Cui Jingnan, Li Shuangshuang, Zhang Tong, Li Chong, Duan Yuxuan, Xu Shanbin, Wang Jingguo, Liu Hualong, Yang Luomiao, Xin Wei, Jia Yan, Bu Qingyun, Zou Detang, Zheng Hongliang
Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
Northeast Institute of Geography and Agroecology, State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, 150081, China.
Theor Appl Genet. 2024 Dec 27;138(1):14. doi: 10.1007/s00122-024-04772-0.
Integrated genome-wide association study and linkage mapping revealed genetic basis of alkalinity tolerance during rice germination. The key gene OsWRKY49 was further verified in transgenic plants. With the widespread use of the rice direct seeding cultivation model, improving the tolerance of rice varieties to salinity-alkalinity at the germination stage has become increasingly important. However, as previous studies have concentrated on neutral salt stress, understanding of alkalinity tolerance is still in its infancy, and the genetic resource data is scarce. Here, we used a natural population composed of 295 japonica rice varieties and a recombinant inbred population including 189 lines derived from Caidao (alkali-sensitive) and WD20342 (alkali-tolerant) to uncover the genetic structure of alkalinity tolerance during rice germination. A total of 15 lead SNPs and six QTLs related to relative germination potential (RGP) and relative germination index (RGI) were detected by genome-wide association study and linkage mapping. Of which, Chr5_28094966, a lead SNP was located in the interval of the mapped major QTL qAT5, that was significantly associated with both RGP and RGI in the two populations. According to the LD block analysis and QTL interval, a 425 kb overlapped region was obtained for screening the candidate genes. After haplotype analysis, qRT-PCR and parental sequence analysis, LOC_Os05g49100 (OsWRKY49) was initially considered as the candidate gene. Having studied the characteristics of rice lines with OsWRKY49 knockout and overexpression, we established that OsWRKY49 could be a positive regulator of alkalinity tolerance in rice at the germination stage. Subcellular localization showed that green fluorescent protein-tagged OsWRKY49 was localized in the nucleus. The application of OsWRKY49 could be useful for increasing alkalinity tolerance of rice direct seeding.
全基因组关联研究与连锁图谱分析揭示了水稻萌发期耐碱性的遗传基础。关键基因OsWRKY49在转基因植株中得到了进一步验证。随着水稻直播栽培模式的广泛应用，提高水稻品种在萌发期对盐碱的耐受性变得越来越重要。然而，由于以往的研究集中在中性盐胁迫上，对耐碱性的了解仍处于起步阶段，遗传资源数据也很匮乏。在此，我们利用一个由295个粳稻品种组成的自然群体和一个包含189个株系的重组自交群体（该群体源于Caidao（碱敏感）和WD20342（耐碱））来揭示水稻萌发期耐碱性的遗传结构。通过全基因组关联研究和连锁图谱分析，共检测到15个与相对萌发势（RGP）和相对萌发指数（RGI）相关的主效单核苷酸多态性（SNP）和6个数量性状基因座（QTL）。其中，Chr5_28094966这个主效SNP位于已定位的主效QTL qAT5区间内，在两个群体中均与RGP和RGI显著相关。根据连锁不平衡（LD）区块分析和QTL区间，获得了一个425 kb的重叠区域用于筛选候选基因。经过单倍型分析、实时定量聚合酶链反应（qRT-PCR）和亲本序列分析，初步认为LOC_Os05g49100（OsWRKY49）是候选基因。通过研究OsWRKY49基因敲除和过表达水稻株系的特性，我们确定OsWRKY49可能是水稻萌发期耐碱性的正调控因子。亚细胞定位显示，绿色荧光蛋白标记的OsWRKY49定位于细胞核。OsWRKY49的应用可能有助于提高水稻直播的耐碱性。
