Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Abstract

Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

Genome‐wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes

“…This confirms earlier findings that advanced lines from the CIMMYT bread wheat breeding program possess moderate resistance to SB (Singh et al., 2015). The continuous distribution of disease scores across all experiments indicates the quantitative character of resistance driven by the additive action of numerous QTLs and genes (Ayana et al., 2018; Joshi et al., 2004; Kumar et al., 2007, 2009; Neupane et al., 2007; Singh et al., 2018; Singh et al., 2023). ANOVA revealed significant effects of year and genotype‐by‐year, highlighting the need for multiple evaluations for SB across years/locations to identify lines with stable resistance and reliable markers for breeding (Chattopadhyay et al., 2022; Roy et al., 2021; Singh et al., 2015).…”

Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat

“…A significance threshold of p < 0.001 (−log10(P) > 3.0) was applied to identify statistically significant MTAs as used previously [12,46,105,106].…”

“…The marker sequences associated with these MTAs were aligned with the wheat genome assembly IWGSC v.1 downloaded from the Ensembl database. Specifically, we analyzed a 200 kb window around each MTA marker (100 kb on each side) to extract highly significant and annotated candidate genes following Singh et al [106] and Feng et al [107]. A 200 kb window is a reasonable size to capture regulatory hubs that may be involved in the expression of a candidate genes.…”