Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm

Abstract

Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.

Genome‐wide SNP discovery and genotyping delineates potential QTLs underlying major yield‐attributing traits in buckwheat

“…Occurrence of common genomic region among more than one environment shows common adaptation and tolerance mechanism of genotypes under these different environments. These results provided a higher correlation for environmental conditions than previ-ous association and linkage mapping studies on wheat (Bálint et al, 2007) model legume Medicago truncatula (Sankaran et al, 2009), pea (Gali et al, 2019), and chickpea (Srungarapu et al, 2022). The moderately significant effect of environmental conditions on the morphological, floral, maturity, and yield traits has also been reported by other researchers in pea (Ma et al, 2017), common bean (Blair et al, 2016), and rice (Garcia-Oliveira et al, 2009).…”

Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies

“…Recent advancements in the sequencing and annotation of the chickpea genome have provided valuable insights into the identification of candidate genes within the genomic regions pinpointed through GWAS. These candidate genes are believed to play a role in modulating the variation observed in heat-responsive traits ( Srungarapu et al., 2022 ). We compiled a table of candidate genes located within 100-kb regions surrounding the identified MTAs, which included information such as their start and stop positions, InterPro IDs, gene ontology (GO) terms, and accessions, as well as the probable proteins they encode.…”

Fatty acid composition and genome-wide associations of a chickpea (Cicer arietinum L.) diversity panel for biofortification efforts

“…Numerous GWAS have been conducted in chickpea to identify SNPs significantly associated with agronomic traits 48 – 51 , stress tolerance 52 , 53 , and nutritional traits 20 , 50 , 54 , 55 . However, no GWAS have been reported for fatty acids in chickpea to date.…”