数字农科院2.0

Comprehensive comparison between structural variants and single-nucleotide polymorphism in genomic selection of rice (Oryza sativa L.)

文献类型： 外文期刊

作者： Liang, Lunping;Zhang, Chaopu;Yu, Linjun;Sheng, Tingting;Zheng, Shuyue;Li, Shijiao;Zhou, Shuran;Feng, Ting;Zhang, Fan;Li, Zhikang;Cui, Yanru;Wang, Wensheng;Li, Min

作者机构：

关键词： Structural variation;QTL;SNP;Predictive ability

期刊名称： CROP JOURNAL

ISSN： 2095-5421

年卷期： 2025 年 13 卷 6 期

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版） ; ; 农林核心（2024版）

摘要： Recent genomic research on plant populations has revealed abundant structural variations (SVs) of > 50 bp within and among genotypes of major crop species, but the application of SVs as a unique type of molecular marker in genetic research and breeding remains limited. In this study, we used a panel of 305 rice accessions from the 3000 Rice Genome Project to compare 26,000 + SVs (> 90% deletions and translocations) and 180,000 + high-quality SNPs in predicting the field performance of 20 traits using nine commonly used genomic selection models. We demonstrated that SVs had slightly lower prediction accuracies (PA) across 20 different traits than SNPs, but saved 53.8%-77.8% of computation time to achieve reasonably high PA. The major advantage of SVs as valuable markers in obtaining reliable genomic estimated breeding values (GEBVs) in GS experiments resulted primarily from their greater phenotypic effects on high heritability traits. Our results suggested that P-0.01 was an appropriate threshold for marker filtering of both SVs and SNPs to achieve high PA in genomic selection experiments. A dataset containing all identified SVs from this study has been deposited at the China National Center for Bioinformation under BioProject: PRJCA038102, a publicly accessible molecular marker resource, enabling broad applications in rice research including gene/QTL discovery, allelic mining, and genomic selection experiments.

分类号：

  • 相关文献

[1]基于SNP遗传图谱定位甘蓝型油菜分枝角度QTL. 汪文祥,储文,梅德圣,成洪涛,朱琳琳,付丽,胡琼,刘佳. 2019

[2]利用双向回交导入系定位水稻苗期耐亚铁毒和锌毒的QTL. 张建,Aijaz Ahmed SOOMRO,柴路,崔彦茹,王小倩,郑天清,徐建龙,黎志康. 2013

[3]QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map. Zhai, Huijie,Feng, Zhiyu,Li, Jiang,Liu, Xinye,Ni, Zhongfu,Sun, Qixin,Zhai, Huijie,Feng, Zhiyu,Li, Jiang,Liu, Xinye,Ni, Zhongfu,Sun, Qixin,Xiao, Shihe. 2016

[4]Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae. Peng, Shasha,Zhang, Yanli,Li, Zhiqiang,Liu, Wende,Ning, Yuese,Wang, Guo-Liang,Wang, Yue,Xiao, Yinghui,Wang, Dan,Wang, Zhilong,Wang, Yue,Xiao, Yinghui,Wang, Dan,Wang, Zhilong,Qu, Shaohong,Yan, Shuangyong,Korniliev, Pavel,Mezey, Jason,McCouch, Susan R.,Leung, Hei,Wang, Guo-Liang.

[5]SNP-and haplotype-based GWAS of flowering-related traits in brassica napus. M. M.U. Helal,Rafaqat Ali Gill,Minqiang Tang,Li Yang,Ming Hu,Lingli Yang,Meili Xie,Chuanji Zhao,Xiaohui Cheng,Yuanyuan Zhang,Xiong Zhang,Shengyi Liu. 2021

[6]Identification of genes for drought resistance and prediction of gene candidates in soybean seedlings based on linkage and association mapping. Yanjun Zhang,Zhangxiong Liu,Xingrong Wang,Yue Li,Yongsheng Li,Zuowang Gou,Xingzhen Zhao,Huilong Hong,Honglei Ren,Xusheng Qi,Lijuan Qiu. 2022

[7]Fine mapping and identification of the gene Cla019481 responsible for patches at the hilum on the testa of watermelon seeds. Runbu Lv,Dan Zhou,Hongyuan Liu,Chengyuan Xie,Yufu Zhang,Xiaoyu Zhang,Dongye Li,Shuangwu Ma,Jifeng Chen. 2025

[8]Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice (Oryza sativa L.). Yuanyuan Zhang,Mengchen Zhang,Junhua Ye,Qun Xu,Yue Feng,Siliang Xu,Dongxiu Hu,Xinghua Wei,Peisong Hu,Yaolong Yang. 2023

[9]Origin and evolution of the kiwifruit Y chromosome. Yue, Junyang,Chen, Qinyao,Zhang, Sijia,Lin, Yunzhi,Ren, Wangmei,Li, Bingjie,Wu, Ying,Wang, Yingzhen,Zhou, Yongfeng,Liu, Yongsheng. 2023

[10]Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum). Xiaoyang Wang,Yuchen Miao,Yingfan Cai,Gaofei Sun,Yinhua Jia,Song Song,Zhaoe Pan,Yuanming Zhang,Liyuan Wang,Guoyong Fu,Qiong Gao,Gaoxiang Ji,Pengpeng Wang,Baojun Chen,Zhen Peng,Xiaomeng Zhang,Xiao Wang,Yi Ding,Daowu Hu,Xiaoli Geng,Liru Wang,Baoyin Pang,Wenfang Gong,Shoupu He,Xiongming Du. 2021

[11]Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. Jie Ma,Hua Wei,Xiaoman Yu,Yang Lv,Yu Zhang,Qian Qian,Lianguang Shang,Longbiao Guo. 2022

[12]Multiple variation patterns of terpene synthases in 26 maize genomes. Sun Y.,Xiao W.,Wang Q.-N.,Wang J.,Kong X.-D.,Ma W.-H.,Liu S.-X.,Ren P.,Xu L.-N.,Zhang Y.-J.. 2023

[13]Five improved sesame reference genomes and genome resequencing unveil the contribution of structural variants to genetic diversity and yield-related traits variation. Song, Shengnan,Dossou, Senouwa Segla Koffi,Meng, Minghui,Sheng, Chen,Li, Huan,Zhou, Rong,Li, Donghua,Xu, Pan,You, Jun,Wang, Linhai. 2023

[14]Genomes of single- and double-petal jasmines (Jasminum sambac) provide insights into their divergence time and structural variations. Wang, Pengjie,Fang, Jingping,Lin, Hongzheng,Yang, Wenwen,Yu, Jiaxin,Hong, Yaping,Jiang, Mengwei,Gu, Mengya,Chen, Qinchang,Zheng, Yucheng,Liao, ZhenYang,Chen, Guixin,Yang, Jiangfan,Jin, Shan,Zhang, Xingtan,Ye, Naixing. 2022

[15]Chromosome-level genome assembly of a regenerable maize inbred line A188. Guifang Lin,Cheng He,Jun Zheng,Dal-Hoe Koo,Ha Le,Huakun Zheng,Tej Man Tamang,Jinguang Lin,Yan Liu,Mingxia Zhao,Yangfan Hao,Frank McFraland,Bo Wang,Yang Qin,Haibao Tang,Donald R. McCarty,Hairong Wei,Myeong-Je Cho,Sunghun Park,Heidi Kaeppler,Shawn M. Kaeppler,Yunjun Liu,Nathan Springer,Patrick S. Schnable,Guoying Wang,Frank F. White,Sanzhen Liu. 2021

[16]Evolutionary Genomics Of Structural Variation In Asian Rice (Oryza Sativa) Domestication. Kou, YX, Liao, Y, Toivainen, T, Lv, YD, Tian, XM, Emerson, JJ, Gaut, BS, Zhou, YF. 2020

[17]Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops. Han Z.,Li F.,Qiao W.,Zheng X.,Cheng Y.,Zhang L.,Huang J.,Wang Y.,Lou D.,Xing M.,Fan W.,Nie Y.,Guo W.,Wang S.,Liu Z.,Yang Q.. 2023

[18]Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Xiaoting Xia,Fengwei Zhang,Shuang Li,Xiaoyu Luo,Lixin Peng,Zheng Dong,Hubert Pausch,Alexander S. Leonard,Danang Crysnanto,Shikang Wang,Bin Tong,Johannes A. Lenstra,Jianlin Han,Fuyong Li,Tieshan Xu,Lihong Gu,Liangliang Jin,Ruihua Dang,Yongzhen Huang,Xianyong Lan,Gang Ren,Yu Wang,Yuanpeng Gao,Zhijie Ma,Haijian Cheng,Yun Ma,Hong Chen,Weijun Pang,Chuzhao Lei,Ningbo Chen. 2023

[19]Adaptive and maladaptive introgression in grapevine domestication. Hua Xiao,Zhongjie Liu,Nan Wang,Qiming Long,Shuo Cao,Guizhou Huang,Wenwen Liu,Yanling Peng,Summaira Riaz,Andrew M. Walker,Brandon S. Gaut,Yongfeng Zhou. 2023

[20]Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments. Jing Long,Wen Chuang He,Huan Wen Peng,Andrey S. Erst,Wei Wang,Kun Li Xiang. 2024

作者其他论文 更多>>