Abstract
Background: Safflower (Carthamus tinctorius L.) has been cultivated worldwide for centuries, originally as a source of textile dyes. Modern safflower breeding has focused on high grain and oil yield and broad adaptability. Here, a genome-wide association study was conducted using a globally diverse Genebank collection of 406 accessions, which included landraces, breeding lines and elite cultivars. We explored the genetic architecture and genotype-by-environment interaction (G × E) patterns of grain yield (YP), days to flowering (DF ), plant height (PH), 500 seed weight (SW), seed oil content (OL), and crude protein content (PR) in four environments (sites) that differed in water availability. Results: Phenotypic variation within the global collection was observed for all traits under differed water stress environments. Two mixed linear models were adopted, and YP exhibited low overall genetic correlations (rGoverall) across sites, while SW and OL had high rGoverall and high pairwise genetic correlations (rGij) across all pairwise sites. Ninety-two marker-trait associations (MTAs) were identified using three methods, single locus genome-wide association studies (GWAS) using a mixed linear model (MLM), the Bayesian multi-locus method (BayesR), and meta-GWAS. MTAs with large effects across all sites were detected for OL, SW, and PR, and MTAs specific for the different water stress sites was identified for all traits. Five MTAs were associated with multiple traits, 4 of 5 MTAs were variously associated with the three traits of SW, OL, and PR and marker effects were consistent with phenotypic observations in different environments. The thresholds of different GWAS methods used in the study affected the number of MTAs identified for complex traits. Conclusions: This study provided insights into the phenotypic variability and genetic architecture of important safflower agronomic traits under different environments. This knowledge is essential to breed for high grain and oil yield and local adaption in safflower.
Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.)
