Association Analysis Identifies Important QTL for Seed Weight in Chickpea

Abstract

Chickpea (Cicer arietinum L.) is an important cool season grain legume crop of the world. Seed size/ weight is an important yield-contributing trait in chickpea and high-quality seed has the potential to attract premium prices. Hence, the breeding for this important trait is of major importance in chickpea improvement programs. Several quantitative trait loci (QTL) mapping studies based on bi-parental mapping populations have been carried out in chickpea and have identified QTL for this trait. However, none of these studies was specifically aimed at seed weight. In the present study, using a diverse set of 187 chickpea genotypes showing substantial variation for seed weight, and a representative set of 23 SSR markers distributed across all the linkage groups (LG) of chickpea genome, association analysis was carried out. Based on a total of 153 alleles amplified, marker-trait association analysis identified four QTL spread across four different LG. One of the most significant associations linked with the marker H2B061 present on LG 2 was identified using all the criteria of analysis and it explained more than 13% of the variation. Presence of important QTL for seed weight on LG 2 has been reported in several earlier studies. The results obtained in the present study are important, as it validate the earlier reported QTL for seed weight in chickpea. The results also showed that for the given set of chickpea genotypes, an approach, such as general linear models that accounts for population structure is more suited than the widely suggested mixed linear models in association analysis.