Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India

Abstract

Barley stripe rust is caused by Puccinia striiformis f.sp. hordei, (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally.

Genome Wide Association Mapping of Spot Blotch Resistance at Seedling and Adult Plant Stages in Barley

“…Out of the 15 QTL for SB resistance at SRT for isolate ICSB3, four were coincident with prior reports and those QTL were identified at both SRT and APS stages using different germplasm and different isolates (Zhou and Steffenson, 2013;Afanasenko et al, 2015;Gutierrez et al, 2015;Bykova et al, 2017;Wang et al, 2017). Furthermore, the QTL SRT-ICSB-12 overlaps with a QTL detected in the same panel for stripe rust and reported in Visioni et al (2018). Within the 9 QTL identified for isolate SB54, SRT-SB54-6 was already reported in a previous studies (chromosome 4H 104 cM) using different isolates and genotypes with different genetic background (Tamang et al, 2015), while QTL SRT-SB54-65 and SRT-SB54-8 were already reported for stripe rust in the same panel (Visioni et al, 2018).…”

“…The extent of LD was estimated by non-linear regression analysis on the basis of intra chromosomal r 2 values (Hill and Weir, 1988;Remington et al, 2001) using nlstools package for R Statistical Software (The R Development Core Team). More information regarding genotyping population structure and LD analysis was reported by Visioni et al (2018).…”

“…Genome wide association mapping was performed combining genotypic data and disease severity scores at the seedling and adult plant stages. Genome scans were performed using both General Linear Model (GLM) and Mixed Linear Model (MLM), the general equations for GLM and MLM were reported by Visioni et al (2018). Genomic scans using the GLM model were performed incorporating population structure (GLM + PCA model) or the Q-matrix (GLM + Q model) as covariate in order to avoid type I errors.…”

“…The critical p-value for marker-trait association was firstly determined according to a liberal approach proposed by Chan et al (2010) rather than using false discovery rate. Considering this approach, markers were declared significant at the p = 0.0001 [−log(p) = 4] with the selected models (Visioni et al, 2018). A further step to increase confidence in QTL identified was done by applying the LD adjusted Bonferroni, proposed by Duggal et al, 2008.…”

“…A further step to increase confidence in QTL identified was done by applying the LD adjusted Bonferroni, proposed by Duggal et al, 2008. The value calculated for LD decay of 4 cM (Visioni et al, 2018), corresponding to 4.3 Mbp, indicated that this association panel interrogated the 987.65 cM of our association mapping panel via 246 "loci hypothesis, " and hence the Bonferroni correction for this panel was set to 3.68 −log(p) (p < 0.05).…”