Journal articles on the topic 'Molecular markers (SNP e SSR)'
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Khatoon, Arifa, Sumeet Verma, Gayatri Wadiye, and Anuprita Zore. "Molecular markers and their potentials." International Journal of Bioassays 5, no. 01 (January 1, 2016): 4706. http://dx.doi.org/10.21746/ijbio.2016.01.003.
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The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant molecular biotechnology and their genetic studies. There are three different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiating in two types 1. Non PCR based (RFLP) and 2. PCR based markers (RAPD, AFLP, SSR, SNP etc.). Amongst others, the microsatellite DNA marker is one of the most widely used marker due to its easy use by simple PCR, followed by a denaturing gel electrophoresis. SNP (Single Nucleotide Polymorphism) is nowadays is the one which is used mainly. In this review, we are going to discuss about the biochemical and molecular markers which are recently developed, the important characteristics of molecular markers their advantages, disadvantages and the applications of these markers in comparison with other markers types.
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Sa, Kyu Jin, Hyeon Park, So Jung Jang, and Ju Kyong Lee. "Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers." Plants 12, no. 2 (January 4, 2023): 239. http://dx.doi.org/10.3390/plants12020239.
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The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses—Q + K and PCA + K mixed linear models (MLMs)—and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker–trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.
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Lyu, Pin, Jianhua Hou, Haifeng Yu, and Huimin Shi. "High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers." Current Bioinformatics 15, no. 8 (January 1, 2021): 889–97. http://dx.doi.org/10.2174/1574893615666200324134725.
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Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.
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Hsu, Te-Hua, Yu-Ting Chiu, Hung-Tai Lee, Hong-Yi Gong, and Chang-Wen Huang. "Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)." Biology 10, no. 1 (January 7, 2021): 36. http://dx.doi.org/10.3390/biology10010036.
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The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Hsu, Te-Hua, Yu-Ting Chiu, Hung-Tai Lee, Hong-Yi Gong, and Chang-Wen Huang. "Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)." Biology 10, no. 1 (January 7, 2021): 36. http://dx.doi.org/10.3390/biology10010036.
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The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Gonzaga, Zennia Jean, Kashif Aslam, Endang M. Septiningsih, and Bertrand C. Y. Collard. "Evaluation of SSR and SNP Markers for Molecular Breeding in Rice." Plant Breeding and Biotechnology 3, no. 2 (June 30, 2015): 139–52. http://dx.doi.org/10.9787/pbb.2015.3.2.139.
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Kang, Sung-Taeg, and M. A. Rouf Mian. "Genetic map of the powdery mildew resistance gene in soybean PI 243540." Genome 53, no. 5 (May 2010): 400–405. http://dx.doi.org/10.1139/g10-015.
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Powdery mildew (caused by Microsphaera diffusa Cooke & Peck) is a common disease of soybean in many soybean-growing regions of the world and under greenhouse conditions. The previously reported Rmd locus of soybean for resistance to powdery mildew was mapped on soybean molecular linkage group J (chromosome 16). We have discovered a single dominant gene in PI 243540 that provides season-long resistance to powdery mildew. The objective of this study was to map the powdery mildew resistance gene in PI 243540 with PCR-based molecular markers. One hundred eighty-four F2 plants and their F2:3 families from a cross between the powdery mildew susceptible cultivar ‘Wyandot’ and PI 243540 were screened with M. diffusa in greenhouses. Bulked segregant analysis (BSA) with SSR markers was used to identify the tentative genomic location of the gene. The BSA localized the gene to a genomic region in soybean chromosome 16. A linkage map with seven SSR and six SNP markers flanking the gene was constructed. We positioned the gene between SSR marker Sat_224 and SNP marker BARC-021875-04228 at distances of 9.6 and 1.3 cM from the markers, respectively. The map position of the gene was slightly different from previously reported map positions of the only known Rmd locus. We have mapped a single dominant gene, tentatively called Rmd_PI243540, near the previously known Rmd locus on chromosome 16. The molecular markers flanking the gene will be useful for marker-assisted selection of this gene.
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Susanto, Untung, Nofi Anisatun Rohmah, and Made Jana Mejaya. "Distinguishing Rice Genotypes using Morphological, Agronomical,." Jurnal Penelitian Pertanian Tanaman Pangan 34, no. 2 (November 12, 2015): 79. http://dx.doi.org/10.21082/jpptp.v34n2.2015.p79-87.
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<p align="LEFT">Complete data on characteristics of a rice variety is very important to race the authenticity of the variety at the field. Sometimes a name of a variety had changed, due to the informal seed distribution among farmers. This could become problem in the property right of the variety. Distinguishing among rice varieties using only morphological and agronomical traits are sometimes not sufficient. Currently, molecular markers such as SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) markers have become available and are powerfull to distinguish rice genotypes. This research was aimed to distinguish nine rice varieties grown by farmers, using morphological characters (47 traits), agronomical characters (9 traits), SSR markers (12 primer pairs, related with important traits of rice plant), and 384 SNP markers, and to compare the effectiveness of each technique in distinguishing among genotypes. A field experiment was conducted in Ranca Jaya village, Patok Beusi, Subang, West Java during Wet Season (WS) of 2011/2012, using a Randomized Complete Block Design in three replications. A modified CTAB method was used to extract DNA for detection using 12 SSR markers and 384 SNP markers. The results revealed that the use of SSR markers that were linked to certain genes was more accurate than that of the SNP markers, agronomic, and morphological characters, in distinguishing differences among the 9 rice genotypes. The complete data of morphologic, agronomic, and molecular are useful to distinguish the authenticity of a variety in order to protect the intelectual property right attached on the variety.</p>
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Fazio, Gennaro, Jack E. Staub, and Sang Min Chung. "Development and Characterization of PCR Markers in Cucumber." Journal of the American Society for Horticultural Science 127, no. 4 (July 2002): 545–57. http://dx.doi.org/10.21273/jashs.127.4.545.
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Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.
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Wu, Jianhui, Qilin Wang, Liangsheng Xu, Xianming Chen, Bei Li, Jingmei Mu, Qingdong Zeng, Lili Huang, Dejun Han, and Zhensheng Kang. "Combining Single Nucleotide Polymorphism Genotyping Array with Bulked Segregant Analysis to Map a Gene Controlling Adult Plant Resistance to Stripe Rust in Wheat Line 03031-1-5 H62." Phytopathology® 108, no. 1 (January 2018): 103–13. http://dx.doi.org/10.1094/phyto-04-17-0153-r.
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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese P. striiformis f. sp. tritici race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and under natural infection in Tianshui, Gansu Province. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers selected together with 84 simple sequence repeat (SSR) markers on 1B were used to screen polymorphism and a chromosome region associated with rust resistance was identified. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8 and 69.3% of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to P. striiformis f. sp. tritici races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/quantitative trait loci on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.
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Jesus, Rafaela de, Gabriel do N. Santos, Andressa S. Piccin, Thiago WA Balsalobre, Fernando C. Sala, and Monalisa S. Carneiro. "Characterization of pepper accessions using molecular markers linked to pungency and SSR." Horticultura Brasileira 37, no. 2 (June 2019): 152–60. http://dx.doi.org/10.1590/s0102-053620190205.
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ABSTRACT Peppers of the genus Capsicum are of great socioeconomic importance, being pungency trait their main attraction. Pungency characterization, genetic distance estimates and population structure analysis of the accessions belonging to germplasm banks are important for parent selection which allows to obtain superior progenies. Therefore, the aims of this study were: i) evaluate 81 accessions of the Capsicum spp. Germplasm Bank of Universidade Federal de São Carlos (BGC-UFSCar) with molecular markers linked to pungency; ii) estimate the genetic diversity among accessions of the BGC-UFSCar using microsatellite markers (SSR); and iii) evaluate the efficiency of these markers in the distinction among species of Capsicum spp. We noticed that pun11 and SNP molecular markers were efficient in predicting the pungent phenotype of BGC-UFSCar accessions in 84.85% and 95.59%, respectively. From a total of 13 amplified microsatellite markers, seven were polymorphic and efficient to discriminate species of Capsicum genus, both through genetic diversity analysis and population structure analysis, which showed three subpopulations. The molecular markers used in this study are useful tools for breeding programs since they were able to characterize and discriminate Capsicum spp. species at DNA level. Information obtained with molecular markers can assist in the selection of contrasting parents for future breeding programs.
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Xu, Yanqin, Shuyun Tian, Renqing Li, Xiaofang Huang, Fengqin Li, Fei Ge, Wenzhen Huang, and Yin Zhou. "Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp." BioMed Research International 2021 (July 7, 2021): 1–11. http://dx.doi.org/10.1155/2021/9990910.
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Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.
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Younis, Adnan, Fahad Ramzan, Yasir Ramzan, Faisal Zulfiqar, Muhammad Ahsan, and Ki Byung Lim. "Molecular Markers Improve Abiotic Stress Tolerance in Crops: A Review." Plants 9, no. 10 (October 15, 2020): 1374. http://dx.doi.org/10.3390/plants9101374.
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Plants endure many abiotic stresses, such as temperature (heat or frost), drought, and salt. Such factors are primary and frequent stressors that reduce agriculture crop yields. Often alterations in nutrient management and constituents, along with variations in biosynthetic capacity, ultimately reduce or halt plant growth. Genetically, stress is an environmental condition that interferes with complete genetic expression. A vast range of molecular genomic markers is available for the analysis of agricultural crops. These markers are classified into various groups based on how the markers are used: RAPD (Random amplified polymorphic DNA) markers serve to identify and screen hybrids based on salinity and drought stress tolerance, while simple sequence repeat (SSR) markers are excellent for the assessment of stress tolerance. Such markers also play an important role in the QTL (Quantitative trait loci) mapping of stress-related genes. Dehydrins for drought and saltol for salinity stresses are primitive genes which regulate responses to these conditions. Further, a focus on traits using single-gene single nucleotide polymorphisms (SNP) markers supports genetic mapping and the sequencing of stress-related traits in inbred lines. DNA markers facilitate marker-assisted breeding to enhance abiotic stress tolerance using advanced techniques and marker modification.
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Francki, Michael G., Esther Walker, Dora A. Li, and Kerrie Forrest. "High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat." Genome 61, no. 2 (February 2018): 145–49. http://dx.doi.org/10.1139/gen-2017-0203.
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The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex, consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, and 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074, and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. The SSR- and DArT-based genetic maps had an average distance of 6.5, 7.8, and 9.7 cM between marker loci for populations EGA/Millewa, P92201D5/P91193D1, and 6HRWSN125/WAWHT2074, respectively. This study used single nucleotide polymorphism (SNP) markers from the iSelect Infinium 90K genotyping array to fine-map genomic regions harbouring QTL for flag leaf and glume SNB resistance, reducing the average distance between markers to 2.9, 3.3, and 3.4 cM for populations P92201D5/P91193D1, EGA/Millewa, and 6HRWSN125/WAWHT2074, respectively. Increasing the marker density of the genetic maps with SNPs did not identify any new QTL for SNB resistance but discriminated previously identified co-located QTL into separate but closely linked QTL.
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Rui, Zhao, Liu Zhen-Zhen, Xu Gui-Yun, and Yang Ning. "Analysis of SNP markers for chicken blue-shelled gene using PCR-SSCP." Chinese Journal of Agricultural Biotechnology 4, no. 1 (April 2007): 53–56. http://dx.doi.org/10.1017/s1479236207001295.
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AbstractThe oocyan (O) gene determines blue shell pigmentation of domesticated chicken. The O locus is closely linked to ALEV1 on chromosome 1 with a genetic distance of 2.3 cM. Blue eggshells contain a protoporphyrin, biliverdin and zinc biliverdin chelating complex, which belongs to the porphyrin metabolic pathway. A bio-informatic approach was first used to BLAST for the genes of the enzymes in the porphyrin pathway; no gene was detected to specify the O locus. Due to a limited number of simple sequence repeat (SSR) markers around the O locus, polymerase chain reaction–single-strand conformational polymorphism (PCR-SSCP) was then employed to search for candidate single nucleotide polymorphism (SNP) markers. The sequence bearing a marker was found to consist of two transversions at Chr1:61754089T→A and Chr1:61754175A→T, respectively. Population screening showed that 81% of homozygous blue-shelled layers (OO) were classified as AA genotype at the SNP loci, while 89% of heterozygous blue-shelled layers (Oo) were AB genotype and 93% of tinted layers (oo) were BB genotype. The results indicated that there is a close association between O locus and SNP locus, suggesting that the marker locus could be used as a molecular marker in breeding for blue-shelled chickens.
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Zhang, Shengrui, Bin Li, Ying Chen, Abdulwahab S. Shaibu, Hongkun Zheng, and Junming Sun. "Molecular-Assisted Distinctness and Uniformity Testing Using SLAF-Sequencing Approach in Soybean." Genes 11, no. 2 (February 6, 2020): 175. http://dx.doi.org/10.3390/genes11020175.
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Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the present study, we assessed the distinctness and uniformity of five soybean cultivars using both single nucleotide polymorphism (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, and simple sequence repeat (SSR) markers. The phylogenetic tree and principal component analysis (PCA) from both the SLAF-seq and SSR methods showed a clear distinction among cultivars Zhonghuang 18, Zhonghuang 68 and Zhonghuang 35, while no clear distinction was observed between cultivars Zhonghuang 13 and Hedou 13. Using the SLAF-seq method, we determined the proportion of homozygous loci for the five soybean cultivars. The heterozygosity of each individual plant was estimated for the assessment of cultivar purity and the purity levels of the five soybean cultivars ranged from 91.89% to 93.96%. To further validate the applicability of the SLAF-seq approach for distinctness testing, we used the SNP information of 150 soybean cultivars with different origins. The cultivars were also distinguished clearly. Taken together, SLAF-seq can be used as an accurate and reliable method in the assessment of the distinctness and uniformity of soybean cultivars.
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Ahn, Yul-Kyun, Swati Tripathi, Young-Il Cho, Jeong-Ho Kim, Hye-Eun Lee, Do-Sun Kim, and Jong-Gyu Woo. "Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology." Plant Genetic Resources 12, S1 (July 2014): S83—S86. http://dx.doi.org/10.1017/s147926211400032x.
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Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.
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Ren, Hailong, Zhenwu Wei, Bo Zhou, Xiang Chen, Qiang Gao, and Zhibin Zhang. "Molecular marker development and genetic diversity exploration in Medicago polymorpha." PeerJ 11 (January 16, 2023): e14698. http://dx.doi.org/10.7717/peerj.14698.
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Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding.
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Jun, Tae-Hwan, and Sung-Taeg Kang. "Genetic map of lps3: a new short petiole gene in soybeans." Genome 55, no. 2 (February 2012): 140–46. http://dx.doi.org/10.1139/g11-086.
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The short petiole trait is valuable for the development of plant ideotypes with high yield by improving the plant canopy. The soybean breeding line SS98206SP has shown extremely short petioles in the greenhouse and fields. A new single recessive gene designated as lps3 confers the short petiole trait in SS98206SP. The objectives of this study were to map the short petiole gene in SS98206SP with PCR-based markers. In total, 187 F2 plants and their F2:3 families from a cross between the short petiole line SS98206SP and the long petiole cultivar ‘Taekwang’ along with the two parental lines were evaluated for their petiole lengths in a greenhouse. An SSR marker from each 10-cM section of a consensus soybean map was selected for bulked segregant analysis (BSA) to identify the tentative genomic location of the gene. The BSA technique was useful to localize the gene to a genomic region in the soybean linkage group F (chromosome 13). A linkage map with six SSR and two SNP markers flanking the gene was constructed. We positioned the gene between two SSR markers, Sat_234 and Sct_033, at distances of 8.5 and 3.5 cM from the marker, respectively. The makers flanking the gene (lps3) were located within 3–4 cM of the gene. These markers will be useful for maker-assisted selection in the development of new ideotype soybean plants.
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Adawiah, Rabiatul, A. R. Shahril Firdaus, A. Norzihan, and A. B. Umi Kalsom. "Mining of single nucleotide polymorphism (SNP) and simple sequence repeats (SSRs) from EST tropical fruits." Asian Journal of Plant Biology 2, no. 2 (December 30, 2014): 48–52. http://dx.doi.org/10.54987/ajpb.v2i2.181.
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The advancement in genomics technology has produced vast amount of expressed sequencetags (ESTs) sequence from tropical fruits. These resources have increased the publicavailability of ESTs sequence from year after year. Therefore, this effort permits mining ofsingle nucleotide polymorphism (SNP) and simple sequence repeat (SSR) from EST tropicalfruits. SNP and SSR are types of molecular marker which commonly used in modern geneticanalysis for wide application such as diversity analysis, linkage analysis and association study.In this study, a small scale EST sequences from tropical fruits (pineapple, mango, coconut andbanana) were retrieved from dbEST database (www.ncbi.nlm.nih.gov/dbEST/ ) as of March2013. Various bioinformatics tools were applied for rapid discovery of SNP and SSR markerfrom EST sequences. We analyzed 31,920 unigenes (contigs and singletons) representing atotal of 77,418 ESTs from four tropical fruits for their potential use in developing SNP and SSRmarkers. A total of 13,709 EST-SNP were discovered while a total of 4853 EST-SSR werediscovered from these four tropical fruits. The most abundant EST-SSR repeat is fromtrinucleotide (15,957 repeats) followed by dinucleotide (13,797 repeats) and tetranucleotide(973 repeats). Here, 1738 primers from SNP while 2033 primers from SSR were passedthrough the setting criteria and were selected for validation using genotyping platform. Thisstudy not only serves as a resource for marker development in tropical fruits but can provide abetter insight into the selection of candidate genes of interest.
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Shukla, Ravi P., Gopal J. Tiwari, Babita Joshi, Satya N. Jena, and Sushma Tamta. "Tightly Linked Molecular DNA Markers with High Predictive Trait Value: A Current Increasing Demand in the Breeding Program of Upland Cotton (Gossypium hirsutum L.)." INTERNATIONAL JOURNAL OF PLANT AND ENVIRONMENT 7, no. 02 (July 15, 2021): 101–18. http://dx.doi.org/10.18811/ijpen.v7i02.01.
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Cotton (Gossypium spp.) is a major cash crop of India and is the second-largest cotton producer in the world after China. Gossypium hirsutum and Gossypium barbadense are two tetraploid species that are majorly cultivated besides two diploid species (desi cotton). In cotton, fiber quality, drought tolerance, boll weight, boll number, and yield are essential quantitative traits with many components that are controlled by several genes present at different loci. Identifying such genes from different genomic resources of cotton using various molecular markers is necessary to accelerate the Quantitative Trait Loci (QTL) analysis. In the public domain of cotton, there is a vast number of molecular markers. However, not all are very useful for trait mapping, as most markers are away from the QTL region. Thereby, cotton improvement programs pay more attention to tightly linked markers with high predictive trait values. The present review provides an overview and updates on the comparative studies and the application of various molecular markers, i.e., RFLP, AFLP, RAPD, SSR, EST-SSR, and SNP in the cotton-breeding program. Insights gained from the study may help in successful cotton breeding and improvement.
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Wang, N., Y. Z. Xie, Y. Z. Li, S. N. Wu, H. S. Wei, and C. S. Wang. "Molecular mapping of a novel early leaf-senescence gene Els2 in common wheat by SNP genotyping arrays." Crop and Pasture Science 71, no. 4 (2020): 356. http://dx.doi.org/10.1071/cp19435.
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Early leaf senescence in wheat (Triticum aestivum L.) is one of the limiting factors for developing high yield potential. In this study, a stably inherited, early leaf-senescence mutant LF2099 was initially identified in an M2 population of the common wheat accession H261 after ethyl methanesulfonate (EMS) mutagenesis. Early leaf senescence was observed in the LF2099 mutant during the three-leaf-stage, and then the etiolated area of the wheat leaf increased gradually from the bottom to the top throughout development. Compared with H261, the chlorophyll (Chl a, Chl b) and carotenoid contents and photosynthetic capacity of the mutant were significantly decreased. All of its yield-related traits except for spike length were also significantly reduced. Dissolved cytoplasm, abnormal chloroplast structure, dissolved chloroplast membrane, abnormal thylakoid development, and more plastoglobules were observed in the senescent leaf region of the mutant by transmission electronic microscope. Genetic analysis indicated that the early leaf-senescence phenotype is controlled by an incomplete-dominance nuclear gene, here designated Els2. Using single nucleotide polymorphisms and bulked segregant analysis, the els2 gene was anchored in a region on chromosome 2BL between simple sequence repeat (SSR) markers gpw4043 and wmc149. Six new polymorphic SSR markers were developed from the Chinese Spring 2BL shotgun survey sequence contigs. By means of comparative genomics analyses, the collinearity genomic regions of the els2 locus on wheat 2BL were identified in Brachypodium distachyon chromosome 5, rice (Oryza sativa) chromosome 4 and sorghum (Sorghum bicolor) chromosome 6. Five intron polymorphism (IP) markers were further developed from this collinearity genomic region. Ultimately, Els2 was mapped in a genetic interval of 0.95 cM flanked by IP markers 2BIP09 and 2BIP14. The co-segregating IP markers 2BIP12 and 2BIP17 provide a starting point for the fine mapping and map-based cloning of Els2.
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You, Frank M., and Sylvie Cloutier. "Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax." Methods and Protocols 3, no. 2 (April 4, 2020): 28. http://dx.doi.org/10.3390/mps3020028.
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Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.
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Hu, Jinghuang, Jingting Li, Peipei Wu, Yahui Li, Dan Qiu, Yunfeng Qu, Jingzhong Xie, et al. "Development of SNP, KASP, and SSR Markers by BSR-Seq Technology for Saturation of Genetic Linkage Map and Efficient Detection of Wheat Powdery Mildew Resistance Gene Pm61." International Journal of Molecular Sciences 20, no. 3 (February 11, 2019): 750. http://dx.doi.org/10.3390/ijms20030750.
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The gene Pm61 that confers powdery mildew resistance has been previously identified on chromosome arm 4AL in Chinese wheat landrace Xuxusanyuehuang (XXSYH). To facilitate the use of Pm61 in breeding practices, the bulked segregant analysis-RNA-Seq (BSR-Seq) analysis, in combination with the information on the Chinese Spring reference genome sequence, was performed in the F2:3 mapping population of XXSYH × Zhongzuo 9504. Two single nucleotide polymorphism (SNP), two Kompetitive Allele Specific PCR (KASP), and six simple sequence repeat (SSR) markers, together with previously identified polymorphic markers, saturated the genetic linkage map for Pm61, especially in the proximal side of the target gene that was short of gene-linked markers. In the newly established genetic linkage map, Pm61 was located in a 0.71 cM genetic interval and can be detected in a high throughput scale by the KASP markers Xicsk8 and Xicsk13 or by the standard PCR-based markers Xicscx497 and Xicsx538. The newly saturated genetic linkage map will be useful in molecular marker assisted-selection of Pm61 in breeding for disease resistant cultivar and in its map-based cloning.
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Jahani, Mojtaba, Ghorbanali Nematzadeh, Behnaz Dolatabadi, Sayyed Hamidreza Hashemi, and Ghasem Mohammadi-Nejad. "Identification and validation of functional markers in a global rice collection by association mapping." Genome 57, no. 6 (June 2014): 355–62. http://dx.doi.org/10.1139/gen-2014-0044.
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Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker–trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.
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Liu, Daofeng, Jing Ma, Jianfeng Yang, Tien V. Nguyen, Huamin Liu, Renwei Huang, Shunzhao Sui, and Mingyang Li. "Mining Simple Sequence Repeat and Single Nucleotide Polymorphism Markers in a Transcriptomic Database of Wintersweet (Chimonanthus praecox)." HortScience 49, no. 11 (November 2014): 1360–64. http://dx.doi.org/10.21273/hortsci.49.11.1360.
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Wintersweet is a woody ornamental plant and has a long history of human cultivation. Few molecular markers have been characterized and remain scant in wintersweet. This study aimed to mine simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) from the transcriptomic database of wintersweet. A total of 3972 SSRs and 97,060 putative SNPs/indels (92,307 SNPs and 4753 indels) were identified in this data set. This study marks the highest number of SSR and SNP markers discovered to date from wintersweet by using transcriptome sequencing data. These identified markers will provide a useful source for molecular genetic studies such as genetic diversity and characterization, association mapping, and map-based gene cloning in wintersweet.
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Gimode, Davis, Damaris A. Odeny, Etienne P. de Villiers, Solomon Wanyonyi, Mathews M. Dida, Emmarold E. Mneney, Alice Muchugi, Jesse Machuka, and Santie M. de Villiers. "Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies." PLOS ONE 11, no. 7 (July 25, 2016): e0159437. http://dx.doi.org/10.1371/journal.pone.0159437.
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Gao, Zexia, Wei Luo, Hong Liu, Cong Zeng, Xiaolian Liu, Shaokui Yi, and Weimin Wang. "Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala)." PLoS ONE 7, no. 8 (August 6, 2012): e42637. http://dx.doi.org/10.1371/journal.pone.0042637.
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Zeng, Weishan, Yan Su, Rong Huang, Dehuo Hu, Shaowei Huang, and Huiquan Zheng. "Insight into the Complex Genetic Relationship of Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets." Forests 14, no. 2 (February 9, 2023): 347. http://dx.doi.org/10.3390/f14020347.
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Accurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted to employ different molecular markers to address the genetic architecture of their target population, but the power of an advanced parent tree population with a complex pedigree relationship is still rather limited. In this study, a partly known pedigree map combined with marker-derived (SSRs and SNPs) information was implemented for the first time in the assessment of the genetic relatedness of a complex advanced parent tree population (n = 50) in Chinese fir. The bivariate analysis showed that relatedness coefficients between individuals based on SSRs were significantly correlated with SNPs (r = 0.690, p < 0.01). Moreover, the heatmap generated by the SSR-based coefficient matrix was largely consistent with that derived from the SNP-based matrix. Additionally, STRUCTURE and ADMIXTURE analyses based on the two markers showed an analogical genetic clustering result. When compared to the recorded pedigree information, the genetic relationships estimated by the two molecular markers were broadly parallel with pedigree relatedness. These results indicated that SSRs and SNPs can be used as effective tools to clarify genetic relationships when complete pedigree records are not available in Chinese fir. Based on the two markers, the present study revealed a relatively wide genetic variation (SSRs: PIC = 0.573; SNPs: PIC = 0.231) in the selected parent trees. This investigation provides important input into the progress of Chinese fir advanced-generation breeding.
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Reis, João M., Ricardo J. Pereira, Paula S. Coelho, and José M. Leitão. "Assessment of Wild Rocket (Diplotaxis tenuifolia (L.) DC.) Germplasm Accessions by NGS Identified SSR and SNP Markers." Plants 11, no. 24 (December 12, 2022): 3482. http://dx.doi.org/10.3390/plants11243482.
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Rocket is the common designation for two baby-leaf salad crops of the Brassicaceae family: Eruca sativa (L.) Cav., usually referred to as annual garden rocket, and Diplotaxis tenuifolia (L.) DC. commonly named to as perennial wild rocket. E. sativa is used for human consumption since antiquity. However, the growing consumer preference for D. tenuifolia is being accompanied by the fast increase in its production area and commercialization of new cultivars. Nevertheless, the worldwide number of wild rocket accessions maintained in germplasm collections is very reduced, the solution for which situation the project “REMIRucula” intends to contribute, establishing a germplasm collection at the INIAV, Oeiras, Portugal. Herein, we report on the establishment via next generation sequencing (NGS) of the first genome assembly of D. tenuifolia and the identification of specific single sequence repeat (SSR) and single nucleotide polymorphisms (SNP) loci for the establishment of specific DNA-markers for this species. A representative set of 87 D. tenuifolia and 3 E. sativa accessions were assessed by 5 SSR and 9 SNP-CAPS markers, allowing a drastic discrimination between both species and the establishment of unequivocal molecular fingerprints for the analyzed accessions. The non-discrimination within six pairs and one trio of D. tenuifolia accessions is discussed.
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Zhao, Jun, Xueqin Tang, Charlene P. Wight, Nicholas A. Tinker, Yunfeng Jiang, Honghai Yan, Jian Ma, et al. "Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.)." Genome 61, no. 7 (July 2018): 497–503. http://dx.doi.org/10.1139/gen-2017-0006.
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Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.
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Schroeder, H., and M. Fladung. "SSR and SNP Markers for the Identification of Clones, Hybrids and Species Within the Genus Populus." Silvae Genetica 59, no. 1-6 (December 1, 2010): 257–63. http://dx.doi.org/10.1515/sg-2010-0036.
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Abstract Several poplar species within a section, but also between sections, are cross-compatible, thus a high number of interspecies-hybrids occur naturally or have been artificially produced during the last 100 years. Very often, systematically kept records on the production or vegetative propagation of poplar hybrids and/or clones have not been available to date. Hence the origin of the poplar plant material used for the generation of hybrids or clones is not quite clear in many cases, thus making the differentiation between the clones a difficult task. Therefore, genetic markers are needed to clearly identify and differentiate the species and hybrids in the genus Populus, including both identification of existing clones and the breeding of new ones. One aspect of this study is therefore to develop molecular markers for the identification and differentiation of species, hybrids, and clones of the genus Populus.
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Feng, J. Y., M. N. Wang, X. M. Chen, D. R. See, Y. L. Zheng, S. M. Chao, and A. M. Wan. "Molecular Mapping of YrSP and Its Relationship with Other Genes for Stripe Rust Resistance in Wheat Chromosome 2BL." Phytopathology® 105, no. 9 (September 2015): 1206–13. http://dx.doi.org/10.1094/phyto-03-15-0060-r.
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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Resistance is the best way to control the disease. YrSP, a gene originally from ‘Spaldings Prolific’ wheat and providing resistance to a broad spectrum of races, is used for differentiating P. striiformis f. sp. tritici races but its chromosomal location is not clear. To map YrSP, a near-isogenic line (AvSYrSPNIL) was backcrossed to the recurrent parent, Avocet S. Genetic analysis of the BC7F1, BC8, BC7F2, and BC7F3 progenies confirmed a single dominant gene for resistance. In total, 182 BC7F2 plants and their derived BC7F3 lines were phenotyped with an avirulent P. striiformis f. sp. tritici race and genotyped with simple-sequence repeat (SSR), single-nucleotide polymorphism (SNP), and sequence-tagged site (STS) markers. A linkage map was constructed with 3 SSR, 17 SNP, and 3 STS markers covering 23.3 centimorgans (cM). Markers IWA638 and dp269 were 0.6 cM proximal and 1.5 cM distal, respectively, to YrSP. The gene was mapped in chromosome bin 2BL-C-0.5, physically within the proximal 50% of the chromosome 2BL arm. Allelism tests based on F2 phenotypes indicated that YrSP is closely linked to but not allelic with genes Yr5, Yr7, Yr43, Yr44, and Yr53. Infection type data from tests with 10 historical and currently predominant P. striiformis f. sp. tritici races in the United States also demonstrated differences in specificity between YrSP and the other genes. The specificity of YrSP is useful in differentiating P. striiformis f. sp. tritici races and studying the plant–pathogen interactions, and the information of chromosomal location of the gene and its tightly linked markers should be useful in developing resistant cultivars when combined with other genes for resistance to stripe rust.
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Ocarez, Nallatt, Nicolás Jiménez, Reynaldo Núñez, Rocco Perniola, Antonio Domenico Marsico, Maria Francesca Cardone, Carlo Bergamini, and Nilo Mejía. "Unraveling the Deep Genetic Architecture for Seedlessness in Grapevine and the Development and Validation of a New Set of Markers for VviAGL11-Based Gene-Assisted Selection." Genes 11, no. 2 (January 30, 2020): 151. http://dx.doi.org/10.3390/genes11020151.
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Seedless inheritance has been considered a quasi-monogenic trait based on the VvAGL11 gene. An intragenic simple sequence repeat (SSR) marker, p3_VvAGL11, is currently used to opportunely discard seeded progeny, which represents up to 50% of seedlings to be established in the field. However, the rate of false positives remains significant, and this lack of accuracy might be due to a more complex genetic architecture, some intrinsic flaws of p3_VvAGL11, or potential recombination events between p3_VvAGL11 and the causal SNP located in the coding region. The purpose of this study was to update the genetic architecture of this trait in order to better understand its implications in breeding strategies. A total of 573 F1 individuals that segregate for seedlessness were genotyped with a 20K SNP chip and characterized phenotypically during four seasons for a fine QTL mapping analysis. Based on the molecular diversity of p3_VvAGL11 alleles, we redesigned this marker, and based on the causal SNP, we developed a qPCR-HRM marker for high-throughput and a Tetra-ARMS-PCR for simple predictive analyses. Up to 10 new QTLs were identified that describe the complex nature of seedlessness, corresponding to small but stable effects. The positive predictive value, based on VvAGL11 alone (0.647), was improved up to 0.814 when adding three small-effect QTLs in a multi-QTL additive model as a proof of concept. The new SSR, 5U_VviAGL11, is more informative and robust, and easier to analyze. However, we demonstrated that the association can be lost by intragenic recombination and that the e7_VviAGL11 SNP-based marker is thus more reliable and decreases the occurrence of false positives. This study highlights the bases of prediction failure based solely on a major gene and a reduced set of candidate genes, in addition to opportunities for molecular breeding following further and larger validation studies.
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Chen, Can, Weihao Hao, Jingchun Wu, Hongqi Si, Xianchun Xia, and Chuanxi Ma. "Fine Mapping of Stripe-Rust-Resistance Gene YrJ22 in Common Wheat by BSR-Seq and MutMap-Based Sequencing." Plants 11, no. 23 (November 25, 2022): 3244. http://dx.doi.org/10.3390/plants11233244.
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Identification and accurate mapping of new resistance genes are essential for gene pyramiding in wheat breeding. The YrJ22 gene is a dominant stripe-rust-resistance gene located at the distal end of chromosome 2AL, which was identified in a leading Chinese-wheat variety, Jimai 22, showing high resistance to CYR32, a prevalent race of Puccinia striiformis tritici (Pst) in China. In the current study, 15 F1 and 2273 F2 plants derived from the cross of Jimai 22/Avocet S were used for the fine-mapping of YrJ22. The RNA-Seq of resistant and susceptible bulks of F2 plants (designated BSR-Seq) identified 10 single-nucleotide polymorphisms (SNP) in a 12.09 Mb physical interval on chromosome 2AL. A total of 1022 EMS-induced M3 lines of Jimai 22 were screened, to identify susceptible mutants for MutMap analysis. Four CAPS markers were developed from SNPs identified using BSR-Seq and MutMap. A linkage map for YrJ22 was constructed with 11 CAPS/STS and three SSR markers. YrJ22 was located at a 0.9 cM genetic interval flanked by markers H736 and H400, corresponding to a 340.46 kb physical region (768.7–769.0 Mb), including 13 high-confidence genes based on the Chinese Spring reference genome. TraesCS2A01G573200 is a potential candidate-gene, according to linkage and quantitative real-time PCR (qPCR) analyses. The CAPS marker H732 designed from an SNP in TraesCS2A01G573200 co-segregated with YrJ22. These results provide a useful stripe-rust-resistance gene and molecular markers for marker-assisted selection in wheat breeding and for further cloning of the gene.
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Akbari, Mahjoubeh, Hossein Sabouri, Sayed Javad Sajadi, Saeed Yarahmadi, Leila Ahangar, Amin Abedi, and Mahnaz Katouzi. "Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses." Genes 13, no. 11 (November 10, 2022): 2087. http://dx.doi.org/10.3390/genes13112087.
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Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.
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Suwabe, Keita, Colin Morgan, and Ian Bancroft. "Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa." Genome 51, no. 3 (March 2008): 169–76. http://dx.doi.org/10.1139/g07-113.
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An integrated linkage map between B. napus and B. rapa was constructed based on a total of 44 common markers comprising 41 SSR (33 BRMS, 6 Saskatoon, and 2 BBSRC) and 3 SNP/indel markers. Between 3 and 7 common markers were mapped onto each of the linkage groups A1 to A10. The position and order of most common markers revealed a high level of colinearity between species, although two small regions on A4, A5, and A10 revealed apparent local inversions between them. These results indicate that the A genome of Brassica has retained a high degree of colinearity between species, despite each species having evolved independently after the integration of the A and C genomes in the amphidiploid state. Our results provide a genetic integration of the Brassica A genome between B. napus and B. rapa. As the analysis employed sequence-based molecular markers, the information will accelerate the exploitation of the B. rapa genome sequence for the improvement of oilseed rape.
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Chitwood, Jessica, Ainong Shi, Beiquan Mou, Michael Evans, John Clark, Dennis Motes, Pengyin Chen, and David Hensley. "Population Structure and Association Analysis of Bolting, Plant Height, and Leaf Erectness in Spinach." HortScience 51, no. 5 (May 2016): 481–86. http://dx.doi.org/10.21273/hortsci.51.5.481.
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Spinach (Spinacia oleracea L.) is an important vegetable worldwide with high nutritional and health-promoting compounds. Bolting is an important trait to consider to grow spinach in different seasons and regions. Plant height and leaf erectness are important traits for machine harvesting. Breeding slow bolting, taller, and more erect spinach cultivars is needed for improved spinach production. A total of 288 United States Department of Agriculture (USDA) spinach accessions were used as the association panel in this research. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Two structured populations and the admixtures were inferred for the 288 spinach accession panel using STRUCTURE and MEGA. Association mapping was conducted using single-marker regression (SMR) in QGene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. Three SNP markers, AYZV02001321_398, AYZV02041012_1060, and AYZV02118171_95 were identified to be associated with bolting. Eight SNP markers, AYZV02014270_540, AYZV02250508_2162, AYZV02091523_19842, AYZV02141794_376, AYZV02077023_64, AYZV02210662_2532, AYZV02153224_2197, and AYZV02003975_248 were found to be associated with plant height. Four SNP markers, AYZV02188832_229, AYZV02219088_79, AYZV02030116_256, and AYZV02129827_197 were associated with erectness. These SNP markers may provide breeders with a tool in spinach molecular breeding to select spinach bolting, plant height, and erectness through marker-assisted selection (MAS).
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Xue, Yongguo, Huawei Gao, Xinlei Liu, Xiaofei Tang, Dan Cao, Xiaoyan Luan, Lin Zhao, and Lijuan Qiu. "QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.)." International Journal of Molecular Sciences 23, no. 19 (September 24, 2022): 11273. http://dx.doi.org/10.3390/ijms231911273.
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Soybeans are essential crops that supply protein and oil. The composition and contents of soybean fatty acids are relevant to human health and have a significant relationship with soybean oil processing and applications. Identifying quantitative trait locus (QTL) genes related to palmitic acid could facilitate the development of a range of nutritive soybean cultivars using molecular marker-assisted selection. In this study, we used a cultivar with higher palmitic acid content, ‘Dongnong42’, and a lower palmitic acid content cultivar, ‘Hobbit’, to establish F2:6 recombinant inbred lines. A high-density genetic map containing 9980 SLAF markers was constructed and distributed across 20 soybean chromosomes. The genetic map contained a total genetic distance of 2602.58 cM and an average genetic distance of 0.39 cM between adjacent markers. Two QTLs related to palmitic acid content were mapped using inclusive composite interval mapping, explaining 4.2–10.1% of the phenotypic variance in three different years and environments, including the QTL included in seed palmitic 7-3, which was validated by developing SSR markers. Based on the SNP/Indel and significant differential expression analyses of Dongnong42 and Hobbit, two genes, Glyma.15g119700 and Glyma.15g119800, were selected as candidate genes. The high-density genetic map, QTLs, and molecular markers will be helpful for the map-based cloning of palmitic acid content genes. These could be used to accelerate breeding for high nutritive value cultivars via molecular marker-assisted breeding.
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Qi, Lili, and Guojia Ma. "Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.)." Genes 11, no. 1 (December 20, 2019): 10. http://dx.doi.org/10.3390/genes11010010.
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Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed at pyramiding rust resistance genes combined with a DM resistance gene, using molecular markers. Four rust resistant lines, HA-R3 (carrying the R4 gene), HA-R2 (R5), HA-R8 (R15), and RHA 397 (R13b), were each crossed with a common line, RHA 464, carrying a rust gene R12 and a DM gene PlArg. An additional cross was made between HA-R8 and RHA 397. Co-dominant simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers linked to the target genes were used to discriminate between homozygotes and heterozygotes in F2 populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition through marker-assisted selection, and three of them were combined with a DM resistance gene PlArg: R4/R12/PlArg, R5/R12/PlArg, R13b/R12/PlArg, R15/R12, and R13b/R15. The pyramiding lines with the stacking of two rust and one DM genes were resistant to all known races of North American sunflower rust and all known races of the pathogen causing DM, potentially providing multiple and durable resistance to both rust and DM. A cluster of 12 SNP markers spanning a region of 34.5 Mb on chromosome 1, which co-segregate with PlArg, were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed.
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Gessese, Mesfin, Harbans Bariana, Debbie Wong, Matthew Hayden, and Urmil Bansal. "Molecular Mapping of Stripe Rust Resistance Gene Yr81 in a Common Wheat Landrace Aus27430." Plant Disease 103, no. 6 (June 2019): 1166–71. http://dx.doi.org/10.1094/pdis-06-18-1055-re.
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The deployment of diverse sources of resistance in new cultivars underpins durable control of rust diseases. Aus27430 exhibited a moderate level of stripe rust resistance against Puccinia striiformis f. sp. tritici (Pst) pathotypes currently prevalent in Australia. Aus27430 was crossed with the susceptible parent Avocet S (AvS) and subsequent filial generations were raised. Monogenic segregation observed among Aus27430/AvS F3 families was confirmed through stripe rust screening of an F6 recombinant inbred line (RIL) population, and the resistance locus was temporarily named YrAW5. Selective genotyping using an Illumina iSelect 90K wheat SNP bead chip array located YrAW5 in chromosome 6A. Genetic mapping of the RIL population with linked 90K SNPs that were converted into PCR-based marker assays, as well as SSR markers previously mapped to chromosome 6A, confirmed the chromosomal assignment for YrAW5. Comparative analysis of other stripe rust resistance genes located in chromosome 6A led to the formal designation of YrAW5 as Yr81. Tests with a marker linked with Yr18 also demonstrated the presence of this gene in Aus27430. Yr18 interacted with Yr81 to produce stripe rust responses lower than those produced by RILs carrying these genes individually. Although gwm459 showed higher recombination with Yr81 compared with the other flanking marker KASP_3077, it amplified the AvS allele in 80 cultivars, whereas KASP_3077 amplified AvS allele in 67 cultivars. Both markers can be used in marker-assisted selection after confirming parental polymorphism.
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Yonet, Nilay, Yıldız Aydin, Goksel Evci, and Ahu Altinkut Uncuoglu. "Genomic Evaluation of Sunflower Broomrape (Orobanche Cumana) Germplasm by KASP Assay." Helia 41, no. 68 (July 26, 2018): 57–72. http://dx.doi.org/10.1515/helia-2017-0016.
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AbstractOrobanche cumana Wallr. is a holoparasitic plant for only sunflower, hence it is called as sunflower broomrape. Yield loss created by O. cumana which is generally 50 % can reach to 100 %. In this study, it was planned to perform molecular characterization of O. cumana germplasm as nine locations of Thrace region obtained from Trakya Agricultural Research Institute by using Single Nucleotide Polymorphism (SNP) markers, widely used in plant breeding programs, in Competitive Allele Specific PCR (KASP) assay which is a fluorescent tagged allele specific PCR method based, economic, reliable and easily repeatable genotyping technology. Databases and literature were scanned to spot variations on O. cumana genome which is not known clearly. So far, four SSR (Simple Sequence Repeat) marker (Ocum-197, Ocum-006, Ocum-023 and Ocum-151) regions showing polymorphic pattern were used for searching possible SNPs. Primer pairs were designed for amplification of the regions possibly having SNPs and PCR amplifications with these primer pairs were performed and 1 candidate deletion was detected on the amplicon which was amplified by Ocum-197 SSR marker. Following, the deletion was converted to KASP primers and KASP assay was performed. The deletion marker, Del-197, has grouped the samples from nine locations in the resulting allelic discrimination plot and infestation was performed according to this grouping, As a conclusion, Del-197 is considered as a selective marker for the ability to rapidly assay allelic variation at DNA markers for O. cumana populations that have effects on infestation results were evaluated as races, F, G, H and I in Thrace region.
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Yu, Ju-Kyung, Qi Sun, Mauricio La Rota, Hugh Edwards, Hailu Tefera, and Mark E. Sorrells. "Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter)." Genome 49, no. 4 (April 1, 2006): 365–72. http://dx.doi.org/10.1139/g05-118.
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Tef (Eragrostis tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA libraries: seedling leaf, seedling root, and inflorescence of E. tef and seedling leaf of Eragrostis pilosa, a wild relative of E. tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 tef unigenes. Ap prox imately 3/4 of tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68% of the putative tef genes with gene ontology categories. Identification of the translated unigenes for conserved protein domains revealed 389 protein family domains (Pfam), the most frequent of which was protein kinase. A total of 170 ESTs containing simple sequence repeats (EST-SSRs) were identified and 80 EST-SSR markers were developed. In addition, 19 single-nucleotide polymorphism (SNP) and (or) insertion–deletion (indel) and 34 intron frag ment length polymorphism (IFLP) markers were developed. The EST database and molecular markers generated in this study will be valuable resources for further tef genetic research.Key words: tef, Ethiopian cereal crop, EST, molecular markers.
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Liu, Cheng, Xianlian Chen, Wubin Wang, Xinyang Hu, Wei Han, Qingyuan He, Hongyan Yang, Shihua Xiang, and Junyi Gai. "Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean." International Journal of Molecular Sciences 22, no. 4 (February 4, 2021): 1559. http://dx.doi.org/10.3390/ijms22041559.
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Annual wild soybean (G. soja) is the ancestor of the cultivated soybean (G. max). To reveal the genetic changes from soja to max, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on SojaCSSLP1 generated from NN1138-2(max)×N24852(soja). The SojaCSSLP5 was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (G, E2 and GmPRR3B) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in SojaCSSLP5. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.
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Luo, Hui, Shijun Xiao, Hua Ye, Zhengshi Zhang, Changhuan Lv, Shuming Zheng, Zhiyong Wang, and Xiaoqing Wang. "Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti." PLOS ONE 11, no. 3 (March 28, 2016): e0152572. http://dx.doi.org/10.1371/journal.pone.0152572.
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Singh, Nivedita, Debjani Roy Choudhury, Amit Kumar Singh, Sundeep Kumar, Kalyani Srinivasan, R. K. Tyagi, N. K. Singh, and Rakesh Singh. "Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties." PLoS ONE 8, no. 12 (December 19, 2013): e84136. http://dx.doi.org/10.1371/journal.pone.0084136.
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Kaya, Hilal Betul, Oznur Cetin, Hulya Kaya, Mustafa Sahin, Filiz Sefer, Abdullah Kahraman, and Bahattin Tanyolac. "SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers." PLoS ONE 8, no. 9 (September 13, 2013): e73674. http://dx.doi.org/10.1371/journal.pone.0073674.
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Tian, Wenlan, Dev Paudel, Wagner Vendrame, and Jianping Wang. "Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies." International Journal of Genomics 2017 (2017): 1–14. http://dx.doi.org/10.1155/2017/8614160.
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Jatropha (Jatropha curcasL.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.
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Carvalho, Marina Santos, Cintia Machado de Oliveira Moulin Carias, Matheus Alves Silva, Marcia Flores da Silva Ferreira, Thiago Lívio Pessoa Oliveira de Souza, Sheila Cristina Prucoli Posse, and Adesio Ferreira. "Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers." Molecular Biology Reports 47, no. 9 (August 17, 2020): 6705–15. http://dx.doi.org/10.1007/s11033-020-05726-7.
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Redjeki, E. S., W. K. Ho, N. Shah, O. O. Molosiwa, N. R. Ardiarini, Kuswanto, and Sean Mayes. "Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins." Genome 63, no. 6 (June 2020): 319–27. http://dx.doi.org/10.1139/gen-2019-0137.
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A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.