A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

Abstract

High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.

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

“…The efficacy of these genes in regulating PH trait was further ascertained by their vegetative tissue-specific expression and pronounced up-regulation in tall than that of dwarf/semi-dwarf mapping parental accessions. The added-advantage of such integrated genomics-assisted breeding strategy for delineation of potential candidate genes regulating important yield-contributing traits have been demonstrated in chickpea232425263132333538. The SNPs-carrying genes (encoding cytochrome c biosynthesis protein, NADH dehydrogenase iron-sulfur protein and malic oxidoreductase) regulating PH trait scaled-down by the integrated genomic approach, are evolutionarily conserved key components of mitochondrial respiratory complex and known to play a central role in classical electron transport chain (ETC) and tricarboxylic acid (TCA) cycle for regulating mitochondrial organization and respiration in crop plants626364656667.…”

“…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.…”

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

“…The grain weight was estimated by measuring the average weight (g) of 1000-matured seeds from 10 representative plants of each mapping individual and parental accession. The frequency distribution, coefficient of variation (CV) and broad-sense heritability ( H 2 ) of grain weight across years/seasons were determined in the mapping population as per Bajaj et al (2015a).…”

“…The additive effect and phenotypic variation explained (PVE) by each major grain weight QTL at a significant LOD were measured following Bajaj et al (2015a).…”

Identification of candidate genes for dissecting complex branch number trait in chickpea

“…Considering the significance of integrated genomics-assisted breeding approach for quantitative dissection of complex yield component traits in crop plants, it would be interesting to employ this strategy in natural and mapping populations to identify functionally relevant molecular tags (markers, genes/QTLs and alleles) regulating branch number in chickpea [20,[24][25][26][27][28][29]. This will provide much needed inputs for genetic dissection of complex branch number trait, which can be subsequently utilized in marker-assisted breeding program leading to development of superior cultivar with a desirable high attribute of branch number/density in chickpea.…”