Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

被引：355

作者：

Fang, Lei ^{[1
,2
]}

Wang, Qiong ^{[1
]}

Hu, Yan ^{[1
,2
]}

Jia, Yinhua ^{[3
]}

Chen, Jiedan ^{[1
,2
]}

Liu, Bingliang ^{[1
]}

Zhang, Zhiyuan ^{[1
,2
]}

Guan, Xueying ^{[1
,2
]}

Chen, Shuqi ^{[1
]}

Zhou, Baoliang ^{[1
]}

Mei, Gaofu ^{[1
]}

Sun, Junling ^{[3
]}

Pan, Zhaoe ^{[3
]}

He, Shoupu ^{[3
]}

Xiao, Songhua ^{[4
]}

Shi, Weijun ^{[5
]}

Gong, Wenfang ^{[3
]}

Liu, Jianguang ^{[4
]}

Ma, Jun ^{[5
]}

Cai, Caiping ^{[1
]}

Zhu, Xiefei ^{[1
]}

Guo, Wangzhen ^{[1
]}

Du, Xiongming ^{[3
]}

Zhang, Tianzhen ^{[1
,2
]}

机构：

[1] Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, Cotton Hybrid R&D Engn Ctr, Minist Educ, Nanjing, Jiangsu, Peoples R China

[2] Zhejiang Univ, Agron Dept, Coll Agr & Biotechnol, Hangzhou, Zhejiang, Peoples R China

[3] Chinese Acad Agr Sci, State Key Lab Cotton Biol, Key Lab Cotton Genet Improvement, ICR,Minist Agr, Anyang, Peoples R China

[4] Jiangsu Acad Agr Sci, Inst Ind Crops, Nanjing, Jiangsu, Peoples R China

[5] Xinjiang Acad Agr Sci, Econ Crop Res Inst, Urumqi, Peoples R China

来源：

NATURE GENETICS | 2017年 / 49卷 / 07期

关键词：

CLASS-XI MYOSINS; GOSSYPIUM-HIRSUTUM; GENETIC DIVERSITY; WIDE ASSOCIATION; AGRONOMIC TRAITS; UPLAND COTTON; POPULATION-STRUCTURE; CULTIVATED RICE; DOMESTICATION; ARABIDOPSIS;

D O I：

10.1038/ng.3887

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits. We found that two ethylene-pathway-related genes were associated with increased lint yield in improved cultivars. We evaluated the population frequency of each elite allele in historically released cultivar groups and found that 54.8% of the elite genome-wide association study (GWAS) alleles detected were transferred from three founder landraces: Deltapine 15, Stoneville 2B and Uganda Mian. Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops.

引用

页码：1089 / +

页数：12

共 56 条

[1] A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals [J].

Browning, Brian L. ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (02) :210-223

[2] REEVALUATING THE ORIGIN OF DOMESTICATED COTTON (GOSSYPIUM-HIRSUTUM MALVACEAE) USING NUCLEAR RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS (RFLPS) [J].

BRUBAKER, CL ;

WENDEL, JF .

AMERICAN JOURNAL OF BOTANY, 1994, 81 (10) :1309-1326

[3]

Calhoun DS., 1994, Pedigrees of Upland and Pima cotton cultivars released between 1970 and 1990

[4] Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars [J].

Cavanagh, Colin R. ;

Chao, Shiaoman ;

Wang, Shichen ;

Huang, Bevan Emma ;

Stephen, Stuart ;

Kiani, Seifollah ;

Forrest, Kerrie ;

Saintenac, Cyrille ;

Brown-Guedira, Gina L. ;

Akhunova, Alina ;

See, Deven ;

Bai, Guihua ;

Pumphrey, Michael ;

Tomar, Luxmi ;

Wong, Debbie ;

Kong, Stephan ;

Reynolds, Matthew ;

da Silva, Marta Lopez ;

Bockelman, Harold ;

Talbert, Luther ;

Anderson, James A. ;

Dreisigacker, Susanne ;

Baenziger, Stephen ;

Carter, Arron ;

Korzun, Viktor ;

Morrell, Peter Laurent ;

Dubcovsky, Jorge ;

Morell, Matthew K. ;

Sorrells, Mark E. ;

Hayden, Matthew J. ;

Akhunov, Eduard .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (20) :8057-8062

[5] Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins [J].

Chao, QM ;

Rothenberg, M ;

Solano, R ;

Roman, G ;

Terzaghi, W ;

Ecker, JR .

CELL, 1997, 89 (07) :1133-1144

[6] Population differentiation as a test for selective sweeps [J].

Chen, Hua ;

Patterson, Nick ;

Reich, David .

GENOME RESEARCH, 2010, 20 (03) :393-402

[7] Ethylene signal transduction [J].

Chen, YF ;

Etheridge, N ;

Schaller, GE .

ANNALS OF BOTANY, 2005, 95 (06) :901-915

[8] Maize HapMap2 identifies extant variation from a genome in flux [J].

Chia, Jer-Ming ;

Song, Chi ;

Bradbury, Peter J. ;

Costich, Denise ;

de Leon, Natalia ;

Doebley, John ;

Elshire, Robert J. ;

Gaut, Brandon ;

Geller, Laura ;

Glaubitz, Jeffrey C. ;

Gore, Michael ;

Guill, Kate E. ;

Holland, Jim ;

Hufford, Matthew B. ;

Lai, Jinsheng ;

Li, Meng ;

Liu, Xin ;

Lu, Yanli ;

McCombie, Richard ;

Nelson, Rebecca ;

Poland, Jesse ;

Prasanna, Boddupalli M. ;

Pyhaejaervi, Tanja ;

Rong, Tingzhao ;

Sekhon, Rajandeep S. ;

Sun, Qi ;

Tenaillon, Maud I. ;

Tian, Feng ;

Wang, Jun ;

Xu, Xun ;

Zhang, Zhiwu ;

Kaeppler, Shawn M. ;

Ross-Ibarra, Jeffrey ;

McMullen, Michael D. ;

Buckler, Edward S. ;

Zhang, Gengyun ;

Xu, Yunbi ;

Ware, Doreen .

NATURE GENETICS, 2012, 44 (07) :803-U238

[9] Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons [J].

Fang, Lei ;

Gong, Hao ;

Hu, Yan ;

Liu, Chunxiao ;

Zhou, Baoliang ;

Huang, Tao ;

Wang, Yangkun ;

Chen, Shuqi ;

Fang, David D. ;

Du, Xiongming ;

Chen, Hong ;

Chen, Jiedan ;

Wang, Sen ;

Wang, Qiong ;

Wan, Qun ;

Liu, Bingliang ;

Pan, Mengqiao ;

Chang, Lijing ;

Wu, Huaitong ;

Mei, Gaofu ;

Xiang, Dan ;

Li, Xinghe ;

Cai, Caiping ;

Zhu, Xiefei ;

Chen, Z. Jeffrey ;

Han, Bin ;

Chen, Xiaoya ;

Guo, Wangzhen ;

Zhang, Tianzhen ;

Huang, Xuehui .

GENOME BIOLOGY, 2017, 18

[10]

Felsenstein J., 2005, PHYLIP (phylogeny inference package) version 3.6

← 1 2 3 4 5 6 →