Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

Abstract

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs

“…Segregation distortion could have resulted from various factors such as residual heterozygosity, gametic or zygotic selections and genotyping errors 31 . It is a common phenomenon observed in both intra-and inter-specific crosses and has been reported in several crops including pigeonpea 9,12,13 and chickpea 32 . Although distorted markers have generally been discarded in earlier studies, evidence indicates that distorted markers can be potentially helpful in the detection of QTLs 33 .…”

“…In pigeonpea, QTLs have been mapped for plant type and earliness including days to flowering and growth habit 10,12,35 and disease resistance 13 . However, such studies have lacked for SPC and it is only till recently that we developed gene-derived sequence-based markers using whole genome resequencing of pigeonpea parental lines 25 .…”

“…DNA isolation and genotyping. Total genomic DNA (gDNA) from 188 F 2 plants and the parents from each of the five mapping populations were isolated and genotyped-by-sequencing as described in Saxena et al 12,13 . Briefly, the sequence reads obtained from the Illumina HiSeq.…”

“…Determining the genetic basis of trait correlations in pigeonpea is essential in designing breeding strategies that aim at improving and stabilizing SPC while maintaining yield and other desirable agronomic attributes. The available genomics, transcriptomics and proteomics resources in pigeonpea coupled with advances in high-throughput genotyping technologies provide opportunity to dissect the genetic architecture of several quantitative traits in the crop 2,[9][10][11][12][13][14][15] . However, genetic architecture of SPC in pigeonpea and the basis of its relationships with other traits of importance has remained untouched by the genomic revolution in the crop.…”

Adapting legume crops to climate change using genomic approaches

“…QTL mapping accompanied by synteny analysis revealed candidate genes for resistance to Macrophomina phaseolina , a fungal pathogen of cowpea (Muchero, Ehlers, Close, & Roberts, ). A recent study in pigeonpea used three different mapping populations and genotyping by sequencing to construct dense genetic maps that revealed 14 significant QTLs for resistance to fusarium wilt (Saxena, Singh, et al, ). Similarly, QTLs have been identified for sterility mosaic disease in pigeonpea (Saxena, Kale, et al, ).…”