Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.
Plant Biotechnol J. 2024 Mar;22(3):662-677. doi: 10.1111/pbi.14215. Epub 2023 Nov 1.
Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.
旱稻是一种具有明显耐旱-需氧生态型的栽培稻，对干旱胁迫具有很强的抗性。然而，由于缺乏基因组资源，旱稻耐旱-需氧适应性的遗传和基因组基础在很大程度上仍不清楚。在这项研究中，我们鉴定了 25 个典型旱稻品种，并组装了一个典型旱稻品种 IRAT109 的高质量基因组，该基因组包含 384Mb，其连续序列 N50 为 19.6Mb。系统发育分析表明，旱稻和水稻在粳稻亚群内具有明显的生态型分化。比较基因组分析表明，水稻的旱、旱性适应分化可能归因于启动子区域的许多基因的自然变异、旱稻中特定基因的形成以及基因家族的扩张。我们揭示了两个生态型叶片和根系的差异表达模式，并发现苯丙烷途径介导的木质素合成在旱稻和水稻的适应性分化中起重要作用。我们鉴定了 28 个在驯化过程中发生的选择区域，并验证了选择区域中的 qRT9 基因可以正向调控水稻的抗旱性。评估了 80 个与抗旱性密切相关的关键基因，以评估其在抗旱性育种中的潜在价值。我们的研究增进了对旱稻适应的理解，并提供了抗旱性育种的基因组导航图，这将有助于培育抗旱水稻和农业的“蓝色革命”。
