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1
Yang, Zhuping, Jeannie Gilbert, George Fedak, and Daryl J. Somers. "Genetic characterization of QTL associated with resistance to Fusarium head blight in a doubled-haploid spring wheat population." Genome 48, no. 2 (April 1, 2005): 187–96. http://dx.doi.org/10.1139/g04-104.
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Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is the key to facilitating the introgression of different FHB resistance genes into adapted wheat. The objectives of the present study were to detect and map quantitative trait loci (QTL) associated with FHB resistance genes and characterize the genetic components of the QTL in a doubled-haploid (DH) spring wheat population using both single-locus and two-locus analysis. A mapping population, consisting of 174 DH lines from the cross between DH181 (resistant) and AC Foremost (susceptible), was evaluated for type I resistance to initial infection during a 2-year period in spray-inoculated field trials, for Type II resistance to fungal spread within the spike in 3 greenhouse experiments using single-floret inoculation, and for resistance to kernel infection in a 2001 field trial. One-locus QTL analysis revealed 7 QTL for type I resistance on chromosome arms 2DS, 3AS, 3BS, 3BC (centromeric), 4DL, 5AS, and 6BS, 4 QTL for type II resistance on chromosomes 2DS, 3BS, 6BS, and 7BL, and 6 QTL for resistance to kernel infection on chromosomes 1DL, 2DS, 3BS, 3BC, 4DL, and 6BS. Two-locus QTL analysis detected 8 QTL with main effects and 4 additive by additive epistatic interactions for FHB resistance and identified novel FHB resistance genes for the first time on chromosomes 1DL, 4AL, and 4DL. Neither significant QTL by environment interactions nor epistatic QTL by environment interactions were found for either type I or type II resistance. The additive effects of QTL explained most of the phenotypic variance for FHB resistance. Marker-assisted selection for the favored alleles at multiple genomic regions appears to be a promising tool to accelerate the introgression and pyramiding of different FHB resistance genes into adapted wheat genetic backgrounds.Key words: Triticum aestivum, Fusarium graminearum, microsatellite, additive effect, additive by additive epistatic effect.
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Colasuonno, Pasqualina, Ilaria Marcotuli, Agata Gadaleta, and Jose Miguel Soriano. "From Genetic Maps to QTL Cloning: An Overview for Durum Wheat." Plants 10, no. 2 (February 6, 2021): 315. http://dx.doi.org/10.3390/plants10020315.
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Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Rosa, Silvia B., Camila M. Zanella, Colin W. Hiebert, Anita L. Brûlé-Babel, Harpinder S. Randhawa, Stephen Shorter, Lesley A. Boyd, and Brent D. McCallum. "Genetic Characterization of Leaf and Stripe Rust Resistance in the Brazilian Wheat Cultivar Toropi." Phytopathology® 109, no. 10 (October 2019): 1760–68. http://dx.doi.org/10.1094/phyto-05-19-0159-r.
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Leaf and stripe rust are major threats to wheat production worldwide. The effective, multiple rust resistances present in the Brazilian cultivar Toropi makes it an excellent choice for a genetic study of rust resistance. Testing of DNA from different seed lots of Toropi with 2,194 polymorphic 90K iSelect single nucleotide polymorphism markers identified significant genetic divergence, with as much as 35% dissimilarity between seed lots. As a result, further work was conducted with a single plant line derived from Toropi variant Toropi-6.4. A double haploid population with 168 lines derived from the cross Toropi-6.4 × Thatcher was phenotyped over multiple years and locations in Canada, New Zealand, and Kenya, with a total of seven field trials undertaken for leaf rust and nine for stripe rust. Genotyping with the 90K iSelect array, simple sequence repeat and Kompetitive allele-specific polymerase chain reaction markers resulted in a genetic map of 3,043 cM, containing 1,208 nonredundant markers. Significant quantitative trait loci (QTL) derived from Toropi-6.4 were identified in multiple environments on chromosomes 1B (QLr.crc-1BL/QYr.crc-1BL), 3B (QLr.crc-3BS), 4B (QYr.crc-4BL), 5A (QLr.crc-5AL and QYr.crc-5AL), and 5D (QLr.crc-5DS). The QTL QLr.crc-1BL/QYr.crc-1BL colocated with the multi-rust resistance locus Lr46/Yr29, while the QTL QLr.crc-5DS located to the Lr78 locus previously found in a wheat backcross population derived from Toropi. Comparisons of QTL combinations showed QLr.crc-1BL to contribute a significantly enhanced leaf rust resistance when combined with QLr.crc-5AL or QLr.crc-5DS, more so than when QLr.crc-5AL and QLr.crc-5DS were combined. A strong additive effect was also seen when the stripe rust resistance QTL QYr.crc-1BL and QYr.crc-5AL were combined.
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Desiderio, Francesca, Salim Bourras, Elisabetta Mazzucotelli, Diego Rubiales, Beat Keller, Luigi Cattivelli, and Giampiero Valè. "Characterization of the Resistance to Powdery Mildew and Leaf Rust Carried by the Bread Wheat Cultivar Victo." International Journal of Molecular Sciences 22, no. 6 (March 18, 2021): 3109. http://dx.doi.org/10.3390/ijms22063109.
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Leaf rust and powdery mildew are two important foliar diseases in wheat. A recombinant inbred line (RIL) population, obtained by crossing two bread wheat cultivars (‘Victo’ and ‘Spada’), was evaluated for resistance to the two pathogens at seedling stage. Upon developing a genetic map of 8726 SNP loci, linkage analysis identified three resistance Quantitative Trait Loci (QTLs), with ‘Victo’ contributing the resistant alleles to all loci. One major QTL (QPm.gb-7A) was detected in response to Blumeria graminis on chromosome 7A, which explained 90% of phenotypic variation (PV). The co-positional relationship with known powdery mildew (Pm) resistance loci suggested that a new source of resistance was identified in T. aestivum. Two QTLs were detected in response to Puccinia triticina: a major gene on chromosome 5D (QLr.gb-5D), explaining a total PV of about 59%, and a minor QTL on chromosome 2B (QLr.gb-2B). A positional relationship was observed between the QLr.gb-5D with the known Lr1 gene, but polymorphisms were found between the cloned Lr1 and the corresponding ‘Victo’ allele, suggesting that QLr.gb-5D could represent a new functional Lr1 allele. Lastly, upon anchoring the QTL on the T. aestivum reference genome, candidate genes were hypothesized on the basis of gene annotation and in silico gene expression analysis.
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Semagn, Kassa, Muhammad Iqbal, Hua Chen, Enid Perez-Lara, Darcy H. Bemister, Rongrong Xiang, Jun Zou, et al. "Physical Mapping of QTL in Four Spring Wheat Populations under Conventional and Organic Management Systems. I. Earliness." Plants 10, no. 5 (April 23, 2021): 853. http://dx.doi.org/10.3390/plants10050853.
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In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the ‘Cutler’ × ‘AC Barrie’ population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the ‘Attila’ × ‘CDC Go’ population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the ‘Peace’ × ‘Carberry’ population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the ‘Peace’ × ‘CDC Stanley’ population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization.
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Raman, Harsh, Kerong Zhang, Mehmet Cakir, Rudi Appels, David F. Garvin, Lyza G. Maron, Leon V. Kochian, et al. "Molecular characterization and mapping of ALMT1, the aluminium-tolerance gene of bread wheat (Triticum aestivum L.)." Genome 48, no. 5 (October 1, 2005): 781–91. http://dx.doi.org/10.1139/g05-054.
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The major aluminum (Al) tolerance gene in wheat ALMT1 confers. An Al-activated efflux of malate from root apices. We determined the genomic structure of the ALMT1 gene and found it consists of 6 exons interrupted by 5 introns. Sequencing a range of wheat genotypes identified 3 alleles for ALMT1, 1 of which was identical to the ALMT1 gene from an Aegilops tauschii accession. The ALMT1 gene was mapped to chromosome 4DL using 'Chinese Spring' deletion lines, and loss of ALMT1 coincided with the loss of both Al tolerance and Al-activated malate efflux. Aluminium tolerance in each of 5 different doubled-haploid populations was found to be conditioned by a single major gene. When ALMT1 was polymorphic between the parental lines, QTL and linkage analyses indicated that ALMT1 mapped to chromosome 4DL and cosegregated with Al tolerance. In 2 populations examined, Al tolerance also segregated with a greater capacity for Al-activated malate efflux. Aluminium tolerance was not associated with a particular coding allele for ALMT1, but was significantly correlated with the relative level of ALMT1 expression. These findings suggest that the Al tolerance in a diverse range of wheat genotypes is primarily conditioned by ALMT1.Key words: aluminum, tolerance, genetic marker, Triticum aestivum, QTL, deletion mapping.
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Beecher, B., J. Bowman, J. M. Martin, A. D. Bettge, C. F. Morris, T. K. Blake, and M. J. Giroux. "Hordoindolines are associated with a major endosperm-texture QTL in Barley (Hordeum vulgare)." Genome 45, no. 3 (June 1, 2002): 584–91. http://dx.doi.org/10.1139/g02-008.
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Endosperm texture has a tremendous impact on the end-use quality of wheat (Triticum aestivum L.). Cultivars of barley (Hordeum vulgare L.), a close relative of wheat, also vary measurably in grain hardness. However, in contrast to wheat, little is known about the genetic control of barley grain hardness. Puroindolines are endosperm-specific proteins found in wheat and its relatives. In wheat, puroindoline sequence variation controls the majority of wheat grain texture variation. Hordoindolines, the puroindoline homologs of barley, have been identified and mapped. Recently, substantial allelic variation was found for hordoindolines among commercial barley cultivars. Our objective was to determine the influence of hordoindoline allelic variation upon grain hardness and dry matter digestibility in the 'Steptoe' × 'Morex' mapping population. This population is segregating for hordoindoline allele type, which was measured by a HinA/HinB/Gsp composite marker. One-hundred and fifty lines of the 'Steptoe' × 'Morex' population were grown in a replicated field trial. Grain hardness was estimated by near-infrared reflectance (NIR) and measured using the single kernel characterization system (SKCS). Variation attributable to the HinA/HinB/Gsp locus averaged 5.7 SKCS hardness units (SKCS U). QTL analysis revealed the presence of several areas of the genome associated with grain hardness. The largest QTL mapped to the HinA/HinB/Gsp region on the short arm of chomosome 7 (5H). This QTL explains 22% of the SKCS hardness difference observed in this study. The results indicate that the Hardness locus is present in barley and implicates the hordoindolines in endosperm texture control.Key words: puroindolines, grain hardness, digestibility.
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Saeed, Muhammad, Muhammad Ibrahim, Waqas Ahmad, Muhammad Tayyab, Safira Attacha, Mudassar Nawaz Khan, Sultan Akbar Jadoon, et al. "Molecular Characterization of Diverse Wheat Genetic Resources for Resistance to Yellow Rust Pathogen (Puccinia striiformis)." Agronomy 12, no. 12 (November 24, 2022): 2951. http://dx.doi.org/10.3390/agronomy12122951.
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Yellow rust (YR) epidemics have affected wheat productivity worldwide. YR resistance (Yr) is eminent in wheat; however, it is continuously invaded by evolving YR pathogen Puccinia striiformis (Pst.). Understanding the Yr genes’ diversity among the available germplasm is paramount to developing YR-resistant cultivars. In this study, 14 wheat genotypes were screened for their relative resistance index (RRI) and Yr genes/QTL via linked microsatellite markers. RRI screening categorized the studied genotypes into susceptible (<5; 4.44 ± 0.75), moderate (5–7; 6.11 ± 0.64), and resistant (>7; 8.45 ± 0.25) bulks (p < 0.001). Genetic analysis using 19 polymorphic microsatellite markers revealed 256 alleles, which were divergent among the three resistance bulks. Markers Xbarc7 and Xgwm429 showed the highest allelic diversity in comparison to Xbarc181, Xwmc419, SCAR1400, and Xgwm130. Resistant bulk showed associated alleles at Yr18 gene-linked markers Xgwm295, cssfr6, and csLV34. Other RRI-associated alleles at markers Xbarc7 and Xbarc101 showed weak and moderate linkages, respectively, with the Yr5 gene; whereas, a moderate association was noted for the Yr15 gene-linked marker Xgwm11. Marker Xwe173 linked with the Yr26 gene showed associated alleles among the susceptible bulk. Cross combinations of the parental lines forming recombinant inbred lines (RILs) demonstrated net higher RRI implying favorable allelic recombination. These results support reports and field observations on novel Pst. races that triggered Yr26, Yr5, and Yr15 busts in recent past. This study further implies that pyramiding all stage resistance genes (Yr5, Yr10, Yr15, and Yr26) with adult plant resistance genes (Yr18 and Yr62) should provide sustained YR resistance. The associated alleles at Yr genes-linked markers provide a basis for marker-assisted YR resistance breeding in wheat.
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Li, Ning, Fanfan Dong, Tongtong Liu, Jinwen Yang, Yugang Shi, Shuguang Wang, Daizhen Sun, and Ruilian Jing. "Quantitative trait loci mapping and candidate gene analysis of stoma-related traits in wheat (Triticum aestivum L.) glumes." PeerJ 10 (April 8, 2022): e13262. http://dx.doi.org/10.7717/peerj.13262.
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The photosynthesis of wheat glumes makes important contributions to the yield. Stomata play a crucial role in regulating photosynthesis and transpiration in plants. However, the genetic base of wheat glume stomata is not fully understood. In this study, stomatal length (SL), stomatal width (SW), stomatal density (SD), potential conductance index (PCI) of stomata, stomatal area (SA), and stomatal relative area (SRA) were measured in different parts of wheat glumes from a doubled haploid (DH) population and their parents. Quantitative trait loci (QTLs) of these traits were anchored on a high-density genetic linkage map of the DH population. A total of 61 QTLs for stoma-related traits were mapped onto 16 chromosomes, and each one accounted for 3.63 to 19.02% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals, AX-109400932∼AX-110985652 and AX-108972184∼AX-108752564, on chromosome 6A. Five possibly candidate genes (TraesCS6A02G105400, TraesCS6A02G106400, TraesCS6A02G115100, TraesCS6A02G115400, and TraesCS6A02G116200) for stoma-related traits of wheat glumes were screened out , according to their predicted expression levels in wheat glumes or spikes. The expression of these genes may be induced by a variety of abiotic stresses. These findings provide insights for cloning and functional characterization of stoma-related candidate genes in wheat glumes.
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Ponce-Molina, L. J., J. Huerta-Espino, R. P. Singh, B. R. Basnet, G. Alvarado, M. S. Randhawa, C. X. Lan, V. H. Aguilar-Rincón, R. Lobato-Ortiz, and J. J. García-Zavala. "Characterization of Leaf Rust and Stripe Rust Resistance in Spring Wheat ‘Chilero’." Plant Disease 102, no. 2 (February 2018): 421–27. http://dx.doi.org/10.1094/pdis-11-16-1545-re.
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Since 1984, the ‘Chilero’ spring wheat line developed by CIMMYT has proven to be highly resistant to leaf rust and stripe rust. Amid efforts to understand the basis of resistance of this line, a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero was studied. The parents and RILs were characterized in field trials for leaf rust and stripe rust in three locations in Mexico between 2012 and 2015 and genotyped with DArT-array, DArT-GBS, and SSR markers. A total of 6,168 polymorphic markers were used to construct genetic linkage maps. Inclusive composite interval mapping detected four colocated resistance loci to both rust diseases and two stripe rust resistant loci in the Avocet × Chilero population. Among these, the quantitative trait locus (QTL) on chromosome 1BL was identified as a pleotropic adult plant resistance gene Lr46/Yr29, whereas QLr.cim-5DS/QYr.cim-5DS was a newly discovered colocated resistance locus to both rust diseases in Chilero. Additionally, one new stripe rust resistance locus on chromosome 7BL was mapped in the current population. Avocet also contributed two minor colocated resistance QTLs situated on chromosomes 1DL and 4BS. The flanking SNP markers can be converted to breeder friendly Kompetitive Allele Specific PCR (KASP) markers for wheat breeding programs.
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Glenn, Priscilla, Junli Zhang, Gina Brown-Guedira, Noah DeWitt, Jason P. Cook, Kun Li, Eduard Akhunov, and Jorge Dubcovsky. "Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat." Theoretical and Applied Genetics 135, no. 2 (November 26, 2021): 679–92. http://dx.doi.org/10.1007/s00122-021-03992-y.
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Abstract Key message We discovered a natural FT-A2 allele that increases grain number per spike in both pasta and bread wheat with limited effect on heading time. Abstract Increases in wheat grain yield are necessary to meet future global food demands. A previous study showed that loss-of-function mutations in FLOWERING LOCUS T2 (FT2) increase spikelet number per spike (SNS), an important grain yield component. However, these mutations were also associated with reduced fertility, offsetting the beneficial effect of the increases in SNS on grain number. Here, we report a natural mutation resulting in an aspartic acid to alanine change at position 10 (D10A) associated with significant increases in SNS and no negative effects on fertility. Using a high-density genetic map, we delimited the SNS candidate region to a 5.2-Mb region on chromosome 3AS including 28 genes. Among them, only FT-A2 showed a non-synonymous polymorphism (D10A) present in two different populations segregating for the SNS QTL on chromosome arm 3AS. These results, together with the known effect of the ft-A2 mutations on SNS, suggest that variation in FT-A2 is the most likely cause of the observed differences in SNS. We validated the positive effects of the A10 allele on SNS, grain number, and grain yield per spike in near-isogenic tetraploid wheat lines and in an hexaploid winter wheat population. The A10 allele is present at very low frequency in durum wheat and at much higher frequency in hexaploid wheat, particularly in winter and fall-planted spring varieties. These results suggest that the FT-A2 A10 allele may be particularly useful for improving grain yield in durum wheat and fall-planted common wheat varieties.
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Oliver, R. E., D. E. Obert, G. Hu, J. M. Bonman, E. O’Leary-Jepsen, and E. W. Jackson. "Development of oat-based markers from barley and wheat microsatellites." Genome 53, no. 6 (June 2010): 458–71. http://dx.doi.org/10.1139/g10-021.
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Although microsatellites are an efficient and reliable genetic marker system, availability is limited in cultivated oat ( Avena sativa L.). Previous research has suggested that microsatellites from related species may be adapted to oat. This study investigated the stability of existing oat microsatellites, sequenced polymorphic oat amplicons derived from wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.) primers, and redesigned primers to develop oat-based markers. We evaluated 161 published oat microsatellites and identified 9 with polymorphism between mapping parents Ogle1040 and TAM O-301 (OT). We also studied 30 wheat, 1 Aegilops tauschii Coss., and 9 barley primers with reported oat polymorphism. Sixteen primers (1 A. tauschii, 10 wheat, 5 barley) amplified random oat sequences and were used to generate 28 new oat STS markers. Eight primers, 4 each from wheat and barley, amplified oat repetitive motifs, generating 10 new oat SSRs. Four additional SSRs were developed from characterization of thaumatin-like pathogenesis-related protein sequences formerly utilized as the Rast1–4 oat marker. These new markers, along with 9 existing oat SSRs and 6 previously identified disease resistance loci, were mapped in the OT population, joining 3 pairs of linkage groups. Map locations of multiallelic SSRs and disease-resistance QTL interactions suggested possible homoeologous relationships among the oat chromosomes.
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Yu, Shuhao, Silvano O. Assanga, Joseph M. Awika, Amir M. H. Ibrahim, Jackie C. Rudd, Qingwu Xue, Mary J. Guttieri, et al. "Genetic Mapping of Quantitative Trait Loci for End-Use Quality and Grain Minerals in Hard Red Winter Wheat." Agronomy 11, no. 12 (December 11, 2021): 2519. http://dx.doi.org/10.3390/agronomy11122519.
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To meet the demands of different wheat-based food products, traits related to end-use quality become indispensable components in wheat improvement. Thus, markers associated with these traits are valuable for the timely evaluation of protein content, kernel physical characteristics, and rheological properties. Hereunder, we report the mapping results of quantitative trait loci (QTLs) linked to end-use quality traits. We used a dense genetic map with 5199 SNPs from a 90K array based on a recombinant inbred line (RIL) population derived from ‘CO960293-2’/‘TAM 111’. The population was evaluated for flour protein concentration, kernel characteristics, dough rheological properties, and grain mineral concentrations. An inclusive composite interval mapping model for individual and across-environment QTL analyses revealed 22 consistent QTLs identified in two or more environments. Chromosomes 1A, 1B, and 1D had clustered QTLs associated with rheological parameters. Glu-D1 loci from CO960293-2 and either low-molecular-weight glutenin subunits or gliadin loci on 1A, 1B, and 1D influenced dough mixing properties substantially, with up to 34.2% of the total phenotypic variation explained (PVE). A total of five QTLs associated with grain Cd, Co, and Mo concentrations were identified on 3B, 5A, and 7B, explaining up to 11.6% of PVE. The results provide important genetic resources towards understanding the genetic bases of end-use quality traits. Information about the novel and consistent QTLs provided solid foundations for further characterization and marker designing to assist selections for end-use quality improvements.
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DOU, BINGDE, BEIWEI HOU, HAIMING XU, XIANGYANG LOU, XIAOFEI CHI, JINBIN YANG, FANG WANG, ZHONGFU NI, and QIXIN SUN. "Efficient mapping of a female sterile gene in wheat (Triticum aestivum L.)." Genetics Research 91, no. 5 (October 2009): 337–43. http://dx.doi.org/10.1017/s0016672309990218.
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SummaryStudies on inheritance of fertility are of great importance in wheat breeding. Although substantial progress has been achieved in molecular characterization of male sterility and fertility restoration recently, little effort has been devoted to female sterility. To identify the gene(s) controlling female sterility in wheat efficiently, an investigation was conducted for the seed setting ratio using a set of F2 populations derived from the cross between a female sterile line XND126 and an elite cultivar Gaocheng 8901. Bulked segregation analysis (BSA) method and recessive class approach were adopted to screen for SSR markers potentially linked to female fertility gene loci in 2005. Out of 1080 SSRs in wheat genome, eight markers on chromosome 2D showed a clear difference between two disparate bulks and small recombination frequency values, suggesting a strong linkage signal to the sterility gene. Based on the candidate linked markers, partial linkage maps were constructed with Mapmaker 3.0 (EXP) instead of whole genome maps, and quantitative trait locus (QTL) mapping was implemented with software QTLNetwork 2.0. A major gene locus designated as taf1, was located on chromosome 2DS. The above result was confirmed by the analysis for 2007 data, and taf1 was identified on the same chromosome 2DS with a confidence interval of 2·4 cM, which could explain 44·99% of phenotypic variation. These results provided fundamental information for fine mapping studies and laid the groundwork for wheat fertility genetic studies.
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Tasma, I. Made. "Gen dan QTL Pengendali Toleransi Tanaman terhadap Keracunan Aluminium dan Aplikasinya untuk Pemuliaan Tanaman di Indonesia." Jurnal AgroBiogen 11, no. 3 (August 10, 2016): 111. http://dx.doi.org/10.21082/jbio.v11n3.2015.p111-124.
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<p>Genetic knowledge of loci controlling Al toxicity tolerance is the key for a successful breeding program in developing Al<br />tolerant cultivars. Tolerance level of crop plants to Al toxicity is genetically controlled. The gene inheritance pattern is mainly<br />resulted from intensive studies of cereal crops, such as wheat, sorghum, maize, and rice. The trait can be controlled by a<br />single dominant gene, a single dominant gene with many alleles, a pair of dominant genes, or by many genes (QTL). The<br />majority of the Al tolerance genes identified so far belongs to two independent groups of gene families, i.e. aluminumactivated<br />malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE), both encoding transport proteins<br />involved in Al-activated organic acid release, mainly citrate and malate. The variations in Al toxicity tolerance phenotypes are<br />strongly correlated with the expressions of such genes in the root apical cells. Many Al tolerance QTLs have been mapped in<br />the genomes of various crop species and were found to be colocated with the ALMT and MATE genes. The genetic maps of<br />the Al tolerance genes and QTLs facilitate breeding programs for developing Al-tolerant cultivars through marker-assisted<br />breeding methods. Al tolerance genes that have been isolated from genetically unrelated species can be used in genetic<br />transformation studies of crop genotypes sexually incompatible to the gene source genotypes. The application of these<br />molecular breeding methods expedites breeding programs to develop crop cultivars tolerance to Al toxicity and acid soils.<br />Genomic technologies by using next-generation sequencing and high-throughput genotyping system accelerate Al toxicity<br />tolerance gene and QTL discoveries of various crop species. The modern genomic technologies also facilitate more<br />comprehensive PGR characterization and utilization to accelerate identification and isolation of the Al tolerance genes and<br />QTLs to be used in a more comprehensive breeding program to support national food self sufficiency and food security<br />programs.</p>
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Fu, Chao, Jiuyuan Du, Xiuling Tian, Zhonghu He, Luping Fu, Yue Wang, Dengan Xu, et al. "Rapid identification and characterization of genetic loci for defective kernel in bread wheat." BMC Plant Biology 19, no. 1 (November 8, 2019). http://dx.doi.org/10.1186/s12870-019-2102-6.
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Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78–18.17%, 16.61–21.83% and 19.08–28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Three major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.
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Zhou, Jieguang, Cong Li, Jianing You, Huaping Tang, Yang Mu, Qiantao Jiang, Yaxi Liu, et al. "Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat." BMC Genomics 22, no. 1 (September 30, 2021). http://dx.doi.org/10.1186/s12864-021-08024-z.
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Abstract Background Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield. Results In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6–695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes. Conclusions Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.
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Ruan, Yuefeng, Wentao Zhang, Ron E. Knox, Samia Berraies, Heather L. Campbell, Raja Ragupathy, Kerry Boyle, et al. "Characterization of the Genetic Architecture for Fusarium Head Blight Resistance in Durum Wheat: The Complex Association of Resistance, Flowering Time, and Height Genes." Frontiers in Plant Science 11 (December 23, 2020). http://dx.doi.org/10.3389/fpls.2020.592064.
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Durum wheat is an economically important crop for Canadian farmers. Fusarium head blight (FHB) is one of the most destructive diseases that threatens durum production in Canada. FHB reduces yield and end-use quality and most commonly contaminates the grain with the fungal mycotoxin deoxynivalenol, also known as DON. Serious outbreaks of FHB can occur in durum wheat in Canada, and combining genetic resistance with fungicide application is a cost effective approach to control this disease. However, there is limited variation for genetic resistance to FHB in elite Canadian durum cultivars. To explore and identify useful genetic FHB resistance variation for the improvement of Canadian durum wheat, we assembled an association mapping (AM) panel of diverse durum germplasms and performed genome wide association analysis (GWAS). Thirty-one quantitative trait loci (QTL) across all 14 chromosomes were significantly associated with FHB resistance. On 3BS, a stable QTL with a larger effect for resistance was located close to the centromere of 3BS. Three haplotypes of Fhb1 QTL were identified, with an emmer wheat haplotype contributing to disease susceptibility. The large number of QTL identified here can provide a rich resource to improve FHB resistance in commercially grown durum wheat. Among the 31 QTL most were associated with plant height and/or flower time. QTL 1A.1, 1A.2, 3B.2, 5A.1, 6A.1, 7A.3 were associated with FHB resistance and not associated or only weakly associated with flowering time nor plant height. These QTL have features that would make them good targets for FHB resistance breeding.
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Sharma, Jyoti Saini, Megan Overlander, Justin D. Faris, Daryl L. Klindworth, Matthew N. Rouse, Houyang Kang, Yunming Long, Yue Jin, Evans S. Lagudah, and Steven S. Xu. "Characterization of synthetic wheat line Largo for resistance to stem rust." G3 Genes|Genomes|Genetics 11, no. 8 (June 4, 2021). http://dx.doi.org/10.1093/g3journal/jkab193.
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Abstract Resistance breeding is an effective approach against wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The synthetic hexaploid wheat line Largo (pedigree: durum wheat “Langdon” × Aegilops tauschii PI 268210) was found to have resistance to a broad spectrum of Pgt races including the Ug99 race group. To identify the stem rust resistance (Sr) genes, we genotyped a population of 188 recombinant inbred lines developed from a cross between the susceptible wheat line ND495 and Largo using the wheat Infinium 90 K SNP iSelect array and evaluated the population for seedling resistance to the Pgt races TTKSK, TRTTF, and TTTTF in the greenhouse conditions. Based on genetic linkage analysis using the marker and rust data, we identified six quantitative trait loci (QTL) with effectiveness against different races. Three QTL on chromosome arms 6AL, 2BL, and 2BS corresponded to Sr genes Sr13c, Sr9e, and a likely new gene from Langdon, respectively. Two other QTL from PI 268210 on 2DS and 1DS were associated with a potentially new allele of Sr46 and a likely new Sr gene, respectively. In addition, Sr7a was identified as the underlying gene for the 4AL QTL from ND495. Knowledge of the Sr genes in Largo will help to design breeding experiments aimed to develop new stem rust-resistant wheat varieties. Largo and its derived lines are particularly useful for introducing two Ug99-effective genes Sr13c and Sr46 into modern bread wheat varieties. The 90 K SNP-based high-density map will be useful for identifying the other important genes in Largo.
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Ramírez-Flores, M. Rosario, Sergio Perez-Limon, Meng Li, Benjamín Barrales-Gamez, Doris Albinsky, Uta Paszkowski, Víctor Olalde-Portugal, and Ruairidh JH Sawers. "The genetic architecture of host response reveals the importance of arbuscular mycorrhizae to maize cultivation." eLife 9 (November 19, 2020). http://dx.doi.org/10.7554/elife.61701.
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Arbuscular mycorrhizal fungi (AMF) are ubiquitous in cultivated soils, forming symbiotic relationships with the roots of major crop species. Studies in controlled conditions have demonstrated the potential of AMF to enhance the growth of host plants. However, it is difficult to estimate the actual benefit in the field, not least because of the lack of suitable AMF-free controls. Here we implement a novel strategy using the selective incorporation of AMF-resistance into a genetic mapping population to evaluate maize response to AMF. We found AMF to account for about one-third of the grain production in a medium input field, as well as to affect the relative performance of different plant genotypes. Characterization of the genetic architecture of the host response indicated a trade-off between mycorrhizal dependence and benefit. We identified several QTL linked to host benefit, supporting the feasibility of breeding crops to maximize profit from symbiosis with AMF.
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Rauf, Yahya, Prabin Bajgain, Matthew Rouse, Khalil A. Khanzada, Sridhar Bhavani, Julio Huerta-Espino, Ravi P. Singh, Muhammad Imtiaz, and Jim A. Anderson. "Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population." Plant Disease, August 5, 2021. http://dx.doi.org/10.1094/pdis-03-21-0672-re.
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Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RIL) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping (CIM) using 762 Genotyping-by-Sequencing (GBS) markers, identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37 and Yr17. Three QTL were mapped on chromosomes 2B, two QTL on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27-39% less stem rust coefficient of infection in all field environments compared to RILs with none of these genes and this gene combination was most effective in the US environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.
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Zhang, Wentao, Kerry Boyle, Peng Gao, Brittany Polley, Jennifer M. Brost, Tammy Francis, Christine Sidebottom, et al. "Systematic characterization of multi-rust resistance genes from a ‘Parula x Thatcher’ population with high-density genetic map." Phytopathology®, January 19, 2023. http://dx.doi.org/10.1094/phyto-06-22-0238-fi.
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Pyramiding multiple resistant genes has been proposed as the most effective way to control wheat rust diseases globally. Identifying the most effective pyramids is challenged by the large pool of rust resistance genes, and limited information about their mechanisms of resistance and interactions. Here, using a high-density genetic map, a double haploid population, and multi-rust field testing, we aimed to systematically characterize the most effective gene pyramids for rust resistance from the durable multi-rust resistant CIMMYT cultivar, Parula. We revealed the Parula resistance gene pyramid contains Lr34/Yr18/Sr57 (Lr34), Lr46/Yr29/Sr58 (Lr46), Lr27/Yr30/Sr2 (Sr2) and Lr68. The efficacy, magnitude of effect and interactions with each other varied for the three rust diseases. A subpopulation mapping approach was applied to characterize the complex interactions of the resistance genes by controlling for the effect of Lr34. Using this approach, we found Lr34 and Lr68 have a strong additive effect for leaf rust, while no additive effects were observed for any rusts between Lr34 and Lr46. Lr34 combined synergistically with Sr12 from Thatcher for stem rust, while the additive effect of Lr34 and Sr2 was dependent on the type of rust and environment. Two novel leaf rust QTL from Parula were identified in this study, a stable QTL QLr-7BS, and QLr-5AS, which showed Lr34 dependent expression. With these findings, we propose combining 2–3 high value genes from Canadian wheat (e.g. Sr12 from Thatcher) with a foundational multi-APR cassette for desirable and durable resistance to all three rusts in Canadian wheat.
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Pradhan, Anjan Kumar, Sundeep Kumar, Amit Kumar Singh, Neeraj Budhlakoti, Dwijesh C. Mishra, Divya Chauhan, Shikha Mittal, et al. "Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India." Frontiers in Genetics 11 (November 27, 2020). http://dx.doi.org/10.3389/fgene.2020.572975.
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Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.
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Shewabez, Elias, Endashaw Bekele, Admas Alemu, Laura Mugnai, and Wuletaw Tadesse. "Genetic characterization and genome-wide association mapping for stem rust resistance in spring bread wheat." BMC Genomic Data 23, no. 1 (February 14, 2022). http://dx.doi.org/10.1186/s12863-022-01030-4.
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Abstract Background Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI). Results Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log10 (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B. Conclusions This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance.
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Xue, Shulin, Mingxue Lu, Shanshan Hu, Hongxing Xu, Yuyu Ma, Nan Lu, Shenglong Bai, Aoyang Gu, Hongshen Wan, and Suoping Li. "Characterization of PmHHXM, a New Broad-spectrum Powdery Mildew Resistance Gene in Chinese Wheat Landrace Honghuaxiaomai." Plant Disease, January 8, 2021. http://dx.doi.org/10.1094/pdis-10-20-2296-re.
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Powdery mildew, caused by fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is one of agronomically important and widespread wheat diseases causing severe yield losses. Deployment of broad‐spectrum disease-resistance genes is the preferred strategy to prevent this pathogen. Chinese wheat landrace Honghuaxiaomai (HHXM) was resistant to all 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:3 progenies derived from the cross HHXM × Yangmai 158 were used in this study, and genetic analysis revealed that a single dominant gene, designated as PmHHXM, conferred resistance to Bgt isolate E09. Bulked segregant analysis and molecular mapping initially located PmHHXM to the distal region of chromosome 4AL. To fine map PmHHXM, two critical recombinants were identified from 592 F2 plants and delimited PmHHXM to a 0.18-cM Xkasp475200–Xhnu552 interval covering 1.77-Mb, in which a number of disease resistance-related gene clusters were annotated. Comparative mapping of this interval revealed a perturbed synteny among Triticeae species. This study reports the new powdery mildew resistance gene PmHHXM that seems different from three known QTL/genes identified on chromosome 4AL and has significant values for further genetic improvement. Analysis of the polymorphisms of 13 co-segregating markers between HHXM and 170 modern wheat cultivars indicates that Xhnu227 and Xsts478700 developed here are ideal for marker-assisted introgression of this resistance gene in wheat breeding.
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Xue, Shulin, Mingxue Lu, Shanshan Hu, Hongxing Xu, Yuyu Ma, Nan Lu, Shenglong Bai, Aoyang Gu, Hongshen Wan, and Suoping Li. "Characterization of PmHHXM, a New Broad-spectrum Powdery Mildew Resistance Gene in Chinese Wheat Landrace Honghuaxiaomai." Plant Disease, January 8, 2021. http://dx.doi.org/10.1094/pdis-10-20-2296-re.
Full textAbstract:
Powdery mildew, caused by fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is one of agronomically important and widespread wheat diseases causing severe yield losses. Deployment of broad‐spectrum disease-resistance genes is the preferred strategy to prevent this pathogen. Chinese wheat landrace Honghuaxiaomai (HHXM) was resistant to all 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:3 progenies derived from the cross HHXM × Yangmai 158 were used in this study, and genetic analysis revealed that a single dominant gene, designated as PmHHXM, conferred resistance to Bgt isolate E09. Bulked segregant analysis and molecular mapping initially located PmHHXM to the distal region of chromosome 4AL. To fine map PmHHXM, two critical recombinants were identified from 592 F2 plants and delimited PmHHXM to a 0.18-cM Xkasp475200–Xhnu552 interval covering 1.77-Mb, in which a number of disease resistance-related gene clusters were annotated. Comparative mapping of this interval revealed a perturbed synteny among Triticeae species. This study reports the new powdery mildew resistance gene PmHHXM that seems different from three known QTL/genes identified on chromosome 4AL and has significant values for further genetic improvement. Analysis of the polymorphisms of 13 co-segregating markers between HHXM and 170 modern wheat cultivars indicates that Xhnu227 and Xsts478700 developed here are ideal for marker-assisted introgression of this resistance gene in wheat breeding.
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Katz, Andrew, Patrick Byrne, Scott Reid, Sarah Bratschun, Scott Haley, and Stephen Pearce. "Identification and validation of a QTL for spikelet number on chromosome arm 6BL of common wheat (Triticum aestivum L.)." Molecular Breeding 42, no. 4 (March 21, 2022). http://dx.doi.org/10.1007/s11032-022-01288-7.
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AbstractTo provide food security for a growing world population, it will be necessary to increase yields of staple crops such as wheat (Triticum aestivum L.). Yield is a complex, polygenic trait influenced by grain weight and number, which are negatively correlated with one another. Spikelet number is an important determinant of grain number, but allelic variants impacting its expression are often associated with heading date, constraining their use in wheat germplasm that must be adapted for specific environments. Identification and characterization of genetic variants affecting spikelet number will increase selection efficiency through their deployment in breeding programs. In this study, a quantitative trait locus (QTL) on chromosome arm 6BL for spikelet number was identified and validated using an association mapping panel, a recombinant inbred line population, and seven derived heterogeneous inbred families. The superior allele, QSn.csu-6Bb, was associated with an increase of 0.248 to 0.808 spikelets per spike across multiple environments that varied for mean spikelet number. Despite epistatic interactions between QSn.csu-6B and three other loci (WAPO-A1, VRN-D3, and PPD-B1), genotypes with a greater number of superior alleles at these loci consistently exhibit higher spikelet number. The frequency of superior alleles at these loci varies among winter wheat varieties adapted to different latitudes of the US Great Plains, revealing opportunities for breeders to select for increased spikelet number using simple molecular markers. This work lays the foundation for the positional cloning of the genetic variant underlying the QSn.csu-6B QTL to strengthen our understanding of spikelet number determination in wheat.
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Vikram, Prashant, Cynthia Ortiz, S. Singh, and Sukhwinder Singh. "Genetic analysis revealed a quantitative trait loci (QTL2A.K) on short arm of chromosome 2A associated with yellow rust resistance in wheat (Triticum aestivum L.)." Indian Journal of Genetics and Plant Breeding (The) 80, no. 03 (September 22, 2020). http://dx.doi.org/10.31742/ijgpb.80.3.1.
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Yellow rust, caused by Puccinia striiformis, is one of the most devastating diseases in wheat. A synthetic by elite recombinant inbred line (RIL) population derived from a cross, Botnol/Aegilops squarrosa (666)//Kachu was evaluated for yellow rust resistance in two different environments in Mexico. The population was subjected to DArT-seq analysis for an in-depth genetic characterization. A major effect rust resistance QTL (QTL2A.K) explaining up to 45% phenotypic variance was found to be contributed by Kachee, an elite line of International Maize and Wheat Improvement Center (CIMMYT) Mexico. The QTL2A.K was found to be contributed by a segment of 2NS Chromosome of Triticum ventricosum translocated into the short arm of bread wheat chromosome 2A (QTL2A.K). The position of QTL2A.K was confirmed using T. ventricosum specific primer VENTRIUP-LN2. Identified genomic regions are being introgressed in to the popular but susceptible wheat varieties through marker-assisted breeding for enhancing yellow rust resistance.
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Zhou, Jingwei, Ravi P. Singh, Yong Ren, Bin Bai, Zhikang Li, Chan Yuan, Shunda Li, Julio Huerta-Espino, Demei LIU, and Caixia Lan. "Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety ‘Neimai 836’." Plant Disease, March 29, 2021. http://dx.doi.org/10.1094/pdis-12-20-2654-re.
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The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety ‘Apav#1’ and resistant variety ‘Neimai 836’ was used to develop a mapping population containing 148 F5 recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico in 2017 and in Mianyang, Ezhou, and Gansu, China in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multi-pathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3-16% of the phenotypic variation in resistance to leaf rust and 7-14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high level resistance to both leaf rust and stripe rust.
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Kumar, Sundeep, Sherry R. Jacob, Reyazul Rouf Mir, V. K. Vikas, Pawan Kulwal, Tilak Chandra, Satinder Kaur, et al. "Indian Wheat Genomics Initiative for Harnessing the Potential of Wheat Germplasm Resources for Breeding Disease-Resistant, Nutrient-Dense, and Climate-Resilient Cultivars." Frontiers in Genetics 13 (June 29, 2022). http://dx.doi.org/10.3389/fgene.2022.834366.
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Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.
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Shi, Xiaohan, Peipei Wu, Jinghuang Hu, Dan Qiu, Yunfeng Qu, Yahui Li, Yi Liu, et al. "Molecular characterization of adult plant resistance loci against powdery mildew in winter wheat cultivar Liangxing 99 using BSR-Seq technology." Plant Disease, May 19, 2021. http://dx.doi.org/10.1094/pdis-03-21-0664-re.
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Winter wheat cultivar Liangxing 99, which carries gene Pm52, is resistant to powdery mildew at both seedling and adult plant stages. An F2:6 recombinant inbred line (RIL) population from cross Liangxing 99 × Zhongzuo 9504 was phenotyped with Blumeria graminis f. sp. tritici isolate Bgt27 at the adult plant stage in four field tests and the seedling stage in a greenhouse test. The analysis of bulk segregant RNA sequences identified an SNP-enriched locus, Qaprpm.caas.2B, on chromosome 2BL in the same genomic interval of Pm52 associated with the all-stage resistance (ASR) and Qaprpm.caas.7A on chromosome 7AL associated with the adult-plant resistance (APR) against the disease. Qaprpm.caas.2B was detected in a 1.3 cM genetic interval between markers Xicscl726 and XicsK128 in which Pm52 was placed with a range of LOD values from 28.1 to 34.6, and the phenotype variations explained in terms of maximum disease severity (MDS) ranged from 45% to 52%. The LOD peak of Qaprpm.caas.7A was localized in a 4.6 cM interval between markers XicsK7A8 and XicsK7A26 and explained the phenotypic variation of MDS ranging from 13% to 16%. The results of this study confirmed Pm52 for ASR and identified Qaprpm.caas.7A for APR to powdery mildew in Liangxing 99. Keywords: Triticum aestivum; Blumeria graminis f. sp. tritici; Pm52; QTL; BSR-Seq