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

Sahadev Singh; Shailendra Singh Gaurav; Neeraj Kumar Vasistha; Uttam Kumar; Arun Kumar Joshi; Vinod Kumar Mishra; Ramesh Chand; Pushpendra Kumar Gupta

doi:10.3389/fpls.2022.1036064

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

Front Plant Sci. 2023 Jan 18:13:1036064. doi: 10.3389/fpls.2022.1036064. eCollection 2022.

Authors

Sahadev Singh¹, Shailendra Singh Gaurav¹, Neeraj Kumar Vasistha², Uttam Kumar³, Arun Kumar Joshi⁴, Vinod Kumar Mishra⁵, Ramesh Chand⁶, Pushpendra Kumar Gupta^{1

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Affiliations

¹ Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India.
² Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, India.
³ Borlaug Institute for South Asia (BISA), Ludhiana, India.
⁴ The International Maize and Wheat Improvement Center (CIMMYT), Borlaug Institute for South Asia (BISA), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, India.
⁵ Department of Genetics and Plant Breeding, Indian Institute of Agricultural Science, Banaras Hindu University, Varanasi, India.
⁶ Department of Mycology and Plant Pathology, Indian Institute of Agricultural Science Banaras Hindu University, Varanasi, India.
⁷ Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA, Australia.

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.

Keywords: GWAS; MTA; Triticum aestivum L; candidate genes; epistasis.