Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration

Abstract

Key message Major QTL on LG 1 and 3 control seed filling and seed coat development, thereby affecting seed shape, size, color, composition and weight, key determinants of crop yield and quality. Abstract A chickpea (Cicer arietinum L.) population consisting of 189 recombinant inbred lines (RILs) derived from a cross between medium-protein ICC 995 and high-protein ICC 5912 genotypes of the desi market class was analyzed for seed properties. Seed from the parental lines and RILs was produced in four different environments for determination of seed shape (SS), 100-seed weight (100-SW), protein (PRO) and starch (STA) concentration. Polymorphic genetic markers for the population were identified by Genotyping by Sequencing and assembled into a 522.5 cM genetic map. Phenotype data from the different growth environments were analyzed by QTL mapping done by single and multi-environment analyses and in addition, single marker association mapping. The analyses identified in total 11 QTL, of which the most significant (P < 0.05) loci were located on LG 1 (q-1.1), LG 2 (q-2.1), LG 3 (q-3.2, q-3.3), LG 4 (q-4.2), and LG 5 (q-5.1). STA was mostly affected by q-1.1, which explained 19.0% of the phenotypic variance for the trait. The largest QTL effects were demonstrated by q-3.2 that explained 52.5% of the phenotypic variances for 100-SW, 44.3% for PRO, and 14.6% for SS. This locus was also highly associated with flower color (COL; 95.2% explained) and showed q-3.2 alleles from the ICC 5912 parent conferred the blue flower color and production of small, round seeds with relatively high protein concentration. Genes affecting seed filling at q-1.1 and seed coat development at q-3.2, respectively, were considered to underlie differences in seed composition and morphology in the RIL population.Communicated by Henry T. Nguyen.Runfeng Wang and Manu P. Gangola have contributed equally to this work.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data

“…A CT repeat region within the 5'UTR of CaIMP is proposed to regulate seed phytic acid content and consequently seed weight (Joshi-Saha and Reddy 2015; Dwivedi et al 2017), possibly through regulation of translation of the CaIMP protein (Dwivedi et al 2017). QTL for seed size have been mapped to this region on Ca1 in several studies (Varshney et al 2014;Jaganathan et al 2015;Das et al 2015;Singh et al 2016;Wang et al 2019). However, Ca1_Vqtl identified in Rupali/Genesis836 in our study is approximately 17 Mb distal to Ca1_6Mb/CaIMP.…”

Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm

“…Two markers, namely S4_2624940 and S4_5775736, were found highly significant among the other markers for grain protein content on chr4 [ 15 ], and interestingly, one highly significant SNP for grain protein content in the current study was positioned between these two SNPs. However, loci on chromosomes 1, 3, and 6 were also found to contribute for protein content [ 60 ]. Thus, the current investigation identified additional markers within the genomic regions on chr4 for grain protein and Fe content, which will help in marker development and further use in the selection process.…”

Evaluation of Seed Dormancy, One of the Key Domestication Traits in Chickpea

“…Chickpea (Cicer arietinum L.) is an annual, self-pollinated legume crop [3] grown mainly in arid and semi-arid regions all over the world. It is the second most important legume crop and is a source of high quality nutrients.…”