Genome‐Wide Association Mapping of Leaf Rust Response in a Durum Wheat Worldwide Germplasm Collection

Abstract

Leaf rust (caused by Puccinia triticina Erikss. [Pt]) is increasingly impacting durum wheat (Triticum turgidum L. var. durum) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent P. triticina race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments. Genome-wide association study (GWAS) was used to identify single-nucleotide polymorphism (SNP) markers associated with leaf rust response in a worldwide durum wheat collection of 496 accessions. Thirteen accessions were resistant across all experiments. Association mapping revealed 88 significant SNPs associated with leaf rust response. Of these, 33 SNPs were located on chromosomes 2A and 2B, and 55 SNPs were distributed across all other chromosomes except for 1B and 7B. Twenty markers were associated with leaf rust response at seedling stage, while 68 markers were associated with leaf rust response at adult plant stage. The current study identified a total of 14 previously uncharacterized loci associated with leaf rust response in durum wheat. The discovery of these loci through association mapping (AM) is a significant step in identifying useful sources of resistance that can be used to broaden the relatively narrow leaf rust resistance spectrum in durum wheat germplasm. Abbreviations: AM, association mapping; ARS, Agricultural Research Service; CDL, Cereal Disease Laboratory; GWAS, genome-wide association study; IT, infection type; LD, linkage disequilibrium; MAF, minor allele frequency; MR, moderately resistant; MS, moderately susceptible; MSD, mean squared difference; NSGC, National Small Grain Collection; PC, principal component; PCA, principal component analysis; pFDR, positive false discovery rate; Pt, Puccinia triticina Erikss.; QTL, quantitative trait loci; R, resistant; S, susceptible; SNP, single-nucleotide polymorphism; SSR, simple-sequence repeat. Core Ideas• Thirteen durum wheat accessions showed resistance to all Puccinia triticina races tested• GWAS revealed 88 SNPs (37 loci) associated with leaf rust response in durum wheat• Associations were identified on all chromosomes except 1B and 7B• GWAS revealed 14 previously uncharacterized loci for leaf rust resistance

Pod indehiscence is a domestication and aridity resilience trait in common bean

“…For association mapping, different panels were used. Two-hundred and eight members of the Andean Diversity Panel (ADP; Cichy et al, 2015) and 278 members of the Middle American Diversity (MDP; Moghaddam et al, 2016) were grown and phenotyped. Sequencing was performed in a diverse panel of 90 varieties representing six species were acquired from the National Plant Germplasm System (NPGS).…”

“…Segregation data of pod shattering data (oven test proportion, force, and shattering in the field) as well as SNP markers in the I9S population have been deposited in the UC Davis Dash public database (doi: 10.25338/B8TW2N:Gepts et al, 2019; doi: 10.25338/B8ZG68: Parker et al, 2019).Genotype data for the Middle American Diversity Panel(Moghaddam et al, 2016) can be accessed at http://arsf tfbean.uprm.edu/beancap/research/. Genotype data for the Andean Diversity Panel can be accessed at http://arsftfbean.…”

Genome‐Wide Analysis of Tar Spot Complex Resistance in Maize Using Genotyping‐by‐Sequencing SNPs and Whole‐Genome Prediction

“…However, the resulting mapping resolution is comparatively low and typically produces a large confidence interval of 10 to 20 cM as a result of the limited number of recombination events occurring in the construction of biparental mapping populations (Li et al, 2010; Manichaikul et al, 2006; Zhu et al, 2008). On the other hand, association mapping explores functional variations within genetically diverse panels through linkage disequilibrium (LD) analysis, which is very efficient and effective for identifying new genes or confirming candidate genes (Aoun et al, 2016; Yu and Edward, 2006). Compared with linkage mapping, association mapping is able to identify historical recombination events in a given population, which improves mapping resolution.…”

Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat

“…The vast majority of the officially named wheat rust resistance genes are based on control by a single (monogenic) or a few (oligogenic) resistance loci, although a few of them are based on truly polygenic quantitative trait loci (Ellis et al, 2014). Recent association genetics studies have indicated that polygenic resistance to wheat rust diseases is paramount (Bajgain et al, 2015; Maccaferri et al, 2015; Bulli et al, 2016; Aoun et al, 2016). Depending on the race composition in a field, environmental conditions for disease development, and the specific trait being measured (assessment method), the wheat rust pathosystem may provide the opportunity to study the effects of trait genetic architecture and assessment methods on GS prediction accuracy.…”