Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat.
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ABSTRACT:
SUBMITTER: Lozano-Ramirez N
PROVIDER: S-EPMC9407756 | biostudies-literature | 2022 Aug
REPOSITORIES: biostudies-literature
Publications
Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat.
Lozano-Ramirez Nerida N Dreisigacker Susanne S Sansaloni Carolina P CP He Xinyao X Sandoval-Islas José Sergio JS Pérez-Rodríguez Paulino P Carballo Aquiles Carballo AC Diaz Cristian Nava CN Kishii Masahiro M Singh Pawan K PK
Genes 20220804 8
Spot blotch (SB) caused by <i>Bipolaris sorokiniana</i> (Sacc.) Shoem is a destructive fungal disease affecting wheat and many other crops. Synthetic hexaploid wheat (SHW) offers opportunities to explore new resistance genes for SB for introgression into elite bread wheat. The objectives of our study were to evaluate a collection of 441 SHWs for resistance to SB and to identify potential new genomic regions associated with the disease. The panel exhibited high SB resistance, with 250 accessions ...[more]
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Project description:Synthetic hexaploid wheat (SHW) has shown effective resistance to a diversity of diseases and insects, including tan spot, which is caused by Pyrenophora tritici-repentis, being an important foliar disease that can attack all types of wheat and several grasses. In this study, 443 SHW plants were evaluated for their resistance to tan spot under controlled environmental conditions. Additionally, a genome-wide association study was conducted by genotyping all entries with the DArTSeq technology to identify marker-trait associations for tan spot resistance. Of the 443 SHW plants, 233 showed resistant and 183 moderately resistant reactions, and only 27 were moderately susceptible or susceptible to tan spot. Durum wheat (DW) parents of the SHW showed moderately susceptible to susceptible reactions. A total of 30 significant marker-trait associations were found on chromosomes 1B (4 markers), 1D (1 marker), 2A (1 marker), 2D (2 markers), 3A (4 markers), 3D (3 markers), 4B (1 marker), 5A (4 markers), 6A (6 markers), 6B (1 marker) and 7D (3 markers). Increased resistance in the SHW in comparison to the DW parents, along with the significant association of resistance with the A and B genome, supported the concept of activating epistasis interaction across the three wheat genomes. Candidate genes coding for F-box and cytochrome P450 proteins that play significant roles in biotic stress resistance were identified for the significant markers. The identified resistant SHW lines can be deployed in wheat breeding for tan spot resistance.
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Project description:Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Project description:Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Project description:Spot blotch caused by the fungus Bipolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions of the world. Hence, the major objective of this study was to identify consistent genotyping-by-sequencing (GBS) markers associated with spot blotch resistance using genome-wide association mapping on a large set of 6,736 advanced bread wheat breeding lines from the International Maize and Wheat Improvement Center. These lines were phenotyped as seven panels at Agua Fria, Mexico between the 2013-2014 and 2019-2020 crop cycles. We identified 214 significant spot blotch associated GBS markers in all the panels, among which only 96 were significant in more than one panel, indicating a strong environmental effect on the trait and highlights the need for multiple phenotypic evaluations to identify lines with stable spot blotch resistance. The 96 consistent GBS markers were on chromosomes 1A, 1B, 1D, 2A, 3B, 4A, 5B, 5D, 6B, 7A, 7B, and 7D, including markers possibly linked to the Lr46, Sb1, Sb2 and Sb3 genes. We also report the association of the 2NS translocation from Aegilops ventricosa with spot blotch resistance in some environments. Moreover, the spot blotch favorable alleles at the 2NS translocation and two markers on chromosome 3BS (3B_2280114 and 3B_5601689) were associated with increased grain yield evaluated at several environments in Mexico and India, implying that selection for favorable alleles at these loci could enable simultaneous improvement for high grain yield and spot blotch resistance. Furthermore, a significant relationship between the percentage of favorable alleles in the lines and their spot blotch response was observed, which taken together with the multiple minor effect loci identified to be associated with spot blotch in this study, indicate quantitative genetic control of resistance. Overall, the results presented here have extended our knowledge on the genetic basis of spot blotch resistance in bread wheat and further efforts to improve genetic resistance to the disease are needed for reducing current and future losses under climate change.
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Project description:Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker-trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.
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Project description:Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most destructive wheat diseases worldwide. FHB infection can dramatically reduce grain yield and quality due to mycotoxins contamination. Wheat resistance to FHB is quantitatively inherited and many low-effect quantitative trait loci (QTL) have been mapped in the wheat genome. Synthetic hexaploid wheat (SHW) represents a novel source of FHB resistance derived from Aegilops tauschii and Triticum turgidum that can be transferred into common wheat (T. aestivum). In this study, a panel of 194 spring Synthetic Hexaploid Derived Wheat (SHDW) lines from the International Maize and Wheat Improvement Center (CIMMYT) was evaluated for FHB response under field conditions over three years (2017-2019). A significant phenotypic variation was found for disease incidence, severity, index, number of Fusarium Damaged Kernels (FDKs), and deoxynivalenol (DON) content. Further, 11 accessions displayed < 10 ppm DON in 2017 and 2019. Genotyping of the SHDW panel using a 90 K Single Nucleotide Polymorphism (SNP) chip array revealed 31 K polymorphic SNPs with a minor allele frequency (MAF) > 5%, which were used for a Genome-Wide Association Study (GWAS) of FHB resistance. A total of 52 significant marker-trait associations for FHB resistance were identified. These included 5 for DON content, 13 for the percentage of FDKs, 11 for the FHB index, 3 for disease incidence, and 20 for disease severity. A survey of genes associated with the markers identified 395 candidate genes that may be involved in FHB resistance. Collectively, our results strongly support the view that utilization of synthetic hexaploid wheat in wheat breeding would enhance diversity and introduce new sources of resistance against FHB into the common wheat gene pool. Further, validated SNP markers associated with FHB resistance may facilitate the screening of wheat populations for FHB resistance.
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