Статті в журналах: "Plant genome mapping"

1

Chaney, Lindsay, Aaron R. Sharp, Carrie R. Evans, and Joshua A. Udall. "Genome Mapping in Plant Comparative Genomics." Trends in Plant Science 21, no. 9 (September 2016): 770–80. http://dx.doi.org/10.1016/j.tplants.2016.05.004.

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2

Doležel, Jaroslav, Marie Kubaláková, Jan Bartoš, and Jiří Macas. "Flow cytogenetics and plant genome mapping." Chromosome Research 12, no. 1 (2004): 77–91. http://dx.doi.org/10.1023/b:chro.0000009293.15189.e5.

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3

Lapitanz, Nora L. V. "Organization and evolution of higher plant nuclear genomes." Genome 35, no. 2 (April 1, 1992): 171–81. http://dx.doi.org/10.1139/g92-028.

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The knowledge gained from studies on eukaryotic genome organization is important for understanding how genomes function and evolve, and it provides the basis for designing strategies for manipulating genomes. Hence, numerous studies on this subject have been conducted over the years, utilizing a variety of methods. In the recent decade, several techniques have been developed that allow the study of eukaryotic genome organization at different levels. Molecular techniques including molecular cloning, DNA sequencing, restriction fragment length polymorphism mapping, in situ hybridization, and pulsed field gel electrophoresis together provide a means of obtaining a comprehensive and detailed view of eukaryotic genomes. This paper summarizes recent findings on the organization and evolution of the nuclear genomes of higher plants, with emphasis on representative species with varying genome sizes, including Arabidopsis thaliana, tomato, maize, and wheat. Common, as well as unique, features in the organization of repeated DNA sequences and low copy sequences in these genomes are described and their evolutionary significance discussed.Key words: genome organization, evolution, higher plants, repeated DNA sequences, low copy number sequences.

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4

Ovesná, J., K. Poláková, and L. Leišová. "DNA analyses and their applications in plant breeding." Czech Journal of Genetics and Plant Breeding 38, No. 1 (July 30, 2012): 29–40. http://dx.doi.org/10.17221/6108-cjgpb.

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In recent years, molecular markers have been developed based on the more detailed knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. This review attempts to give an account of different molecular markers currently available for genome mapping and for tagging different traits – restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites. Other markers, expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also mentioned. The importance of structural, functional genomic and comparative mapping is also discussed.

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5

Staňková, Helena, Alex R. Hastie, Saki Chan, Jan Vrána, Zuzana Tulpová, Marie Kubaláková, Paul Visendi, et al. "BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes." Plant Biotechnology Journal 14, no. 7 (January 23, 2016): 1523–31. http://dx.doi.org/10.1111/pbi.12513.

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6

Hou, Yuze, Li Wang, and Weihua Pan. "Comparison of Hi-C-Based Scaffolding Tools on Plant Genomes." Genes 14, no. 12 (November 27, 2023): 2147. http://dx.doi.org/10.3390/genes14122147.

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De novo genome assembly holds paramount significance in the field of genomics. Scaffolding, as a pivotal component within the genome assembly process, is instrumental in determining the orientation and arrangement of contigs, ultimately facilitating the generation of a chromosome-level assembly. Scaffolding is contingent on supplementary linkage information, including paired-end reads, bionano, physical mapping, genetic mapping, and Hi-C (an abbreviation for High-throughput Chromosome Conformation Capture). In recent years, Hi-C has emerged as the predominant source of linkage information in scaffolding, attributed to its capacity to offer long-range signals, leading to the development of numerous Hi-C-based scaffolding tools. However, to the best of our knowledge, there has been a paucity of comprehensive studies assessing and comparing the efficacy of these tools. In order to address this gap, we meticulously selected six tools, namely LACHESIS, pin_hic, YaHS, SALSA2, 3d-DNA, and ALLHiC, and conducted a comparative analysis of their performance across haploid, diploid, and polyploid genomes. This endeavor has yielded valuable insights in advancing the field of genome scaffolding research.

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7

Vlk, D., and J. Řepková. "Application of next-generation sequencing in plant breeding." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 89–96. http://dx.doi.org/10.17221/192/2016-cjgpb.

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

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8

Wu, Xing, Wei Jiang, Christopher Fragoso, Jing Huang, Geyu Zhou, Hongyu Zhao, and Stephen Dellaporta. "Prioritized candidate causal haplotype blocks in plant genome-wide association studies." PLOS Genetics 18, no. 10 (October 17, 2022): e1010437. http://dx.doi.org/10.1371/journal.pgen.1010437.

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Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to prioritize the candidate causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, GMMAT, and BLINK in both simulated and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in high polygenicity simulation setting. Moreover, it resulted in smaller mapping intervals, especially in regions of high LD, achieved by prioritizing small candidate causal blocks in the larger haplotype blocks. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and the average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved on mapping resolution to facilitate crop improvement.

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9

Lindeberg, Magdalen, Christopher R. Myers, Alan Collmer, and David J. Schneider. "Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization." Molecular Plant-Microbe Interactions® 21, no. 6 (June 2008): 685–700. http://dx.doi.org/10.1094/mpmi-21-6-0685.

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Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syringae genome organization was analyzed to distinguish patterns of conservation among genomes and association between genes and mobile genetic elements. Variable regions were identified on the basis of deviation in sequence composition and gaps in syntenic alignment among the three genomes. Mapping gene location relative to the genome structure revealed strong segregation of the HrpL regulon with variable genome regions (VR), divergent distribution patterns for toxin genes depending on association with plant or insect pathogenesis, and patterns of distribution for other virulence genes that highlight potential sources of strain-to-strain differences in host interaction. Distribution of VR among other sequenced bacterial genomes was analyzed and future plans for characterization of this potential reservoir of virulence genes are discussed.

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10

Foolad, Majid R. "Genome Mapping and Molecular Breeding of Tomato." International Journal of Plant Genomics 2007 (August 22, 2007): 1–52. http://dx.doi.org/10.1155/2007/64358.

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The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum×L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs.

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11

Yazaki, Junshi, Brian D. Gregory, and Joseph R. Ecker. "Mapping the genome landscape using tiling array technology." Current Opinion in Plant Biology 10, no. 5 (October 2007): 534–42. http://dx.doi.org/10.1016/j.pbi.2007.07.006.

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12

Dutta, Anik, Bruce A. McDonald, and Daniel Croll. "Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen." PLOS Pathogens 19, no. 11 (November 16, 2023): e1011801. http://dx.doi.org/10.1371/journal.ppat.1011801.

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Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.

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13

Jiang, Jiming, and Bikram S. Gill. "Nonisotopic in situ hybridization and plant genome mapping: the first 10 years." Genome 37, no. 5 (October 1, 1994): 717–25. http://dx.doi.org/10.1139/g94-102.

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Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopolyploid species. GISH also provides a powerful technique for monitoring chromatin introgession during interspecific hybridization. A sequential chromosome banding and ISH technique was developed. The sequential technique is very useful for more precise and efficient mapping as well as cytogenetic determination of genomic affinities of individual chromosomes in allopolyploid species. A critical review is made on the present resolution of the ISH technique and the future outlook of ISH research is discussed.Key words: in situ hybridization, physical mapping, genome mapping, molecular cytogenetics.

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14

Schmidt, Renate. "Physical mapping of the Arabidopsis thaliana genome." Plant Physiology and Biochemistry 36, no. 1-2 (January 1998): 1–8. http://dx.doi.org/10.1016/s0981-9428(98)80086-7.

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15

Tuberosa, Roberto. "Principles and practices of plant penomics. Volume 1. Genome mapping." Annals of Botany 102, no. 5 (November 2008): 879–80. http://dx.doi.org/10.1093/aob/mcn169.

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16

Krishna, Thumadath P. A., Maharajan Theivanayagam, Gurusunathan V. Roch, Veeramuthu Duraipandiyan, and Savarimuthu Ignacimuthu. "Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)." Current Biotechnology 9, no. 3 (December 21, 2020): 160–70. http://dx.doi.org/10.2174/2211550109999200908090745.

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Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

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17

Wixon, Jo. "UK CropNet." Yeast 1, no. 3 (January 1, 2000): 244–54. http://dx.doi.org/10.1155/2000/124868.

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This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC).

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18

Wixon, Jo. "UK CropNet." Yeast 1, no. 3 (2000): 244–54. http://dx.doi.org/10.1002/1097-0061(20000930)17:3<244::aid-yea38>3.0.co;2-p.

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This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, NottinghamArabidopsisStock Centre (NASC).

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19

Zhang, Hong-Bin, Yaning Li, Baohua Wang, and Peng W. Chee. "Recent Advances in Cotton Genomics." International Journal of Plant Genomics 2008 (January 23, 2008): 1–20. http://dx.doi.org/10.1155/2008/742304.

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Genome research promises to promote continued and enhanced plant genetic improvement. As a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression profiling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the current status of each of the genome research areas suggests that the areas of physical mapping, QTL fine mapping, genome sequencing, nonfiber and nonovule EST development, gene expression profiling, and association studies between gene expression and fiber trait performance should be emphasized currently and in near future to accelerate utilization of the genomics research achievements for enhancing cotton genetic improvement.

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20

Soundararajan, Prabhakaran, So Youn Won, and Jung Sun Kim. "Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective." BioMed Research International 2019 (February 19, 2019): 1–12. http://dx.doi.org/10.1155/2019/7519687.

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Rosaceae is one of the important families possessing a variety of diversified plant species. It includes many economically valuable crops that provide nutritional and health benefits for the human. Whole genome sequences of valuable crop plants were released in recent years. Understanding of genomics helps to decipher the plant physiology and developmental process. With the information of cultivating species and its wild relative genomes, genome sequence-based molecular markers and mapping loci for economically important traits can be used to accelerate the genome assisted breeding. Identification and characterization of disease resistant capacities and abiotic stress tolerance related genes are feasible to study across species with genome information. Further breeding studies based on the identification of gene loci for aesthetic values, flowering molecular circuit controls, fruit firmness, nonacid fruits, etc. is required for producing new cultivars with valuable traits. This review discusses the whole genome sequencing reports of Malus, Pyrus, Fragaria, Prunus, and Rosa and status of functional genomics of representative traits in individual crops.

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21

Lin, Jing-Zhong, and Kermit Ritland. "Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers." Genome 39, no. 1 (February 1, 1996): 63–70. http://dx.doi.org/10.1139/g96-009.

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As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated genome. The genome length of Mimulus is estimated at 2474 ± 35 cM; bootstrapping indicates that only ca. 40 markers are needed to give an accurate estimate of genome length. Further statistical analyses indicate that many RAPD markers cannot be ordered with certainty and that uncertain linkage groups tend to map nonlinearly even under commonly used mapping functions. Strategies for speeding up the mapping process for a wild species and possible applications of a partial linkage map in evolutionary studies are discussed. Key words : linkage map, mating system, Mimulus, RAPD.

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22

Mascher, Martin, Thomas Wicker, Jerry Jenkins, Christopher Plott, Thomas Lux, Chu Shin Koh, Jennifer Ens, et al. "Long-read sequence assembly: a technical evaluation in barley." Plant Cell 33, no. 6 (March 12, 2021): 1888–906. http://dx.doi.org/10.1093/plcell/koab077.

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Abstract Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.

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23

Hanson, Anthony A., Aaron J. Lorenz, Louis S. Hesler, Siddhi J. Bhusal, Raman Bansal, Andy P. Michel, Guo‐Liang Jiang, and Robert L. Koch. "Genome‐Wide Association Mapping of Host‐Plant Resistance to Soybean Aphid." Plant Genome 11, no. 3 (November 2018): 180011. http://dx.doi.org/10.3835/plantgenome2018.02.0011.

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24

Darzentas, N., A. Bousios, V. Apostolidou, and A. S. Tsaftaris. "MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences." Bioinformatics 26, no. 19 (August 9, 2010): 2452–54. http://dx.doi.org/10.1093/bioinformatics/btq454.

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25

Chang, Caren, and Elliot M. Meyerowitz. "Plant genome studies: Restriction fragment length polymorphism and chromosome mapping information." Current Opinion in Biotechnology 2, no. 2 (April 1991): 178–83. http://dx.doi.org/10.1016/0958-1669(91)90007-r.

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26

Chang, Caren, and Elliot M. Meyerowitz. "Plant genome studies: restriction fragment length polymorphism and chromosome mapping information." Current Opinion in Genetics & Development 1, no. 1 (June 1991): 112–18. http://dx.doi.org/10.1016/0959-437x(91)80051-m.

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27

Dey, T., and P. D. Ghosh. "Application of molecular markers in plant genome study." NBU Journal of Plant Sciences 4, no. 1 (2010): 1–9. http://dx.doi.org/10.55734/nbujps.2010.v04i01.001.

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The development of molecular techniques for genetic analysis has led to a great increase in our knowledge of plant genetics and our understanding of the structure and behaviour of plant genome. During last three decades, several powerful DNA based marker technologies have been developed for the assessment of genetic diversities and molecular marker assisted breeding technology. In plant systems, the prospects of DNA profiling and fingerprinting is becoming indispensable in the context of establishment of molecular phylogeny, assessment of somaclonal variants, characterization of plant genomics, marker- based gene tags, map-based cloning of agronomically important genes, variability studies, synteny mapping, marker-assisted selection of desirable genotypes etc. In this review article, various molecular markers are reviewed with emphasis on specific areas of their application in higher plants.

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28

Dey, T., and P. D. Ghosh. "Application of molecular markers in plant genome study." NBU Journal of Plant Sciences 4, no. 1 (2010): 1–9. http://dx.doi.org/10.55734/nbujps.2010.v04i01.001.

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Анотація:

The development of molecular techniques for genetic analysis has led to a great increase in our knowledge of plant genetics and our understanding of the structure and behaviour of plant genome. During last three decades, several powerful DNA based marker technologies have been developed for the assessment of genetic diversities and molecular marker assisted breeding technology. In plant systems, the prospects of DNA profiling and fingerprinting is becoming indispensable in the context of establishment of molecular phylogeny, assessment of somaclonal variants, characterization of plant genomics, marker- based gene tags, map-based cloning of agronomically important genes, variability studies, synteny mapping, marker-assisted selection of desirable genotypes etc. In this review article, various molecular markers are reviewed with emphasis on specific areas of their application in higher plants.

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29

Dodeweerd, Anne-Marie van, Caroline R. Hall, Elisabeth G. Bent, Samantha J. Johnson, Michael W. Bevan, and Ian Bancroft. "Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana." Genome 42, no. 5 (October 1, 1999): 887–92. http://dx.doi.org/10.1139/g99-033.

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Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

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30

Yu, Li, Yanshen Nie, Jinxia Jiao, Liufang Jian, and Jie Zhao. "The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes." International Journal of Molecular Sciences 22, no. 12 (June 9, 2021): 6224. http://dx.doi.org/10.3390/ijms22126224.

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A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.

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31

Kikuchi, Shinji, Raju Bheemanahalli, Krishna S. V. Jagadish, Etsushi Kumagai, Yusuke Masuya, Eiki Kuroda, Chitra Raghavan, Michael Dingkuhn, Akira Abe, and Hiroyuki Shimono. "Genome-wide association mapping for phenotypic plasticity in rice." Plant, Cell & Environment 40, no. 8 (June 2, 2017): 1565–75. http://dx.doi.org/10.1111/pce.12955.

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32

Gardiner, Susan E., Ji Mei Zhu, Heather C. M. Whitehead, and Charlotte Madie. "The New Zealand apple genome mapping project." Euphytica 77, no. 1-2 (February 1994): 77–81. http://dx.doi.org/10.1007/bf02551465.

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33

Uceda-Campos, Guillermo, Oseias R. Feitosa-Junior, Caio R. N. Santiago, Paulo M. Pierry, Paulo A. Zaini, Wesley O. de Santana, Joaquim Martins-Junior, et al. "Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems." Microorganisms 10, no. 5 (April 27, 2022): 914. http://dx.doi.org/10.3390/microorganisms10050914.

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Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.

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34

Zhang, Taifeng, Jiajun Liu, Sikandar Amanullah, Zhuo Ding, Haonan Cui, Feishi Luan, and Peng Gao. "Fine Mapping of Cla015407 Controlling Plant Height in Watermelon." Journal of the American Society for Horticultural Science 146, no. 3 (May 2021): 196–205. http://dx.doi.org/10.21273/jashs04934-20.

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The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (P2), was performed and preliminarily mapped through a bulked segregant analysis of F2 individuals that revealed the Cldw gene locus on chromosome 9. Two candidate genes, Cla015407 and Cla015408, were discovered at the delimited region of 43.2 kb by fine mapping, and gene annotation exposed that the Cla015407 gene encodes gibberellic acid 3β-hydroxylase protein. In addition, a comparative analysis of gene sequence and cultivars sequences across the reference genome of watermelon revealed the splice site mutation in the intron region of the Cldw gene in dwarf-type cultivar 812. The quantitative real-time polymerase chain reaction exhibited a significantly higher expression of the Cla015407 gene in cultivar W1-1 compared with 812. There was no significant difference in the vine length of both cultivars after gibberellic acid treatment. In brief, our fine mapping demonstrated that Cla015407 is a candidate gene controlling dwarfism of watermelon plants.

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35

Benchimol-Reis, Luciana L. "Molecular Markers in Plant Breeding." Journal of Agricultural Science 15, no. 3 (February 15, 2023): 58. http://dx.doi.org/10.5539/jas.v15n3p58.

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Molecular markers are an important tool for plant breeding. Since the 1980s, in response to the technology development, molecular marker approaches have been further diversified. The establishment of new-generation sequencing and high-throughput plant phenotyping has greatly decreased the time to genotype large numbers of individuals. For breeders who are not very familiar with molecular techniques and want to catch up with the advances in the field, this review offers basic knowledge. Each molecular marker technology has specific advantages as well as limitations. Molecular marker types, diversity studies, QTL mapping, associative mapping, marker-assisted backcrossing and genomic selection are explored. Marker application in plant breeding is also described. In the genome, molecular markers can detect the genetic architecture of a trait, but also identify candidate genes with an important role in plant breeding programs.

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36

Kumar, Ajay, Kristin Simons, Muhammad J. Iqbal, Monika de Jiménez, Filippo M. Bassi, Farhad Ghavami, Omar Al-Azzam, et al. "Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii." BMC Genomics 13, no. 1 (2012): 597. http://dx.doi.org/10.1186/1471-2164-13-597.

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37

Sher, Muhammad Ali, Abdus Salam Khan, Zulfiqar Ali, and Sultan Habibullah Khan. "Association Mapping of Agronomic traits in Bread Wheat using a high Density 90k SNP Array." Pakistan Journal of Biochemistry and Biotechnology 2, no. 2 (December 31, 2021): 236–47. http://dx.doi.org/10.52700/pjbb.v2i2.91.

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A genome-wide association study (GWAS) was performed using a high-density infinium 90K SNP array. We identified a total markers traits associations (MTAs) (p ?0.000) for the following plant traits; days taken to 50% heading(DH), days to 50% maturity (DM), plant height (Ph) cm, flag leaf area cm2 (FLA), tillers number per plant, spike length (SL) cm and grain yield per plant (GP) g. Most of the SNPs were identified in the A and B genome as compared to the D genome. The significant associated SNPs were mainly distributed on the chromosome 2B, 3B, 5A, and 5B. Nine SNPs on chromosome 5A, 2B and 2D were identified having pleiotropic effects The correlation analysis showed a significant positive association among SL, NT, GP. Which depicted that these traits are promising for breeding high yielding wheat cultivars. This study provided useful information of the valuable genetic loci for marker-assisted breeding.

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38

Ling, Maurice H. T., Roel C. Rabara, Prateek Tripathi, Paul J. Rushton, and Xijin Ge. "Extending MapMan Ontology to Tobacco for Visualization of Gene Expression." Dataset Papers in Biology 2013 (February 20, 2013): 1–7. http://dx.doi.org/10.7167/2013/706465.

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Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

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39

Yang, Fangping, Jindong Liu, Ying Guo, Zhonghu He, Awais Rasheed, Ling Wu, Shiqin Cao, Hai Nan, and Xianchun Xia. "Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)." Plant Disease 104, no. 8 (August 2020): 2174–80. http://dx.doi.org/10.1094/pdis-10-19-2116-re.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

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40

Mandal, Lincoln, Sunil Kumar Verma, Saugata Sasmal, Anju Rani Ekka, Jawahar Lal Katara, and Anil S. Kotasthane. "Multi-Parent Advanced Generation Intercross (Magic) Population for Genome Mapping in Plant." International Journal of Genetics 10, no. 2 (March 30, 2018): 343. http://dx.doi.org/10.9735/0975-2862.10.2.343-345.

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41

Thoen, Manus P. M., Nelson H. Davila Olivas, Karen J. Kloth, Silvia Coolen, Ping-Ping Huang, Mark G. M. Aarts, Johanna A. Bac-Molenaar, et al. "Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping." New Phytologist 213, no. 3 (October 4, 2016): 1346–62. http://dx.doi.org/10.1111/nph.14220.

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42

Gupta, S. K., and T. Gopalakrishna. "Advances in genome mapping in orphan grain legumes of genusVigna." Indian Journal of Genetics and Plant Breeding (The) 73, no. 1 (2013): 1. http://dx.doi.org/10.5958/j.0019-5200.73.1.001.

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43

Weir, Bruce S. "Statistical genetic issues for genome-wide association studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”." Genome 53, no. 11 (November 2010): 869–75. http://dx.doi.org/10.1139/g10-062.

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Genotyping technology now allows the rapid and affordable generation of million-SNP profiles for humans, leading to considerable activity in association mapping. Similar activity is anticipated for many plant species, including Brassica . These plant association mapping activities will require the same care in quality control and quality assurance as for humans. The subsequent analyses may draw upon the same body of theory that is described here in the language of quantitative genetics.

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44

Kudryavtseva, Natalya, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, and Ludmila Khrustaleva. "A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps." International Journal of Molecular Sciences 22, no. 11 (May 30, 2021): 5860. http://dx.doi.org/10.3390/ijms22115860.

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In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.

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45

Siezen, Roland J., Marjo J. C. Starrenburg, Jos Boekhorst, Bernadet Renckens, Douwe Molenaar, and Johan E. T. van Hylckama Vlieg. "Genome-Scale Genotype-Phenotype Matching of Two Lactococcus lactis Isolates from Plants Identifies Mechanisms of Adaptation to the Plant Niche." Applied and Environmental Microbiology 74, no. 2 (November 26, 2007): 424–36. http://dx.doi.org/10.1128/aem.01850-07.

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ABSTRACT Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various nondairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL-1403, SK11, and MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two L. lactis plant isolates. Diagnostic sequencing of their genomes resulted in over 2.5 Mb of sequence for each strain. A high synteny was found with the genome of L. lactis IL-1403, which was used as a template for contig mapping and locating deletions and insertions in the plant L. lactis genomes. Numerous genes were identified that do not have homologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the degradation of complex plant polymers such as xylan, arabinan, glucans, and fructans but also for the uptake and conversion of typical plant cell wall degradation products such as α-galactosides, β-glucosides, arabinose, xylose, galacturonate, glucuronate, and gluconate. Further niche-specific differences are found in genes for defense (nisin biosynthesis), stress response (nonribosomal peptide synthesis and various transporters), and exopolysaccharide biosynthesis, as well as the expected differences in various mobile elements such as prophages, plasmids, restriction-modification systems, and insertion sequence elements. Many of these genes were identified for the first time in Lactococcus lactis. In most cases good correspondence was found with the phenotypic characteristics of these two strains.

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46

Zhang, Guobin, Chunxia Ge, Pingping Xu, Shukai Wang, Senan Cheng, Yanbin Han, Yancui Wang, et al. "The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae." Nature Plants 7, no. 5 (May 2021): 608–18. http://dx.doi.org/10.1038/s41477-021-00908-y.

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AbstractMiscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus. Fusion of two chromosomes occurred during rediploidization in M. floridulus and no significant subgenome dominance was observed. A survey of cellulose synthases (CesA) in M. floridulus revealed quite high expression of most CesA genes in growing stems, which is in agreement with the high cellulose content of this species. Resequencing and comparisons of 75 Miscanthus accessions suggest that M. lutarioriparius is genetically close to M. sacchariflorus and that M. floridulus is more distantly related to other species and is more genetically diverse. This study provides a valuable genomic resource for molecular breeding and improvement of Miscanthus and Saccharinae crops.

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47

Wischnitzki, Elisabeth, Eva Maria Sehr, Karin Hansel-Hohl, Maria Berenyi, Kornel Burg, and Silvia Fluch. "How to Isolate a Plant’s Hypomethylome in One Shot." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/570568.

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Genome assembly remains a challenge for large and/or complex plant genomes due to their abundant repetitive regions resulting in studies focusing on gene space instead of the whole genome. Thus, DNA enrichment strategies facilitate the assembly by increasing the coverage and simultaneously reducing the complexity of the whole genome. In this paper we provide an easy, fast, and cost-effective variant of MRE-seq to obtain a plant’s hypomethylome by an optimized methyl filtration protocol followed by next generation sequencing. The method is demonstrated on three plant species with knowingly large and/or complex (polyploid) genomes:Oryza sativa,Picea abies, andCrocus sativus. The identified hypomethylomes show clear enrichment for genes and their flanking regions and clear reduction of transposable elements. Additionally, genomic sequences around genes are captured including regulatory elements in introns and up- and downstream flanks. High similarity of the results obtained by ade novoassembly approach with a reference based mapping in rice supports the applicability for studying and understanding the genomes of nonmodel organisms. Hence we show the high potential of MRE-seq in a wide range of scenarios for the direct analysis of methylation differences, for example, between ecotypes, individuals, within or across species harbouring large, and complex genomes.

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48

Jiang, Jiming, and Bikram S. Gill. "Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research." Genome 49, no. 9 (September 2006): 1057–68. http://dx.doi.org/10.1139/g06-076.

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Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.

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49

King, Graham J. "Progress in mapping agronomic genes in apple (The European Apple Genome Mapping Project)." Euphytica 77, no. 1-2 (February 1994): 65–69. http://dx.doi.org/10.1007/bf02551463.

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50

Bellinger, M. Renee, Roshan Paudel, Steven Starnes, Lukas Kambic, Michael B. Kantar, Thomas Wolfgruber, Kurt Lamour, et al. "Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight." G3: Genes|Genomes|Genetics 10, no. 8 (June 16, 2020): 2763–75. http://dx.doi.org/10.1534/g3.120.401367.

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Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. A comparison of family-level (Araceae) genome features reveals the repeat content of taro to be 82%, >3.5x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ∼391 vs. ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTL) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species.

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