Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops
文献类型: 外文期刊
第一作者: Han, Zhenyun
作者: Han, Zhenyun;Li, Fei;Qiao, Weihua;Zheng, Xiaoming;Cheng, Yunlian;Zhang, Lifang;Huang, Jingfen;Wang, Yanyan;Lou, Danjing;Xing, Meng;Fan, Weiya;Nie, Yamin;Guo, Wenlong;Wang, Shizhuang;Liu, Ziran;Yang, Qingwen;Qiao, Weihua;Zheng, Xiaoming;Yang, Qingwen;Zheng, Xiaoming
作者机构:
关键词: weedy rice; population classification; structural variation; WRKY; NBS
期刊名称:FRONTIERS IN PLANT SCIENCE ( 影响因子:5.6; 五年影响因子:6.8 )
ISSN: 1664-462X
年卷期: 2023 年 13 卷
页码:
收录情况: SCI
摘要: Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs.
分类号:
- 相关文献
作者其他论文 更多>>
-
Spatiotemporal variation of autumn phenology responses to preseason drought and temperature in alpine and temperate grasslands in China
作者:Yuan, Zhihui;Tong, Siqin;Bao, Gang;Yin, Shan;Sa, Chula;Bao, Yuhai;Yuan, Zhihui;Bao, Gang;Bao, Yuhai;Yuan, Zhihui;Chen, Jiquan;Li, Fei
关键词:End of the vegetation growing season; Temperate and alpine grasslands; Drought; Temperature; Spatiotemporal pattern
-
Chromosome-level genome assembly of the Colorado potato beetle, Leptinotarsa decemlineata
作者:Yan, Junjie;Zhang, Mengdi;Gao, Yulin;Zhang, Chaowei;Zhou, Hang;Zuo, Zhangqi;Li, Fei;Zhang, Chaowei;Zhou, Hang;Zuo, Zhangqi;Li, Fei;Zhang, Chaowei;Zhou, Hang;Zuo, Zhangqi;Li, Fei;Ding, Xinhua;Zhang, Runzhi
关键词:
-
Genome-wide differences of alternative splicing between Oryza sativa ssp. indica and Oryza sativa ssp. japonica
作者:Pang, Hongbo;Wu, Yuanming;Liu, Ziran;Xie, Yuankun;Li, Yueying;Wang, Ze;Chen, Qiang;Wu, Longkun;Ahmed, Zeeshan;Zheng, Xiaoming
关键词:Oryza sativa L; Transcriptome sequencing; Alternative splicing; Abiotic stress; GO enrichment
-
The low ferric chelate reductase activity and high apoplastic pH in leaves cause iron deficiency chlorosis in 'Huangguan' pears grafted onto quince A grown in calcareous soil
作者:Zhao, Yanyan;Li, Fei;Sun, Zhi;Li, Haigang;Zhao, Yanyan;Liu, Songzhong;Sun, Mingde;Liang, Zhenxu;Yu, Futong
关键词:Pears; Quince A; Iron deficiency; Calcareous soil; Apoplastic pH
-
A novel seed balling technology and its effect on cotton emergence, yield and fiber quality
作者:Xie, Zhangshu;Zhou, Chengxuan;Li, Kan;Yang, Dan;Tu, Xiaoju;Qin, Yeling;Xu, Doudou;Li, Jiarui;Liu, Aiyu;Zhou, Zhonghua;Xie, Zhangshu;Zhou, Chengxuan;Li, Kan;Yang, Dan;Tu, Xiaoju;Qin, Yeling;Xu, Doudou;Li, Jiarui;Liu, Aiyu;Zhou, Zhonghua;Xie, Xuefang;Li, Fei;Jiang, Jie;He, Yunxin;Wu, Bibo;Zhou, Zhonghua;Zhou, Zhonghua;Wu, Bibo
关键词:cotton seed pretreatment; seed balling technology; direct seeding
-
Xoo-YOLO: a detection method for wild rice bacterial blight in the field from the perspective of unmanned aerial vehicles
作者:Pan, Pan;Hu, Lin;Zhou, Guomin;Zhang, Jianhua;Pan, Pan;Zheng, Xiaoming;Hu, Lin;Zhou, Guomin;Zhang, Jianhua;Guo, Wenlong;Zheng, Xiaoming;Zhou, Guomin
关键词:wild rice; UAV; bacterial blight; disease detection; deep learning; YOLOv8
-
The Effect of Drip Irrigation Quota on Biochemical Activities and Yield-Related Traits in Different Drought-Tolerant Maize Varieties
作者:Xu, Chen;Li, Fei;Zhuang, Yan;Zhang, Zhian;Zhao, Renjie;Qi, Zexin;Xu, Chen;Li, Qian;Zhang, Lihua;Zhao, Hongxiang;Bian, Shaofeng;Wang, Hongjun
关键词:maize (Zea mays L.); drip irrigation; grain filling; yield; starch synthesis