QTL analysis of cold tolerance in chickpea

Deus Mugabe

Yield of fall-sown chickpea (Cicer arietinum L.) can be nearly twice that of spring-sown chickpea in regions that have mild winters. However, winter kill can limit the productivity of fall-sown chickpea. Currently, there are no chickpea cultivars that can successfully overwinter in the northern tier of US states. Developing cold tolerant chickpea cultivars may allow expansion of the current geographic range where the crop is grown, and improve productivity. This study focused on screening an interspecific chickpea recombinant inbred line (RIL) population, CRIL 2, in field and controlled environments and identifying quantitative trait loci (QTL) associated with cold tolerance. CRIL 2 was derived from the cross between a cultivated, cold susceptible parent (ICC 4958; C. arietinum) and a wild type, cold tolerant parent (PI 489777; C. reticulatum). The population was evaluated for cold tolerance in the fields at two locations in Washington for location-years. Cold tolerance was also evaluated in controlled environments. Cold tolerance, scored as leaf damage, was confirmed in the population in all trial environments. Line ranks of post-winter leaf damage in field environments was highly correlated to mean spring stand count. Controlled environment freezing tests were an efficient method to screen for cold tolerance. For the QTL study, CRIL 2 was genotyped using genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) markers. The SNPs were used to construct a linkage map and conduct QTL analysis. Three significant QTL were found on linkage group (LG) 1B, 3 and 8. QTL on LG 3 and 8 were consistent in six environments with LOD score ranges of 5.16 - 15.11 and 5.68 - 23.96 respectively. The QTL on LG 3 explained 7.17 - 34.6% of the variance across all environments, while the LG 8 QTL explained 11.5 - 48.4% phenotypic variance in all environments. Understanding the genetic basis of cold tolerance in chickpea can facilitate the introgression of novel alleles from wild relatives into adapted cultivars. The QTL associated SNP markers have potential after validation for assisting in the breeding of increased cold tolerance in cultivated chickpea.

QTL analysis of cold tolerance in chickpea

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