Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)

Abstract

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations ( = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.

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

“…Investigating the genomic resources such as simple sequence repeat markers (SSRs) and single nucleotide polymorphism (SNPs) is vital for mapping of genes/QTL as well as for identifying genes related to drought and heat tolerance in QTL intervals. In the last decade, unprecedented advancements in molecular marker development and construction of high-density linkage maps have enabled precise mapping of various traits of breeding interest at specific locations across linkage groups in chickpea (Thudi et al, 2011;Jha et al, 2018b). Considering drought and heat stress tolerance, family-based bi-parental mating scheme derived mapping populations were limitedly devoted to elucidating QTLs controlling traits associated with various morpho-physiological and yield and yield-related traits under drought and heat stress in chickpea (Rehman et al, 2011;Hamwieh et al, 2013;.…”

“…A total of 312 significant MTAs related to various drought and heat stressrelated traits were identified providing a great opportunity for targeting those genomic regions for drought and heat stress tolerance breeding (Thudi et al, 2014). Similarly, five significant MTAs for cell membrane stability and chlorophyll content related to heat stress tolerance were deciphered from 71 chickpea genotypes containing historically released varieties of Indian and improved breeding lines (Jha et al, 2018b). Likewise, recently given the 3.65 million SNPs emanating from resequencing 429 globally collected chickpea germplasm, FIGURE 1 | Integration of genomic approaches with physiological traits for breeding drought and temperature extreme resilient chickpea cultivar.…”

QTL mapping for heat stress tolerance in chickpea (Cicer arietinum L.)

“…In the last decade significant progress has been achieved in terms of developing chickpea genomic resources (for details see Jha, 2018), providing great opportunity to the chickpea breeding community for performing genomic assisted selection for increasing genetic gain. However, progress in genetic dissection of HS tolerance in chickpea remains limited (Thudi et al 2014;Jha et al 2018b;Jha, 2018;Paul et al 2018b). Here, we captured wide range of genetic variability for seventeen traits of morpho-physiological and breeding importance in F 2 based mapping population developed from DCP 92-3 × ICCV 92944 cross under HS.…”

Genetic Variability and Marker Trait Association analysis of Various Phenological and Yield Related Traits for Heat Tolerance in Chickpea (Cicer arietinum L.)

“…However, progress in development in designing HS tolerant chickpea remains slow. In parallel surge of various advanced molecular markers have offered great opportunity to the breeder community to exploit them in marker assisted breeding scheme for improving various complex traits including HS in chickpea (Bajaj et al, 2015a;Thudi et al, 2014;Varshney et al, 2014;Kale et al, 2015;Jha et al, 2018). Thus, role of (MTA) analysis an approach of marker assisted molecular breeding could be of great importance for identifying genomic regions conferring HS tolerance thereby, accelerating the HS tolerance breeding in chickpea.…”