National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
International Rice Research Institute, DAPO box 7777, Metro Manila, the Philippines.
BMC Biol. 2023 Feb 1;21(1):20. doi: 10.1186/s12915-023-01512-6.
DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication.
In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length.
We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.
不同类型的 DNA 突变为表型变异和进化提供了所需的原材料。 在作物物种的情况下，以前的研究旨在阐明重复序列、单核苷酸多态性 (SNP) 和小插入缺失 (InDel) 在驯化过程中的变化模式，以解释形态进化和对不同环境的适应。 此外，结构变异 (SV) 包含更大的 DNA 片段更有可能改变基因表达水平，导致表型变异，从而影响植物表型和抗逆性。 以前对水稻中 SV 的研究受到对短读测序的依赖的限制，限制了 SV 识别的数量和质量，而 SV 数据目前仅可用于栽培稻，野生稻则基本上没有特征。 在这里，我们使用长读测序为 O. rufipogon 生成了两个基因组组装，并提供了有关 SV 在水稻驯化过程中对形态特征进化模式和影响的见解。
在这项研究中，我们通过对 13 个高质量水稻基因组的全面分析，在栽培稻和野生稻群体中鉴定出 318589 个 SV，并发现野生稻基因组包含 49%的独特 SV，并且在水稻驯化过程中平均有 1.76%的基因丢失。 这些 SV 进一步对 649 个水稻品种进行了基因分型，研究了它们在水稻驯化过程中的进化模式及其与重要农艺性状多样性的潜在关联。 对这些 SV 与九个农艺性状之间的全基因组关联研究确定了 413 个候选因果变异，这些变异共同影响 361 个基因。 粳稻中一个 824bp 的缺失，该缺失编码丝氨酸羧肽酶家族蛋白，与粒长有关。
通过比较 13 个代表性品种的长读测序数据，我们为栽培稻和野生稻提供了相对准确和完整的 SV 数据集，特别是在富含 TE 的区域。 综合的水稻 SV 图谱以及鉴定的候选基因和变异为未来的水稻基因组研究和育种提供了有价值的资源。
