High-resolution genetic mapping of maize pan-genome sequence anchors

文献类型: 外文期刊

第一作者: Lu, Fei

作者: Lu, Fei;Romay, Maria C.;Glaubitz, Jeffrey C.;Elshire, Robert J.;Buckler, Edward S.;Bradbury, Peter J.;Buckler, Edward S.;Wang, Tianyu;Li, Yu;Li, Yongxiang;Semagn, Kassa;Zhang, Xuecai;Hernandez, Alvaro G.;Mikel, Mark A.;Mikel, Mark A.;Soifer, Ilya;Barad, Omer

作者机构:

关键词: COPY NUMBER VARIATION;TRANSPOSABLE ELEMENTS;WIDE ASSOCIATION;WHOLE-GENOME;EVOLUTION;POPULATION;DIVERSITY;PLANTS;DUPLICATION;ALIGNMENT

期刊名称:NATURE COMMUNICATIONS ( 影响因子:14.919; 五年影响因子:15.805 )

ISSN:

年卷期:

页码:

收录情况: SCI

摘要: In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.

分类号: N

  • 相关文献

[1]Paleo-evolutionary plasticity of plant disease resistance genes. Zhang, Rongzhi,Murat, Florent,Pont, Caroline,Langin, Thierry,Salse, Jerome,Zhang, Rongzhi. 2014

[2]Evolution and expression analysis of the soybean glutamate decarboxylase gene family. Hyun, Tae Kyung,Eom, Seung Hee,Han, Xiao,Kim, Ju-Sung,Kim, Ju-Sung.

[3]Isolation, characterization and phylogenetic analysis of the resistance gene analogues (RGAs) in banana (Musa spp.). Pei, Xinwu,Li, Shengjun,Jiang, Ying,Zhang, Yongqiang,Wang, Zhixing,Jia, Shirong.

[4]Evolution of the cyclin gene family in plants. Jia, Rui-Dong,Guo, Chun-Ce,Xu, Gui-Xia,Shan, Hong-Yan,Kong, Hong-Zhi,Jia, Rui-Dong,Jia, Rui-Dong. 2014

[5]In situ expression of the GmNMH7 gene is photoperiod-dependent in a unique soybean (Glycine max [L.] Merr.) flowering reversion system. Wu, CX,Ma, QB,Yam, KM,Cheung, MY,Xu, YY,Han, TF,Lam, HM,Chong, K.

[6]Phylogenetic relationships of wild roses in China based on nrDNA and matK data. Qiu, Xianqin,Zhang, Hao,Wang, Qigang,Jian, Hongying,Yan, Huijun,Zhang, Ting,Wang, Jihua,Tang, Kaixue.

[7]Antimicrobial activity of an endophytic Xylaria sp.YX-28 and identification of its antimicrobial compound 7-amino-4-methylcoumarin. Liu, Xiaoli,Dong, Mingsheng,Chen, Xiaohong,Jiang, Mei,Lv, Xin,Lv, Xin,Zhou, Jianzhong.

[8]Desmoglein 4 diversity and correlation analysis with coat color in goat. E, G. X.,Zhao, Y. J.,Na, R. S.,Zhao, Z. Q.,Jiang, C. D.,Zhang, J. H.,Chen, L. P.,Qiu, X. Y.,Hu, W.,Huang, Y. F.,Ma, Y. H.,Cao, G. L.,He, J. N.,Arlvd, S.. 2016

[9]Characterization and genetic diversity of the sturgeon Acipenser schrenskil Ig heavy chain. Wang Di,Lu Tong-yan,Liu Hong-bai. 2009

[10]Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.). Jiang, Jiahuan,Tan, Lubin,Zhu, Zuofeng,Fu, Yongcai,Liu, Fengxia,Cai, Hongwei,Sun, Chuanqing,Jiang, Jiahuan. 2012

[11]A Unique Evolution of the S2 Gene of Equine Infectious Anemia Virus in Hosts Correlated with Particular Infection Statuses. Wang, Xue-Feng,Wang, Shuai,Liu, Qiang,Lin, Yue-Zhi,Du, Cheng,Tang, Yan-Dong,Na, Lei,Wang, Xiaojun,Zhou, Jian-Hua,Zhou, Jian-Hua. 2014

[12]A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based on Adh1a sequences. Xu, Xin-wei,Ge, Song,Xu, Xin-wei,Ke, Wei-dong,Yu, Xiao-ping,Wen, Jun,Ge, Song.

[13]Warfarin resistance in Rattus losea in Guangdong Province, China. Wang, Hanshe,Zhong, Wenqin,Li, Ming,Dai, Jiayin,Feng, Zhiyong,Yao, Dandan,Sui, Jingjing. 2008

[14]Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Huang, Xuehui,Zhao, Yan,Feng, Qi,Gong, Hao,Li, Wenjun,Zhan, Qilin,Liu, Kunyan,Zhu, Chuanrang,Huang, Tao,Zhao, Qiang,Zhang, Lei,Fan, Danlin,Zhou, Congcong,Lu, Yiqi,Weng, Qijun,Wang, Zi-Xuan,Han, Bin,Yang, Shihua,Gong, Junyi,Cheng, Benyi,Xia, Junhui,Chen, Neng,Hao, Zhongna,Li, Jiayang.

[15]A 90-day safety study of genetically modified rice expressing rhIGF-1 protein in C57BL/6J rats. Tang, Maoxue,Cheng, Wenke,Qian, Lili,Yang, Shulin,Cui, Wentao,Li, Kui,Tang, Maoxue,Cheng, Wenke,Qian, Lili,Yang, Shulin,Cui, Wentao,Li, Kui,Xie, Tingting,Yang, Daichang.

[16]Genetic and cytological analysis of a new spontaneous male sterility in radish (Raphanus sativus L.). Wang, Zhi-Wei,Gao, Lei,Zhou, Yuan,Wang, Ting,Wang, Zhi-Wei,Xiang, Chang Ping,Liu, Hai Zhou,Mei, Shi Yong.

[17]Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice. Li, Siyuan,Xia, Qiong,Yu, Xiaoming,Gao, Xiang,Liu, Bao,Li, Siyuan,Wang, Fang,Ma, Jian,Kou, Hongping,Lin, Xiuyun. 2017

[18]Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces. Choulet, Frederic,Rustenholz, Camille,Paux, Etienne,Salse, Jerome,Leroy, Philippe,Feuillet, Catherine,Wicker, Thomas,Keller, Beat,Schlub, Stephane,Le Paslier, Marie-Christine,Brunel, Dominique,Magdelenat, Ghislaine,Gonthier, Catherine,Couloux, Arnaud,Budak, Hikmet,Breen, James,Appels, Rudi,Pumphrey, Michael,Gill, Bikram S.,Liu, Sixin,Anderson, James A.,Kong, Xiuying,Jia, Jizeng,Gut, Marta.

[19]Functional analysis of GUS expression patterns and T-DNA integration characteristics in rice enhancer trap lines. Peng, H,Huang, HM,Yang, YZ,Zhai, Y,Wu, JX,Huang, DF,Lu, TG.

[20]SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Ding, Yong,Wang, Xia,Su, Lei,Zhai, JiXian,Cao, ShouYun,Zhang, DongFen,Liu, ChunYan,Bi, YuPing,Qian, Qian,Cheng, ZhuKuan,Chu, ChengCai,Cao, XiaoFeng.

作者其他论文 更多>>