Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height

Abstract

Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.

Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits

“…Changes of the isoflavones content upon germination has very likely a genetic regulation explanation, although no QTLs/genes associated with this phenomenon have been reported so far. Most of the genetic studies of chickpea have focused on the identification of genetic regions using different methodologies associated to improving agronomic traits, such as increasing seed yield and the yield of components [95,96,97,98,99,100,101,102,103]. In addition, a genetic approach has been used to develop drought/heat tolerance [70,104,105,106,107,108], as well as disease resistance, for example, Ascochyta blight [109,110].…”

Elucidating genetic diversity and association mapping to identify SSR markers linked to 100 seed weight in chickpea (Cicer arietinum L.)

“…In the current study, TAA60 on LG2, H1B04 on LG3 and CakTpSSR02719 marker exhibited significant MTA for both years 2016-2017 and 2017-18. Similarly, one QTL for 100 SWwas found on LG6 (Verma et al 2015;Bajaj et al 2015), one QTL on LG3 (Bajaj et al 2015) and one QTL on LG2 (Gupta et al 2015) was reported. In 2017-18, each significant MTAs were identified on LG1, LG2, LG3, LG6 and LG7, respectively.…”

“…In 2017-18, each significant MTAs were identified on LG1, LG2, LG3, LG6 and LG7, respectively. Similarly, two QTLs on LG1 (Kujur et al 2014), one QTL on LG1 by employing QTL-seq approach in ICC4958 × ICC1882 mapping population (Singh et al 2016), one QTL on LG1 (Gupta et al 2015;Verma et al 2015) and one major SW QTL CaqSW1.1 (Das et al 2015), one QTL on LG1 (Dwivedi et al 2017), 5 QTLs on LG1 (Wang et al2019) and three QTL on LG1 (Bajaj et al 2015) were reported for this trait. While one QTL on LG2 and three QTLs on LG7 (Kujur et al 2014;Verma et al 2015) and five QTLs on LG3 (Wang et al 2019) were mapped for this trait.…”

Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292

“…Using GBS approach four QTLs for yield per plant located on chromosome 4, 6, 7 and 8 were reported [ 75 ]. Two QTLs for seed weight on chromosome 6 (LOD = 2.6) and 7 (LOD = 2.7) and two QTLs for plant height on chromosome 1 (LOD = 3.25) and 3 (LOD = 2.7) were identified [ 76 ]. QTL for 100-seed weight was identified [ 77 ] on chromosome 4 which was in accordance to our results.…”