Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

Abstract

A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.

Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

“…Henceforth, novelty and population-specific characteristics of the identified six major and robust QTLs governing PH trait was apparent in chickpea. A number of QTL mapping studies involving high resolution intra- and inter-specific genetic linkage maps as references/anchors have been undertaken for rapid molecular mapping as well as fine mapping/map-based cloning of major genes/QTLs governing multiple stress tolerance- and yield-component traits to expedite marker-assisted genetic enhancement in chickpea26282935363759. Interestingly, with the use of an ultra-high density genetic linkage map as a reference in the present investigation, the major PH QTLs significantly scaled-down into the marker intervals of 0.058–0.688 cM (average <0.5 cM) in chickpea.…”

“…These available genomic resources have accelerated the process of NGS (next-generation sequencing)-based whole genome and transcriptome sequencing of numerous cultivated ( desi and kabuli ) and wild accessions as well as NGS-/array-based large-scale discovery and high-throughput genotyping of informative microsatellite and SNP (single nucleotide polymorphism) markers in natural and mapping populations of chickpea101112131415161718. Consequently, these efforts have significantly driven the process of constructing high-density intra- and inter-specific genetic linkage maps and genetic/association mapping to identify QTLs (quantitative trait loci)/genes governing useful agronomic traits in chickpea121920212223242526272829303132333435. One such most promising outcome includes the use of GBS (genotyping-by-sequencing) assay in discovery/genotyping of genome-wide SNPs in natural germplasm lines and mapping populations for understanding domestication and LD (linkage disequilibrium) pattern and constructing ultra-high density genetic linkage maps.…”

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

“…QTL-seq has also been used in cucumber to map a QTL involved in flowering trait [101]. Likewise, the deployment of QTL-seq for rapid identification and fine mapping of QTLs was reported in chickpea [102] and sorghum [103].…”

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

“…The parameter of average base quality score was much higher than what was usually suggested (i.e. 20) (Clevenger et al, 2015;Das et al, 2015;Nagy et al, 2013). Only three out of 40 SNPs were hom-het which link to an enzyme (EC:6.3.1.2 -synthetase) that form Lglutamate which enter to the IMP biosynthetic pathways (Figure 6.7 -D and Table 6.5), and two enzymes (EC:3.6.1.3 -adenylpyrophosphatase and EC:3.6.1.15 -phosphatase) in purine metabolism pathways that converts ATP to ADP which entered into xanthosine synthesis pathways ( Figure 6.7 -C and Table 6.5).…”

“…The average coverage at the location where SNPs were called was very high for the two bulks (30x for B1 and 45x for B2) compared to a number of studies both pooled-seq (Das et al, 2015;Takagi et al, 2013) and non-pooled-seq (Byers et al, 2012;Clarke et al, 2016;Hamilton et al, 2011;Hulse-Kemp et al, 2015;Zhu et al, 2014) indicating the high quality and confidence of these SNPs. The confidence was supported with the high F/R balance in reads (0.38 in B1 and 0.39 in B2) and the average base quality score (36 in B1 and 35 in B2) as these are a reflection of read quality used in SNP detection.…”