Quantitative Trait Loci for Cold Tolerance in Chickpea

Abstract

Fall‐sown chickpea (Cicer arietinum L.) yields are often double those of spring‐sown chickpea in regions with Mediterranean climates that have mild winters. However, winter kill can limit the productivity of fall‐sown chickpea. Developing cold‐tolerant chickpea would allow the expansion of the current geographic range where chickpea is grown and also improve productivity. The objective of this study was to identify the quantitative trait loci (QTL) associated with cold tolerance in chickpea. An interspecific recombinant inbred line population of 129 lines derived from a cross between ICC 4958, a cold‐sensitive desi type (C. arietinum), and PI 489777, a cold‐tolerant wild relative (C. reticulatum Ladiz), was used in this study. The population was phenotyped for cold tolerance in the field over four field seasons (September 2011–March 2015) and under controlled conditions two times. The population was genotyped using genotyping‐by‐sequencing, and an interspecific genetic linkage map consisting of 747 single nucleotide polymorphism (SNP) markers, spanning a distance of 393.7 cM, was developed. Three significant QTL were found on linkage groups (LGs) 1B, 3, and 8. The QTL on LGs 3 and 8 were consistently detected in six environments with logarithm of odds score ranges of 5.16 to 15.11 and 5.68 to 23.96, respectively. The QTL CT Ca‐3.1 explained 7.15 to 34.6% of the phenotypic variance in all environments, whereas QTL CT Ca‐8.1 explained 11.5 to 48.4%. The QTL‐associated SNP markers may become useful for breeding with further fine mapping for increasing cold tolerance in domestic chickpea.

Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses

“…Whole genome sequencing (WGS) has also provided insights into cold-tolerance mechanisms in chickpea. The technique has been exploited to generate genomic resources for better understanding of cold-tolerance and cold-susceptibility in chickpea, such as identification of a flowering repressor gene MtVRN2 in the confidence interval of a QTL (Mugabe et al, 2019), using the reference genome of CDC Frontier chickpea. GWS has also been used to identify mitogen-activated protein kinases (MAPKs) in chickpea and the impact of cold on their expression.…”

“…The lack of adequate marker density appears to explain the non-detection of QTLs linked to cold tolerance as only 64 AFLP markers were used. Recently, a mapping population of 129 recombinant inbred lines (RILs), derived from an interspecific cross between ICC 4958 (cold-sensitive, desi type, C. arietinum) and PI 489777 (cold-tolerant wild relative, C. reticulatum Ladiz), followed by genotyping-by-sequencing was used to identify QTLs linked to cold tolerance (Mugabe et al, 2019). A total of 747 SNP markers, spanning 393.7 cM, were used in this study.…”

“…The SNPs were more abundant than traditional markers and had considerably higher marker density, with an average of 1.8 SNPs cM −1 . Freezing tolerance in PI48977 was governed by three QTLs situated on linkage groups (LGs) 1B, 3, and 8 (Mugabe et al, 2019); CT Ca-3.1 (on LG3) and CT Ca-8.1 (on LG8) were more important and accounted for 34 and 48% of the phenotypic variance for cold, respectively. One of the parents used in the study, C. reticulatum, requires vernalization, i.e., acceleration of flowering following brief spells of cold exposure (van Oss et al, 2015) and QTLs for vernalization response were also identified using a RIL population where one of the parents was PI 489777 (Samineni et al, 2016).…”

“…The QTL spanned 22 cM on LG3 and explained 47.9 to 54.9% of the phenotypic variation. Both studies, Samineni et al(2016) and Mugabe et al(2019) used the same coldtolerant and vernalization responsive parent (PI 489777), and identified the same QTL (CT Ca-3.1) linked to the cold tolerance and vernalization response. This finding necessitates further research to determine the relationship between cold tolerance and vernalization response machinery in Cicer species.…”

“…This finding necessitates further research to determine the relationship between cold tolerance and vernalization response machinery in Cicer species. Using CDC Frontier chickpea as a reference genome, a homolog of the M e d i c a g o t r u n c a t u l a v e r n a l i z a t i o n g e n e n a m e d VERNALISATION2-LIKEVEFS box gene (MtVRN2) was mapped in CTCa-3.1 confidence interval (Mugabe et al, 2019).…”