Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines

Abstract

BackgroundAlthough chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance.ResultsIn the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions.ConclusionIdentification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0491-8) contains supplementary material, which is available to authorized users.

The Chickpea Early Flowering 1 (Efl1) Locus Is an Ortholog of Arabidopsis ELF3

“…The most notable of these was a QTL on Ca5 (qdf-SD5) that accounted for approximately 59% of phenotypic variation in flowering time under SD (Table I). This is consistent with previous reports of a large flowering time QTL on Ca5 in crosses involving ICCV 2, one of the parents of ICCV 96029 (Jamalabadi et al, 2013;Pushpavalli et al, 2015).…”

“…A number of QTLs within these regions have been reported previously, including the QTLs on Ca4 (Cobos et al, 2007;Varshney et al, 2014) and Ca5 (Cho et al, 2002;Vadez et al, 2012;Jamalabadi et al, 2013;Pushpavalli et al, 2015). GI remains a potential candidate for qdf-SD4, with markers for CDC Frontier and ICCV 96029 alleles showing a strong association with flowering time under SD (Supplemental Fig.…”

“…Efl1 has been associated previously with several QTLs on Ca3 (Cho et al, 2002;Jamalabadi et al, 2013), Ca4 (Upadhyaya et al, 2015), and Ca5 (Vadez et al, 2012;Pushpavalli et al, 2015). Changes to the naming convention and a lack of common markers between maps are likely to account for some of the reports of Efl1 on different chromosomes.…”

“…Currently, only four loci controlling the crucial trait of flowering time (Efl1-Efl4) have been identified in domesticated chickpea germplasm, and the genes responsible for these loci are unknown. Efl1, the first major flowering time locus described in chickpea, was initially defined in ICCV 2 (Kumar and van Rheenen, 2000), which has been used as a common parent in several crosses that report major QTLs on Ca5, suggesting a likely map position for Efl1 (Cho et al, 2002;Vadez et al, 2012;Jamalabadi et al, 2013;Pushpavalli et al, 2015). Allelism tests have provided strong genetic evidence that this earlyflowering efl1 gene also is present in ICCV 96029, a direct descendent of ICCV 2 .…”

“…In addition, six quantitative trait loci (QTLs) have been reported from chickpea linkage studies (Weller and Ortega, 2015). Several of these studies have involved ICCV 2, which is known to carry efl1, and each of these reported a major QTL on what is now known to be Ca5 (Cho et al, 2002;Vadez et al, 2012;Jamalabadi et al, 2013;Pushpavalli et al, 2015), while Efl2 has been shown to be associated with a QTL on Ca1 (Lichtenzveig et al, 2006). A recent genome-wide association study identified five further flowering time QTLs and put forward eight candidate genes for these QTLs, including an ortholog of the Arabidopsis gene PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1) on Ca4 that is proposed to be synonymous with the Efl1 locus (Upadhyaya et al, 2015).…”