Huang Chujun, Cheng Yu, Hu Yan, Zhang Xuemei, Chen Jinwen, Zhao Ting, Si Zhanfeng, Cao Yiwen, Li Yiqian, Fang Lei, Guan Xueying, Zhang Tianzhen
Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
J Adv Res. 2024 Aug 6. doi: 10.1016/j.jare.2024.08.010.
Heterosis has revolutionized crop breeding, enhancing global agricultural production. However, the mechanisms underlying heterosis remain obscure. Xiangzamian 2# (XZM2), a super hybrid upland cotton (Gossypium hirsutum L.) characterized by high-yield heterosis, has been developed and extensively planted in China.
We conducted a systematic analysis of CRI12 and J8891, two parents of XZM2. We aimed to reveal the precise genetic information and the role of non-syntenic divergence in shaping heterosis, laying a foundation for advancing understanding of heterosis.
We de novo assembled high-quality genomes of CRI12 and J8891, and further uncovered abundant genetic variations and non-syntenic regions between the parents. Whole-genome comparison, association analysis, transcriptomic analysis and relative identity-by-descent (rIBD) estimation were conducted to identify structural variations (SVs) and introgressions within non-syntenic blocks and to analyze their impacts on promoting heterosis.
Parental genetic divergence increased in non-syntenic regions. Furthermore, these regions, accounting for only 16.71% of the total genome, contained more loci with significantly higher heterotic effects, far exceeding the syntenic background. SVs covered 97.26% of non-syntenic sequences and caused widespread gene expression differences in these regions, driving dynamic complementation of gene expression in the hybrid. A set of SVs were responsible for trait improvement and had positive effects on heterosis, contributing larger heritability than short variations. We characterized numerous parental-specific introgressions from G. barbadense. Specifically, a functional introgression segment within non-syntenic blocks introduced an elite haplotype, which significantly increased lint yield and enhanced heterosis.
Our study clarified non-syntenic regions to harbor more loci with higher heterotic effects, revealed their importance in promoting heterosis and supported the crucial role of genetic complementation in heterosis. SVs and introgressions were identified as key factors responsible for non-syntenic divergence between the parents. They had important effects on gene expression and trait improvement, positively contributing to heterosis.
杂种优势彻底改变了作物育种，提高了全球农业产量。然而，杂种优势的潜在机制仍不清楚。湘杂棉2号（XZM2）是一种具有高产杂种优势的超级杂交陆地棉（陆地棉），已在中国培育并广泛种植。
我们对XZM2的两个亲本CRI12和J8891进行了系统分析。我们旨在揭示精确的遗传信息以及非共线性差异在塑造杂种优势中的作用，为增进对杂种优势的理解奠定基础。
我们对CRI12和J8891的高质量基因组进行了从头组装，并进一步揭示了亲本之间丰富的遗传变异和非共线性区域。进行全基因组比较、关联分析、转录组分析和相对同源片段估计，以识别非共线性区域内的结构变异（SVs）和渗入片段，并分析它们对促进杂种优势的影响。
亲本的遗传差异在非共线性区域增加。此外，这些区域仅占基因组总量的16.71%，却包含更多具有显著更高杂种优势效应的位点，远远超过共线性背景。SVs覆盖了97.26%的非共线性序列，并在这些区域引起广泛的基因表达差异，推动杂种中基因表达的动态互补。一组SVs负责性状改良，并对杂种优势有积极影响，其遗传力贡献大于短变异。我们鉴定了许多来自海岛棉的亲本特异性渗入片段。具体而言，非共线性区域内的一个功能性渗入片段引入了一个优良单倍型，显著提高了皮棉产量并增强了杂种优势。
我们的研究阐明了非共线性区域含有更多具有更高杂种优势效应的位点，揭示了它们在促进杂种优势中的重要性，并支持了遗传互补在杂种优势中的关键作用。SVs和渗入片段被确定为亲本间非共线性差异的关键因素。它们对基因表达和性状改良有重要影响，对杂种优势有积极贡献。
