EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea

Abstract

The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10–15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.

Global transcriptome and coexpression network analyses reveal cultivar‐specific molecular signatures associated with seed development and seed size/weight determination in chickpea

“…Further, we sought to identify genetic variations among the small‐ and large‐seeded cultivars that might be responsible for differential gene expression and determine seed weight/size in chickpea. For this analysis, we integrated the known QTLs (based on genomic coordinates) and candidate genes (based on gene identifiers) associated with seed size/weight reported in previous studies (Kujur et al ., , ; Saxena et al ., ; Bajaj et al ., , ; Verma et al ., ; Singh et al ., ) with our differential gene expression results. A total of 34 genes, including those located in the QTLs, genes associated with seed weight/size, involved in cell cycle/cell division, endoreduplication and seed storage protein accumulation and/or showing higher transcript abundance in JGK 3 at S3 and/or S5 stages as compared with Himchana 1, were identified (Figure a; Dataset 4).…”

“…Quite a few studies have identified QTLs and/or candidate genes associated with seed size/weight in chickpea using different biparental populations or diverse germplasm via various approaches (Kujur et al ., , ; Saxena et al ., ; Verma et al ., ; Bajaj et al ., , ; Singh et al ., ). In most of these studies, large genomic regions harboring several genes have been identified as QTLs.…”

“…Although huge variations in seed size have been observed among chickpea genotypes, this phenotypic variability could not be harnessed to improve seed size in important chickpea cultivars due to poor understanding of molecular mechanisms underlying this important trait. Recently, a few quantitative trait loci (QTLs) and candidate genes involved in regulation of seed size have been identified via marker‐based, QTL mapping or association analysis studies (Kujur et al ., , ; Saxena et al ., ; Bajaj et al ., , ; Verma et al ., ; Singh et al ., ).…”

Winged bean (Psophocarpus tetragonolobus (L.) DC.) for food and nutritional security: synthesis of past research and future direction

“…Renewed efforts could mirror, to an extent, what the dedicated international centre did back during the 70 s and 80 s, by creating a panel of common accessions for phenotypic screening, and for development of populations with shared molecular information. Such steps are critical also in the development of mapping populations, linkage mapping, and Genome Wide Association Studies (GWAS) for trait discovery, as shown in soybean (Li et al 2018), chickpea (Bajaj et al 2016;Saeed and Darvishzadeh 2017), mung bean (Noble et al 2018), and common bean (Tock et al 2017). This would allow us also to combine phenotypic and genetic data across different environments and assess the degree of adaptability and plasticity of winged bean.…”

Efficient Discovery of Single-Nucleotide Variations in Cochliobolus sativus Vegetative Compatibility Groups by Ecotilling

“…Ecotilling, a variant of Tilling (Targeting Induced Local Lesions IN Genomes) method, allows high-throughput analyses of natural genetic diversity in populations [12][13][14]. In this technique, a single-strand specific endonuclease extracted from celery (CEL I) is used to cleave DNA where there are mismatched bases in the DNA heteroduplexes of PCR products.…”