Molecular Mapping and Characterization of Genes Governing Time to Flowering, Seed Weight, and Plant Height in an Intraspecific Genetic Linkage Map of Chickpea (Cicer arietinum)

Abstract

Drought is the major constraint to chickpea productivity worldwide. Utilizing early flowering genotypes and larger seed size have been suggested as strategies for breeding in drought zones. Therefore, this study aimed to identify potential markers linked to days-to-flowering, 100-seed weight, and plant height in a chickpea intraspecific F(2:3) population derived from the cross ILC3279 × ICCV2. A closely linked marker (TA117) on linkage group LG3 was identified for the days-to-flowering trait, explaining 33% of the variation. In relation to plant height, a quantitative trait loci (QTL) was located in LG3, close to the Ts5 marker, that explained 29% of phenotypic variation. A QTL for 100-seed weight located in LG4, close to TA176, explained 51% of variation. The identification of a locus linked both to high 100-seed weight and days-to-flowering may account for the correlation observed between these traits in this and other breeding attempts.

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.…”

“…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).…”

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

“…Several SSR markers were developed and used in chickpea (Hüttel et al 1999;Udupa and Baum 2001;Lichtenzveig et al 2005;Sethy et al 2006;Choudhary et al 2006;Saxena et al 2014;Parida et al 2015;Khajuria et al 2015). Most of them have a known genomic localization, following linkage analysis (Winter et al 2000;Nayak et al 2010;Jamalabadi et al 2013;Khajuria et al 2015).…”