Kong Weilong, Deng Xiaoxiao, Yang Jing, Zhang Chenhao, Sun Tong, Ji Wenjie, Zhong Hua, Fu Xiaopeng, Li Yangsheng
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Plant J. 2022 May;110(3):814-827. doi: 10.1111/tpj.15705. Epub 2022 Mar 5.
Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.
株高（PH）是影响植株形态、种子产量和收获指数的重要性状。然而，PH杂种优势的分子机制仍不清楚。此外，迫切需要鉴定与PH相关的有用基因，以促进水稻（Oryza sativa L.）理想株型育种。在本研究中，为了探索水稻中PH的数量性状位点（QTL）和杂种优势相关位点，我们利用两个优良品种罗恢9（籼稻/籼）×RPY粳（粳稻/粳）杂交构建了一个由272个重组自交系（RIL）组成的高世代（>F）群体，以及两个由RIL与两个细胞质雄性不育系（YTA[籼稻]和Z7A[粳稻]）杂交产生的测交杂种群体。利用深度重测序数据，构建了一个包含4758个bin标记的高密度遗传图谱，总图距为2356.41 cM。最终，在五个季节中鉴定出31个与不同PH组成部分长度或分蘖数相关的PH QTL。在海南（qPH-3.1）或湖北（qPH-5.1）稳定检测到两个主要的环境特异性PH QTL，随着地理环境的变化，它们在水稻中发生了显著的功能改变。基于比较基因组学、基因功能注释、同源物鉴定和现有文献（开创性研究），对多个QTL的候选基因进行了精细定位，并利用CRISPR-Cas9基因编辑进一步验证了PH的候选基因qPH-3.1和qPH-5.1。具体而言，qPH-3.1被鉴定为一个多效基因，qPH-3.1敲除系表现出株高降低、抽穗延迟、结实率降低和分蘖数增加。重要的是，在测交群体中鉴定出10个与PH杂种优势相关的QTL，一个较好亲本杂种优势位点（qBPH-5.2）完全覆盖了qPH-5.1。此外，固定基因型RIL的杂交结果验证了qPH-3.1和qPH-（此处原文可能有误，推测为qPH-5.1）的显性效应。总之，这些发现进一步加深了我们对PH遗传机制的理解，并为在不久的将来培育具有理想株型和高产潜力的水稻品种提供了多个高度可靠的基因靶点。
