Abstract
Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150–200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10–20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21–22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.
Highlights
Chickpea (Cicer arietinum L.) is the second most consumed important food legume crop globally and stands third in production among all legume crops world-wide (Kumar et al, 2011; FAOSTAT: Production-Crops, 2012; Varshney et al, 2013b)
The chickpea seeds being significantly rich in almost all essential amino acids can be consumed along with cereals as a daily human diet to mitigate the problem of proteincalorie malnutrition (Monti and Grillo, 1983; Haider and Haider, 1984; Duranti and Gius, 1997; Jukanti et al, 2012; World Health Organization [WHO], 2013)
To perform genome-wide association study (GWAS), the high-throughput genotyping data of 16376 reference genome-based GBS-single nucleotide polymorphism (SNP) generated from 92 sequenced and genotyped accessions were utilized. This included genotyping information of 3072 SNPs generated by their high-throughput genotyping in 244 accessions using Illumina GoldenGate assay (Supplementary Table S2)
Summary
Chickpea (Cicer arietinum L.) is the second most consumed important food legume crop globally and stands third in production among all legume crops world-wide (Kumar et al, 2011; FAOSTAT: Production-Crops, 2012; Varshney et al, 2013b). The seed-protein content (SPC) is an extremely vital component of nutrition for both humans and animals (Millerd, 1975; Monti and Grillo, 1983; Duranti and Gius, 1997; Kumar et al, 2011; Varshney et al, 2013b; Jadhav et al, 2015). The chickpea seeds being significantly rich in almost all essential amino acids (except sulfur-containing types) can be consumed along with cereals as a daily human diet to mitigate the problem of proteincalorie malnutrition (Monti and Grillo, 1983; Haider and Haider, 1984; Duranti and Gius, 1997; Jukanti et al, 2012; World Health Organization [WHO], 2013). It would be interesting to decipher the genetic factors and functional gene regulatory mechanism underlying SPC variation in chickpea
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