Genome wide association mapping through 90K SNP array against Leaf rust pathogen in bread wheat genotypes under field conditions

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

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Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes

Frontiers in Plant Science ◽

10.3389/fpls.2021.640739 ◽

2021 ◽

Vol 12 ◽

Author(s):

Meriem Aoun ◽

Matthew N. Rouse ◽

James A. Kolmer ◽

Ajay Kumar ◽

Elias M. Elias

Keyword(s):

Durum Wheat ◽

Leaf Rust ◽

Stripe Rust ◽

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Genome Wide Association ◽

Genome Wide ◽

Rust Pathogen ◽

Rust Resistance Genes

Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.

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Genome-wide association analyses for yield and yield-related traits in bread wheat (Triticum aestivum L.) under pre-anthesis combined heat and drought stress in field conditions

PLoS ONE ◽

10.1371/journal.pone.0213407 ◽

2019 ◽

Vol 14 (3) ◽

pp. e0213407 ◽

Cited By ~ 6

Author(s):

Mirza Faisal Qaseem ◽

Rahmatullah Qureshi ◽

Humaira Shaheen ◽

Noshin Shafqat

Keyword(s):

Triticum Aestivum ◽

Drought Stress ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Field Conditions ◽

Genome Wide Association ◽

Association Analyses ◽

Genome Wide

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Incorporating Genome-Wide Association Mapping Results Into Genomic Prediction Models for Grain Yield and Yield Stability in CIMMYT Spring Bread Wheat

Frontiers in Plant Science ◽

10.3389/fpls.2020.00197 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 2

Author(s):

Deepmala Sehgal ◽

Umesh Rosyara ◽

Suchismita Mondal ◽

Ravi Singh ◽

Jesse Poland ◽

...

Keyword(s):

Grain Yield ◽

Association Mapping ◽

Bread Wheat ◽

Genomic Prediction ◽

Prediction Models ◽

Yield Stability ◽

Genome Wide Association ◽

Spring Bread Wheat ◽

Genome Wide

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Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.0156 ◽

2015 ◽

Vol 282 (1806) ◽

pp. 20150156 ◽

Cited By ~ 34

Author(s):

Arild Husby ◽

Takeshi Kawakami ◽

Lars Rönnegård ◽

Linnéa Smeds ◽

Hans Ellegren ◽

...

Keyword(s):

Life History ◽

Association Mapping ◽

Genetic Basis ◽

Snp Array ◽

Genome Wide Association ◽

Life History Trait ◽

Lifetime Reproductive Success ◽

Phenotypic Variance ◽

Sexual Antagonism ◽

Genome Wide

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

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