Genome-wide association study of stripe rust (Puccinia striiformis f.sp. hordei) resistance in a world collection of barley (Hordeum vulgare L.)

Abstract

Stripe rust (Puccicina striiformis f.sp. hordei) (PSH) is one of the major diseases that causes significant yield losses of barley (Hordeium vulgare L.) worldwide. Frequent breakdown of resistance genes and emergence of new races have necessitated research for new sources of resistance. The genetic map of PSH resistance in barley is unknown against Indian races. We performed genome-wide association study (GWAS) of stripe rust resistance using 336 barley genotypes collected world-wide. Barley genotypes were evaluated for stripe rust resistance using six races prevalent in India; Q (5S0), 24 (0S0-1), 57 (0S0), M (1S0), G (4S0) and 7S0 (newly reported race). Seedling screening with individual race was carried out in ICAR-IIWBR Regional Station, Shimla, while field screening was carried out at adult stage with mixed inoculum of all the races in Durgapura, Rajasthan, India in 2015. Barley genotypes were genotyped using 9K SNP array based on iSelect Illumina Inifinium Assay in USDA-ARS, Fargo, USA. GWAS was carried out in TASSEL using mixed linear model (MLM) where population structure and Kinship were used as fixed and random effects, respectively. Out of 336 genotypes, 87 (25.9%), 101 (30.1%), 119 (35.4%), 100 (29.8%), 91 (27.1%), 70 (20%) were resistant to races M (1S0), 24 (0S0-1), 57 (0S0), G (4S0), Q (5S0), and 7S0 races, respectively. Both population structure and PCA analyses revealed two sub-populations predominantly based on row types. GWAS revealed 12 race-specific seedling resistance QTL for stripe rust, while seven adult-plant stage QTL were mapped in different chromosomes. Gene annotation using BLAST search revealed genes encoding 1-Phosphatidylinositol-3-phosphate 5-kinase, Glycine-rich domain-containing protein, Purine biosynthesis PurH-like protein, Dof-type zinc finger protein 15 (Dof15), RNA polymerase II transcription subunit 27, NAC transcription factor (NAC012 gene), WUSCHEL-related homeobox 8, Ubiquitin-conjugating enzyme (UBC) and uncharacterized proteins. The QTL mapped in the current study shall be important for PSH resistant barley breeding in India and elsewhere.