ArticleBMC genomics2025
EMS-induced genomic variation and QTL-seq analysis of safflower spininess through whole genome sequencing (WGS).
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Phenotypic variation is detrimental for deciphering the genetic control of valuable traits in crop plants. Safflower (Carthamus tinctorius L.) is an industrial and medicinal plant with natural stress-resilience. In this study, we used two bulk samples of safflower (spiny and spineless) developed after ethyl methanesulfonate (EMS) induced mutagenesis, aimed to find genomic variation between two phenotypes through whole genome sequencing (WGS) and to find putative associations with spine formation on the plant organs. More than 890,000 EMS-induced SNPs were obtained, and comparison of the G: C > A:T canonical mutation rate in EMS-induced and 93 natural safflower samples obtained via genotyping-by-sequencing (GBS) showed that the canonical mutation rate in two studies was significantly different (38.03% vs. 32.4%). Most of the mutations affected the intergenic regions (46.81%) and only 3.94% were located in exome which could have a high putative impact on gene function. More than 137,000 filtered SNPs were used for marker-trait association (MTA) via QTL-seq analysis which resulted in identifying a genomic region on short arm of chromosome 7 (qSpiny7) to be associated with spininess. The qSpiny7 contains 24 genes carrying 151 SNPs in their exons, 40 of which were functional SNPs. RNA-seq assay indicated that 14 and 8 genes within qSpiny7, respectively, were up- and down-regulated in spineless mutant. The expression patterns of 6 selected genes were confirmed using real-time qRT-PCR. A new candidate gene (BG1-like E) involved in cell division and different organ`s enlargement, and a recently identified gene, Lonely Guy (LOG), for controlling spine/prickle formation in higher plants, also locate within qSpiny7 in safflower. The latter gene harbors a SNP in its first intron. Based on our results, the major effect genomic region qSpiny7 harbors important genes for developmental processes and stress responses. These findings can open new insight into the nature of natural and induced genomic variations of safflower and the applicability of them in MTA studies.
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