Li Zhiyong, Li Chunhui, Zhang Ruyang, Duan Minxiao, Tian Hongli, Yi Hongmei, Xu Liwen, Wang Fengge, Shi Zi, Wang Xiaqing, Wang Jidong, Su Aiguo, Wang Shuai, Sun Xuan, Zhao Yanxin, Wang Shuaishuai, Zhang Yunxia, Wang Yuandong, Song Wei, Zhao Jiuran
Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Front Plant Sci. 2023 Aug 11;14:1213675. doi: 10.3389/fpls.2023.1213675. eCollection 2023.
Genome-wide analyses of maize populations have clarified the genetic basis of crop domestication and improvement. However, limited information is available on how breeding improvement reshaped the genome in the process of the formation of heterotic groups. In this study, we identified a new heterotic group (X group) based on an examination of 512 Chinese maize inbred lines. The X group was clearly distinct from the other non-H&L groups, implying that X × HIL is a new heterotic pattern. We selected the core inbred lines for an analysis of yield-related traits. Almost all yield-related traits were better in the X lines than those in the parental lines, indicating that the primary genetic improvement in the X group during breeding was yield-related traits. We generated whole-genome sequences of these lines with an average coverage of 17.35× to explore genome changes further. We analyzed the identity-by-descent (IBD) segments transferred from the two parents to the X lines and identified 29 and 28 IBD conserved regions (ICRs) from the parents PH4CV and PH6WC, respectively, accounting for 28.8% and 12.8% of the genome. We also identified 103, 89, and 131 selective sweeps (SSWs) using methods that involved the π, Tajima's D, and CLR values, respectively. Notably, 96.13% of the ICRs co-localized with SSWs, indicating that SSW signals concentrated in ICRs. We identified 171 annotated genes associated with yield-related traits in maize both in ICRs and SSWs. To identify the genetic factors associated with yield improvement, we conducted QTL mapping for 240 lines from a DH population (PH4CV × PH6WC, which are the parents of X1132X) for ten key yield-related traits and identified a total of 55 QTLs. Furthermore, we detected three QTL clusters both in ICRs and SSWs. Based on the genetic evidence, we finally identified three key genes contributing to yield improvement in breeding the X group. These findings reveal key loci and genes targeted during pedigree breeding and provide new insights for future genomic breeding.
对玉米群体的全基因组分析已经阐明了作物驯化和改良的遗传基础。然而，关于杂种优势群形成过程中育种改良如何重塑基因组的信息有限。在本研究中，我们通过对512个中国玉米自交系的检测，鉴定出一个新的杂种优势群（X群）。X群与其他非H&L群明显不同，这意味着X×HIL是一种新的杂种优势模式。我们选择核心自交系分析产量相关性状。几乎所有产量相关性状在X系中都比在亲本系中更好，这表明在育种过程中X群的主要遗传改良是产量相关性状。我们生成了这些品系的全基因组序列，平均覆盖度为17.35×，以进一步探索基因组变化。我们分析了从两个亲本转移到X系的同源片段（IBD），分别从亲本PH4CV和PH6WC中鉴定出29个和28个IBD保守区域（ICR），分别占基因组的28.8%和12.8%。我们还分别使用涉及π值、Tajima's D值和CLR值的方法鉴定出103个、89个和131个选择清除（SSW）区域。值得注意的是，96.13%的ICR与SSW共定位，表明SSW信号集中在ICR中。我们在ICR和SSW中鉴定出171个与玉米产量相关性状相关的注释基因。为了鉴定与产量提高相关的遗传因素，我们对来自DH群体（PH4CV×PH6WC，即X1132X的亲本）的240个品系的十个关键产量相关性状进行了QTL定位，共鉴定出55个QTL。此外，我们在ICR和SSW中都检测到三个QTL簇。基于遗传证据，我们最终鉴定出三个在X群育种过程中对产量提高有贡献的关键基因。这些发现揭示了系谱育种过程中靶向的关键位点和基因，并为未来的基因组育种提供了新的见解。
