Genotyping-by-sequencing based genetic mapping reveals large number of epistatic interactions for stem rot resistance in groundnut

Abstract

Key message Genetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance. Abstract Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, diverse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, linkage analysis and quantitative trait locus (QTL) mapping for resistance to stem rot disease was performed in a bi-parental recombinant inbred line population developed from TG37A (susceptible) × NRCG-CS85 (resistant) comprising of 270 individuals. Genotyping-bysequencing approach was deployed to generate single nucleotide polymorphism (SNP) genotyping data leading to development of a genetic map with 585 SNP loci spanning map distance of 2430 cM. QTL analysis using multi-season phenotyping and genotyping data could not detect any major main-effect QTL but identified 44 major epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%. Large number interactions indicate the complexity of genetic architecture of resistance to stem rot disease. A QTL of physical map length 5.2 Mb identified on B04 comprising 170 different genes especially leucine reach repeats, zinc finger motifs and ethyleneresponsivefactors, etc., was identified. The identified genomic regions and candidate genes will further validate and facilitate marker development to deploy GAB for developing stem rot disease resistance groundnut varieties.Communicated by Henry T. Nguyen. Electronic supplementary materialThe online version of this article (https ://doi.org/10.1007/s0012 2-018-3255-7) contains supplementary material, which is available to authorized users. * Rajeev K. Varshney

Translational genomics for achieving higher genetic gains in groundnut

“…Nevertheless, the improved technology named ddRADseq provided much better results when deployed for construction of dense genetic maps (1,621 SNP loci) in RIL population derived from Zhonghua 5 and ICGV86699 (Zhou et al 2014). The GBS-based sequencing approach was utilized for developing three dense genetic maps (585 to 2753 SNP loci) and successful discovery of genomic regions and candidate genes for resistance to rust and LLS in TAG 24 × GPBD 4 (Pandey et al 2017c), stem rot in TG37A × NRCG-CS85 (Dodia et al 2019) and early leaf spot (ELS) and LLS in Florida-07 × GP-NC WS 16 (Han et al 2018). Deployment of another technology, SLAF-seq, helped in developing denser genetic maps with 2266 SNP loci in RIL population (Huayu28 × P76) and with 2808 SNP loci in RIL population (Jihua 5 × M130), respectively, leading to high-resolution mapping of oil (Hu et al 2018) and growth habit-related traits within 0.17 Mb with putative genes (Li et al 2019).…”

Unraveling the mechanisms of resistance to Sclerotium rolfsii in peanut (Arachis hypogaea L.) using comparative RNA-Seq analysis of resistant and susceptible genotypes

“…Stem rot disease is caused by a necrotrophic, soil-borne fungal pathogen Sclerotium rolfsii Sacc. (Athelia rolfsii), which may incur yield losses of 10-40%, especially under irrigated conditions [4,5]. Moreover, the oxalic acid produced by S. rolfsii causes a blue discoloration on the seed surface and ultimately affects the overall seed quality [6].…”

“…In order to manage the stem rot infection, the development of resistant varieties is considered a more economical and environmentally friendly approach compared to the fungicide application. Although no peanut genotype has yet been reported to be resistant to Sclerotium rolfsii infection, some genotypes have field resistance [5,10,11].…”

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

“…Earlier constructed genetic maps for individual RIL populations were not very dense due to less allelic diversity and few recombination events. Recently, a genetic map of 585 loci using genotyping‐by‐sequencing (GBS) was used for mapping stem rot resistance in peanut (Dodia et al , ). A SSR‐based genetic map was developed for mapping aflatoxin resistance with 1219 loci (1175 SSR markers and 42 transposon markers) in 2037.75 cM (Yu et al , ).…”