Linkage and association mapping in multi‐parental populations reveal the genetic basis of carotenoid variation in maize kernels

作者：Pengfei Yin, Xiuyi Fu, Haiying Feng, Yanyan Yang, Jing Xu, Xuan Zhang, Min Wang, Shenghui Ji, Binghao Zhao, Hui Fang, Xiaoxia Du, Yaru Li, Shuting Hu, Kun Li, Shutu Xu, Zhigang Li, Fang Liu, Yingni Xiao, Yuandong Wang, Jiansheng Li, Xiaohong Yang · 发表于：Plant Biotechnology Journal · 年份：2024 · DOI：10.1111/pbi.14346 · 被引用次数：9 · 研究领域：Antioxidant Activity and Oxidative Stress、Genetic Mapping and Diversity in Plants and Animals、Plant Reproductive Biology

Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to a...