Genome-wide association studies provide insights on genetic architecture of resistance to leaf rust in a worldwide barley collection

Abstract

We assembled an international barley panel comprising 282 entries from 26 countries with various levels of field resistance to leaf rust caused by Puccinia hordei. The panel was screened for leaf rust response with an array of pathotypes at the seedling stage, and at the adult plant stage in multiple environments (2013–2015) in Australia and Uruguay, and genotyped using > 13 K polymorphic DArT-Seq markers. Multipathotype testing in the greenhouse postulated the presence of seedling resistance genes Rph1, Rph2, Rph3, Rph4, Rph7, Rph9.am, Rph12, Rph14, Rph15, Rph19, and Rph25. Genome-wide association studies (GWAS) based on field data identified 13 QTLs significantly associated with DArT-Seq markers on chromosomes 2H (Rph_G_Q1, Rph_G_Q2, Rph_G_Q3, and Rph_G_Q4), 4H (Rph_G_Q5), 5H (Rph_G_Q6, Rph_G_Q7, Rph_G_Q8), 6H (Rph_G_Q9 and Rph_G_Q10), and 7H (Rph_G_Q11, Rph_G_Q12, and Rph_G_Q13). Three QTLs (Rph_G_Q3, Rph_G_Q5, and Rph_G_Q6) were detected under all environments, whereas the other ten were variable, being detected in 1–4 environments; Rph_G_Q1 and Rph_G_Q13 being detected only in Uruguay. Among the three QTLs detected under all environments, Rph_G_Q6 on chromosome 5H had the largest effect and corresponded to a region where the cataloged APR gene Rph20 is located. Rph_G_Q3 and Rph_G_Q5 detected on chromosome 2H and 4H aligned with QTLs reported in at least three previous studies. The studies provide useful information towards better understanding of the genetic architecture of seedling and adult plant resistance to leaf rust in diverse global barley germplasm.