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 alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.

中文翻译：

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多亲本群体中的连锁和关联作图揭示了玉米籽粒中类胡萝卜素变异的遗传基础

类胡萝卜素是植物不可缺少的，也是人类饮食的重要组成部分。类胡萝卜素代谢途径在植物物种中是保守的，但对于大多数谷类作物的种子，我们对类胡萝卜素变异遗传基础的理解仍然有限。为了解决这个问题，我们使用六个重组自交系（RIL）群体系统地对八个类胡萝卜素性状进行了连锁和关联作图。单连锁作图 (SLM) 和联合连锁作图 (JLM) 鉴定了 77 个独特的加性 QTL 和 104 对上位 QTL。在这些QTL中，我们鉴定了22个加性和上位基因座的重叠热点，强调了一些QTL通过加性或上位机制对类胡萝卜素水平的重要贡献。基于所有RIL的全基因组关联研究检测到244个与类胡萝卜素性状显着相关的候选基因，其中23个被注释为类胡萝卜素途径基因。效果比较表明，少数与途径基因相关的基因座对我们测试的群体中的类胡萝卜素变异具有重大影响，但许多与途径基因无关的基因座也对类胡萝卜素变异做出了重要贡献。我们将ZmPTOX确定为 QTL 热点 ( Q10 / JLM10 / GWAS019 ) 的因果基因；该基因编码一种推定的质体末端氧化酶，该酶产生类胡萝卜素途径中两种酶所使用的质体醌-9。发现ZmPTOX启动子和第二外显子中的天然变异会改变类胡萝卜素水平。对类胡萝卜素变异背后的遗传机制的全面评估为重新连接类胡萝卜素代谢和积累以实现有效的类胡萝卜素生物强化奠定了基础。