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Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm.

ABSTRACT:

Key message

Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an association mapping approach. African races of the stem rust pathogen (Puccinia graminis f. sp. tritici) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an association mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg-qtl-7H-12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg-qtl-5H-11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg-qtl-5H-11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding.

SUBMITTER: Zhou H

PROVIDER: S-EPMC4035542 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Stem rust of wheat caused by Puccinia graminis Pers. f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year × season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64-83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22, and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.

Project description:Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is a dangerous disease of common wheat worldwide. Development and cultivation of the varieties with genetic resistance is one of the most effective and environmentally important ways for protection of wheat against fungal pathogens. Field phytopathological screening and genome-wide association study (GWAS) were used for assessment of the genetic diversity of a collection of spring wheat genotypes on stem rust resistance loci. The collection consisting of Russian varieties of spring wheat and introgression lines with alien genetic materials was evaluated over three seasons (2016, 2017 and 2018) for resistance to the native population of stem rust specific to the West Siberian region of Russia. The results indicate that most varieties displayed from moderate to high levels of susceptibility to P. graminis; 16% of genotypes had resistance or immune response. In total, 13,006 single-nucleotide polymorphism (SNP) markers obtained from the Infinium 15K array were used to perform genome-wide association analysis. GWAS detected 35 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1A, 2A, 2B, 3B, 5A, 5B, 6A, 7A and 7B. The most significant associations were found on chromosomes 7A and 6A where known resistance genes Sr25 and Sr6Ai = 2 originated from Thinopyrum ssp. are located. Common wheat lines containing introgressed fragments from Triticum timopheevii and Triticum kiharae were found to carry Sr36 gene on 2B chromosome. It has been suggested that the quantitative trait loci (QTL) mapped to the chromosome 5BL may be new loci inherited from the T. timopheevii. It can be inferred that a number of Russian wheat varieties may contain the Sr17 gene, which does not currently provide effective protection against pathogen. This is the first report describing the results of analysis of the genetic factors conferring resistance of Russian spring wheat varieties to stem rust.

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Project description:Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.

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Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm.

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