Wang Junjie, Ma Qi, Zhang Yuyang, Duan Qian, Zhen Xiaoxi, Zhang Yaoyuan, Li Hongying, Han Yuanhuai, Zhang Bin
College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China.
BMC Plant Biol. 2025 Apr 25;25(1):529. doi: 10.1186/s12870-025-06585-9.
Kernel color is an important characteristic of foxtail millet (Setaria italica) associated with its market ability, quality, and nutritional value, which is mainly due to the accumulation of carotenoids. Despite its importance, the genetic basis of carotenoid variation in foxtail millet remains largely unexplored. Herein, the molecular mechanisms governing carotenoid accumulation in the kernel of foxtail millet were investigated by an exhaustive methodology encompassing Genome-Wide Association Study (GWAS), Bulk Segregant Analysis sequencing (BSA-seq), and integrated transcriptomic and metabolomic analyses.
The total carotenoid content in kernels across 201 foxtail millet germplasms showed a spectrum of variations, which indicated that the kernel color is a quantitative genetic trait controlled by multiple genes. Using GWAS on these germplasms and BSA-seq on an F generation Recombinant Inbred Line (RIL) population derived from the GBS (yellow kernel) and NMB (white kernel) cross, we identified genome regions linked with total carotenoid content in foxtail millet kernels. Integrated transcriptomic and metabolomic profiling during grain filling in both yellow and white varieties pinpointed SiPSY1 and SiCCD1 as key genes controlling carotenoid accumulation. Notably, the SNP (G/A) at 364 bp and the Indel (29 bp insertion) at 856 bp within the SiPSY1 promoter predominantly contributed to the variance in promoter activity. These variations markedly affected SiPSY1 expression levels, ultimately determining the phenotypic difference between yellow and white kernels.
These findings provide crucial genetic insights for the molecular mechanisms involved in carotenoid metabolism and lay a solid foundation for millet color breeding in foxtail millet.
谷粒颜色是谷子（Setaria italica）的一个重要特征，与其市场竞争力、品质和营养价值相关，这主要归因于类胡萝卜素的积累。尽管其很重要，但谷子中类胡萝卜素变异的遗传基础在很大程度上仍未被探索。在此，通过全基因组关联研究（GWAS）、混合分组分析法测序（BSA-seq）以及整合转录组和代谢组分析等详尽方法，对调控谷子谷粒中类胡萝卜素积累的分子机制进行了研究。
201份谷子种质资源谷粒中的总类胡萝卜素含量呈现出一系列变异，这表明谷粒颜色是一个受多基因控制的数量遗传性状。利用这些种质资源进行GWAS，并对GBS（黄粒）和NMB（白粒）杂交产生的F代重组自交系（RIL）群体进行BSA-seq，我们鉴定出了与谷子谷粒总类胡萝卜素含量相关的基因组区域。对黄粒和白粒品种灌浆期进行的整合转录组和代谢组分析确定了SiPSY1和SiCCD1是控制类胡萝卜素积累的关键基因。值得注意的是，SiPSY1启动子内364 bp处的单核苷酸多态性（SNP，G/A）和856 bp处的插入缺失（29 bp插入）主要导致了启动子活性的差异。这些变异显著影响了SiPSY1的表达水平，最终决定了黄粒和白粒之间的表型差异。
这些发现为类胡萝卜素代谢所涉及的分子机制提供了关键的遗传学见解，并为谷子的颜色育种奠定了坚实基础。
