A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea.

Deepak Bajaj,Saurabh Badoni,Shouvik Das,Shivali Sharma,Sube Singh,Hari D Upadhyaya,Vinod Kumar,Akhilesh K Tyagi,C L Laxmipathi Gowda,Shailesh Tripathi,Swarup K Parida,Rajeev Ranjan

doi:10.3389/fpls.2015.00979

Abstract

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Highlights

Chickpea (Cicer arietinum L.) is the third largest produced food legume crop globally that serves as a vital human dietary source of protein enriched with essential amino acids (Kumar et al, 2011; Gaur et al, 2012; Varshney et al, 2013)
79 diverse Cicer accessions belonging to five annual wild species, namely C. reticulatum (14), C. echinospermum (8), C. judaicum (22), C. bijugum (19), and C. pinnatifidum (15) and one perennial species C. microphyllum were chosen for haplotype-based evolutionary study (Table S1)
The sequencing of 2 × 96-plex ApeKI GBS libraries generated on an average of 200.7 million high-quality sequence reads that are evenly distributed across 172, including 93 cultivated and 79 wild chickpea accessions (Table S1)

Summary

Introduction

Chickpea (Cicer arietinum L.) is the third largest produced food legume crop globally that serves as a vital human dietary source of protein enriched with essential amino acids (Kumar et al, 2011; Gaur et al, 2012; Varshney et al, 2013).

Results

Conclusion