Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Plant Physiol. 2023 Oct 26;193(3):1913-1932. doi: 10.1093/plphys/kiad432.
Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses between a semiwild and 2 domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the 2 hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multiomic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.
减数分裂重组驱动遗传多样性和作物基因组优化。在植物育种中，将具有优良性状的亲本进行杂交，以培育出优良品种。不同的杂交产生同源染色体之间不同类型的片段重排。然而，对于导致杂种特异性交叉（COs）变化的因素知之甚少。在这里，我们构建了 2 个来自半野生和 2 个栽培黄瓜（ Cucumis sativus ）品系之间杂交的 F2 群体，并检查了 CO 事件。CO 主要发生在基因周围，在两个杂种之间的染色体上不均匀分布。杂合结构变异（SVs）区域的精细 CO 分布受到抑制，而高序列多态性则加速了 CO 的分布。黄瓜辐射敏感 51A（ CsRAD51A ）结合、组蛋白 H3 赖氨酸 4 三甲基化（H3K4me3）修饰、染色质可及性和低甲基化与全局 CO 景观以及局部 DNA 双链断裂（DSB）热点和基因呈正相关。CO 的频率和抑制可以根据多组学信息进行大致预测。杂种之间 CO 事件的差异部分可以追溯到不同的遗传和表观遗传特征，并且与特定的 DSB 热点和杂合性 SVs 显著相关。我们的研究结果确定了导致黄瓜 CO 形成和杂种特异性分化的基因组和表观遗传特征，为选择亲本组合和在植物育种过程中操纵目标基因组区域的重组事件提供了理论支持。
