哪有情可长
(2023-01-31 19:16):
#paper # De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis, Nature Genetics,16 January 2023,doi.org/10.1038/s41588-022-01283-w.玉米是三大粮食作物中杂种优势研究最多的物种，只是证明玉米存在杂种优势，但是关于对不同的育种目标对父母本的选择还没有文章说明，所以作者想对现在的骨干亲本组装想鉴定发现前人杂种优势形成的缘由。作者首先通过进化树分析对现在玉米常用的350自交系进行分析，对进化树每个分支上选取目前世界范围内广泛使用的12个骨干自交系，通过三代测序组装高质量基因组，同时结合玉米中之前已经发表的B73和Mo17基因组，构建了温带玉米核心育种种质泛基因组。作者对14个材料之间进行基因组比较分析发现存在广泛的遗传变异，通过对对玉米中现在 常用的自交系350份对花期、穗行数、穗粒数等表型进行鉴定和关键基因的单倍型分析，发现结构变异对杂种有事的形成和表型分化具有重要的贡献。通过对131份自交系雌穗的转录组数据分析，鉴定到306,868个调控基因表达的顺式eQTL，并挖掘到了一批调控玉米雄穗分枝数、穗位高及穗腐病抗性相关的候选基因及其关键结构变异；进一步结合14 个自交系的双列杂交群体 (91个F1)及3个环境的表型数据分析发现，玉米杂种优势与双亲基因组间结构变异的数量呈显著正相关，而与双亲基因组间共线性程度呈显著负相关，说明玉米杂种优势与双亲在全基因组水平的遗传互补性密切相关，为杂种优势的遗传互补模型提供了强有力的支持。同时结合遗传和分子生物学证据，挖掘到了ZmACO2 （编码一个乙烯合成酶）和ARGOS1 (ZAR1, 编码一个乙烯信号传导相关蛋白) 2个关键产量杂种优势位点，证明了其以超显性效应发挥作用。
De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis
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Abstract:
Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F hybrids, we found strong positive correlations between better-parent heterosis of the F hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.
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