Genome-wide association mapping in safflower (Carthamus tinctorius L.) for genetic dissection of drought tolerance using DArTseq markers

Abstract

Understanding the genetic basis of drought tolerance in safflower (Carthamus tinctorius L.) is essential for developing resilient varieties. In this study, we performed a genome-wide association study (GWAS) using DArTseq markers to identify marker-trait associations (MTAs) linked to drought tolerance across 90 globally diverse safflower genotypes. These genotypes were evaluated under both rainfed (drought) and irrigated conditions over three consecutive years (2016-2018). Significant variation in seed yield and morphological traits was observed between genotypes and across environments, with notably reduced performance under rainfed conditions. A total of 66 MTAs were identified for key agronomic traits, including seed yield, 1000-seed weight, number of heads per plant, and days to maturity, with 45 MTAs showing significant associations with the stress-tolerance index (STI). Twelve MTAs were consistently detected across both stress and non-stress conditions, suggesting stable loci for breeding applications. BLAST searches indicated that several identified markers corresponded to genes involved in abiotic stress response, including biotin carboxylase, serine/threonine-protein kinase, and zinc finger domain proteins. The clustering of genotypes based on drought-tolerance coefficient (DC) and STI values grouped genotypes into drought-susceptible and drought-tolerant categories, with no strong correlation to geographic origin. These findings provide valuable insights into the genetic architecture of drought tolerance in safflower and highlight candidate loci for marker-assisted selection, supporting the development of drought-resilient varieties.

Keywords: DArTseq; Drought; GWAS; Safflower.

Fig. 1

Correlation coefficients between seed yield and agro-morphological traits under irrigated (a), and rainfed condition (b) based on BLUE value of the measured traits of 3 years from 2016–2018. *significance at level of 0.05; **significance at level of 0.01; ***significance at level of 0.001.

Fig. 2

Principal component bi-plot analysis of 90 safflower genotypes grown during three seasons (2016–2018) under the irrigated and rainfed environments.

Fig. 3

Cluster analysis of 90 safflower genotypes under rainfed (a) and irrigated (b) environments based on BLUEs value of seed yield and related traits.

Fig. 4

Cluster analysis of 90 safflower genotypes based on drought-tolerance coefficient (DC) and stress-tolerance index (STI) values. Cluster I, Cluster II, Cluster III and Cluster IV represent different drought resistance levels.

Fig. 5

Heatmap of genomic relationships based on genetic distances (a), Delta K (b), Bayesian model-based genetic structure analysis (c) and neighbor-joining cluster analysis (d) show the three subpopulations in the main population of 90 safflower genotypes based on 7029 DArTSeq markers.

Fig. 6

Circular Manhattan plot representing the markers-traits association for morphological traits in 90 safflower genotypes under supplementary irrigation environment. The trait indicators used for constructing the circular Manhattan plot from outside to inside are TSW, Yp, RWC, PH, OIL, NSH, NHP, HD, DTM and DTF, respectively.

Fig. 7

Circular Manhattan plot representing the markers-traits association for morphological traits in 90 safflower genotypes under rainfed environment. The trait indicators used for constructing the circular Manhattan plot from outside to inside are DTF, DTM, HD, NHP, NSH, OIL, PH, RWC, Ys and TSW, respectively.

Fig. 8

Circular Manhattan plot representing the markers-traits association for STI values of traits. The trait indicators used for constructing the circular Manhattan plot from outside to inside are STI-SY, STI-TSW, STI-RWC, STI-PH, STI-OIL, STI-NSH, STI-NHP, STI-HD, STI-DTM and STI-DTF, respectively.