Genomic insights into the genetic signatures of selection and seed trait loci in cultivated peanut
文献类型: 外文期刊
第一作者: Liu, Yiyang
作者: Liu, Yiyang;Li, Rongchong;Cui, Feng;Zhang, Jialei;Guo, Feng;Li, Xinguo;Li, Guowei;Wan, Shubo;Shao, Libin;Zhou, Jing;Fan, Guangyi;Pandey, Manish K.;Varshney, Rajeev K.;Han, Yan;Li, Guowei;Shan, Shihua;Fan, Guangyi;Zhang, He;Seim, Inge;Seim, Inge;Varshney, Rajeev K.;Varshney, Rajeev K.
作者机构:
关键词: Peanut; Genomic diversity; Evolution; GWAS; Seed traits
期刊名称:JOURNAL OF ADVANCED RESEARCH ( 影响因子:10.7; 五年影响因子:11.4 )
ISSN: 2090-1232
年卷期: 2022 年 42 卷
页码:
收录情况: SCI
摘要: Introduction: Cultivated peanut (Arachis hypogaea L.) is an important oil crop for human nutrition and is cultivated in >100 countries. However, the present knowledge of its genomic diversity, evolution, and loci related to the seed traits is limited. Objectives: Our study intended to (1) uncover the population structure and the demographic history of peanuts, (2) identify signatures of selection that occurred during peanut improvement breeding, and (3) detect and verify the functions of candidate genes associated with seed traits. Methods: We explored the population relationship and the evolution of peanuts using a largescale single nucleotide polymorphism dataset generated from the genome-wide resequencing of 203 cultivated peanuts. Genetic diversity and genomic scan analyses were applied to identify selective loci for genomicselection breeding. Genome-wide association studies, transgenic experiments, and RNA-seq were employed to identify the candidate genes associated with seed traits. Results: Our study revealed that the 203 resequenced accessions were divided into four genetic groups, consistent with their botanical classification. Moreover, the var. peruviana and var. fastigiata subpopulations have diverged to a greater extent than the others, and var. peruviana may be the earliest variant in the evolution from tetraploid ancestors. A recent dramatic expansion in the effective population size of the cultivated peanuts ca. 300-500 years ago was also noted. Selective sweeps underlying quantitative trait loci and genes of seed size, plant architecture, and disease resistance coincide with the major goals of improved peanut breeding compared with the landrace and cultivar populations. Genome-wide association testing with functional analysis led to the identification of two genes involved in seed weight and seed length regulation. Conclusion: Our study provides valuable information for understanding the genomic diversity and the evolution of peanuts and serves as a genomic basis for improving peanut cultivars. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article
分类号:
- 相关文献
作者其他论文 更多>>
-
Peanut NAC Transcription Factor AhNAPa Negatively Regulates Salt Tolerance in Transgenic Arabidopsis
作者:Yuan, Cuiling;Sun, Quanxi;Shan, Shihua;Miao, Haocui
关键词:AhNAPa; NAC transcription factor; salt tolerance; negative regulator; peanut
-
Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut
作者:Wang, Lihui;Chen, Kun;Fu, Huiwen;Chen, Hua;Zhang, Chong;Cai, Tiecheng;Yang, Qiang;Zhuang, Weijian;Zhuang, Yuhui;Chen, Xiangyu;Chitkineni, Annapurna;Varshney, Rajeev K.;Wang, Xiyin
关键词:peanut; alternative splicing; chromatin structures; Iso-Seq; 6mA
-
Temperature-smart plants: A new horizon with omics-driven plant breeding
作者:Raza, Ali;Raza, Ali;Bashir, Shanza;Khare, Tushar;Jamla, Monica;Karikari, Benjamin;Karikari, Benjamin;Copeland, Rhys G. R.;Varshney, Rajeev K.;Abbas, Saghir;Charagh, Sidra;Nayak, Spurthi N.;Djalovic, Ivica;Rivero, Rosa M.;Siddique, Kadambot H. M.
关键词:
-
Peanut-based intercropping systems altered soil bacterial communities, potential functions, and crop yield
作者:Liu, Zhu;Nan, Zhenwu;Lin, Songming;Meng, Weiwei;Xie, Liyong;Zhang, Zheng;Wan, Shubo;Liu, Zhu;Xie, Liyong;Yu, Haiqiu;Lin, Songming
关键词:Sorghum; Millet; Peanut; Intercropping; Yield; Soil bacterial community
-
Multiomics analysis reveals that microbiota regulate fat and muscle synthesis in chickens
作者:Yin, Hai Chang;Yao, Wan Qi;Liu, Song;Ma, Tian Yi;Yin, Hai Chang;Yao, Wan Qi;Zhang, He;Ma, Tian Yi;Zhang, He;Xia, Chang You
关键词:Key words: intestinal microbes; GF chicken; metabolism; fat accumulation; muscle development
-
Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity
作者:Raza, Ali;Salehi, Hajar;Bashir, Shanza;Tabassum, Javaria;Javed, Muhammad Arshad;Jamla, Monica;Charagh, Sidra;Barmukh, Rutwik;Varshney, Rajeev K.;Mir, Rakeeb Ahmad;Bhat, Basharat Ahmad;Guan, Dong-Xing;Mir, Reyazul Rouf;Siddique, Kadambot H. M.
关键词:Artificial intelligence; Bioinformatic tools; Climate change; Defense responses; Environmental pollution; Metal toxicity; Omics approaches
-
ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L.
作者:Deng, Quanqing;Du, Puxuan;Hong, Yanbin;Hu, Dongxiu;Li, Haifen;Lu, Qing;Li, Shaoxiong;Liu, Haiyan;Wang, Runfeng;Huang, Lu;Liang, Xuanqiang;Chen, Xiaoping;Liu, Hao;Gangurde, Sunil S.;Xiao, Yuan;Wang, Wenyi;Varshney, Rajeev K.;Garg, Vanika
关键词:scRNA-seq; peanut leaf; single cell; light; gene atlases