Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China.
The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China.
Plant Biotechnol J. 2024 Nov;22(11):3135-3150. doi: 10.1111/pbi.14436. Epub 2024 Jul 24.
The elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene-environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near-isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre-quality-related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis-expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co-expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.
阐明复杂性状的遗传结构和分子调控网络仍然是生命科学中的一个重大挑战，这主要是由于上位性和基因-环境相互作用产生的大量背景效应。染色体片段代换系（CSSL）由于其近等基因特性，是遗传和分子剖析复杂性状的理想材料；然而，从基本的代换片段鉴定到先进的调控网络分析，仍然不够全面。在这里，我们在陆地棉背景上开发了两个具有广泛适应性和高皮棉产量的棉花 CSSL 群体，来自于具有优异纤维品质的海岛棉的渐渗；我们对 99 个在纤维方面与陆地棉表现出显著差异的 CSSL 进行了测序，并在三个关键发育阶段对 836 个动态纤维转录组进行了特征描述。我们开发了一种用于精确解析染色体代换片段的工作流程；基因组测序揭示了共代表现 87.25%的海岛棉基因组的代换。总的来说，基因组和转录组调查确定了 18 个具有高遗传贡献的新纤维品质相关数量性状位点和纤维发育调控的综合景观。此外，分析确定了 CSSL 中独特的顺式表达模式是纤维品质改变的驱动力；在此基础上，共表达调控网络揭示了所关注途径之间的生物学关系，并准确描述了 GhHOX3、GhRDL1 和 GhEXPA1 在纤维伸长过程中的分子相互作用，以及对它们与 GhTBA8A5 相互作用的可靠预测。我们的研究将增强 CSSL 在作物分子生物学和育种计划中的更战略性应用。
