Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor

被引：144

作者：

Zhao, Jiantao ^{[1
]}

Sauvage, Christopher ^{[1
,7
]}

Zhao, Jinghua ^{[2
,3
,8
]}

Bitton, Frederique ^{[1
]}

Bauchet, Guillaume ^{[1
,9
]}

Liu, Dan ^{[4
]}

Huang, Sanwen ^{[4
,5
]}

Tieman, Denise M. ^{[6
]}

Klee, Harry J. ^{[6
]}

Causse, Mathilde ^{[1
]}

机构：

[1] INRA, Genet & Ameliorat Fruits & Legumes, UR1052, 67 Allee Chenes CS 60094, F-84143 Montfavet, France

[2] Univ Cambridge, Addrenbrookes Hosp, MRC Epidemiol Unit, Box 285Hills Rd, Cambridge CB2 0QQ, England

[3] Univ Cambridge, Addrenbrookes Hosp, Inst Metab Sci, Box 285Hills Rd, Cambridge CB2 0QQ, England

[4] Chinese Acad Agr Sci, Minist Agr, Agr Genom Inst Shenzhen, Genome Anal Lab, Shenzhen 518124, Guangdong, Peoples R China

[5] Chinese Acad Agr Sci, Inst Vegetables & Flowers, Key Lab Biol & Genet Improvement Hort Crops, Sino Dutch Joint Lab Hort Genom,Minist Agr, Beijing 100081, Peoples R China

[6] Univ Florida, Plant Innovat Ctr, Hort Sci, POB 110690, Gainesville, FL 32611 USA

[7] Syngenta, 12 Chemin Hobit, F-31790 St Sauveur, France

[8] Univ Cambridge, Dept Publ Hlth & Primary Care, Cardiovasc Epidemiol Unit, Strangeways Res Lab, Worts Causeway, Cambridge CB1 8RN, England

[9] Cornell Univ, Boyce Thompson Inst, 533 Tower Rd, Ithaca, NY 14853 USA

来源：

NATURE COMMUNICATIONS | 2019年 / 10卷 / 1期

关键词：

MISSING HERITABILITY; GENOTYPE IMPUTATION; CULTIVATED TOMATO; IDENTIFICATION; TRAITS; MODEL; LOCI; POLYMORPHISM; PREFERENCES; GENERATION;

D O I：

10.1038/s41467-019-09462-w

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, acids, amino acids, and flavor-related volatiles. We demonstrate that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. We suggest that it may be possible to significantly increase volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis.

引用

页数：12

共 70 条

[61] Quality control and conduct of genome-wide association meta-analyses [J].

Winkler, Thomas W. ;

Day, Felix R. ;

Croteau-Chonka, Damien C. ;

Wood, Andrew R. ;

Locke, Adam E. ;

Maegi, Reedik ;

Ferreira, Teresa ;

Fall, Tove ;

Graff, Mariaelisa ;

Justice, Anne E. ;

Luan, Jian'an ;

Gustafsson, Stefan ;

Randall, Joshua C. ;

Vedantam, Sailaja ;

Workalemahu, Tsegaselassie ;

Kilpelainen, Tuomas O. ;

Scherag, Andre ;

Esko, Tonu ;

Kutalik, Zoltan ;

Heid, Iris M. ;

Loos, Ruth J. F. .

NATURE PROTOCOLS, 2014, 9 (05) :1192-1212

[62] Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species [J].

Xu, Jiaxin ;

Ranc, Nicolas ;

Munos, Stephane ;

Rolland, Sophie ;

Bouchet, Jean-Paul ;

Desplat, Nelly ;

Le Paslier, Marie-Christine ;

Liang, Yan ;

Brunel, Dominique ;

Causse, Mathilde .

THEORETICAL AND APPLIED GENETICS, 2013, 126 (03) :567-581

[63] Concepts, estimation and interpretation of SNP-based heritability [J].

Yang, Jian ;

Zeng, Jian ;

Goddard, Michael E. ;

Wray, Naomi R. ;

Visscher, Peter M. .

NATURE GENETICS, 2017, 49 (09) :1304-U243

[64] Genomic inflation factors under polygenic inheritance [J].

Yang, Jian ;

Weedon, Michael N. ;

Purcell, Shaun ;

Lettre, Guillaume ;

Estrada, Karol ;

Willer, Cristen J. ;

Smith, Albert V. ;

Ingelsson, Erik ;

O'Connell, Jeffrey R. ;

Mangino, Massimo ;

Maegi, Reedik ;

Madden, Pamela A. ;

Heath, Andrew C. ;

Nyholt, Dale R. ;

Martin, Nicholas G. ;

Montgomery, Grant W. ;

Frayling, Timothy M. ;

Hirschhorn, Joel N. ;

McCarthy, Mark I. ;

Goddard, Michael E. ;

Visscher, Peter M. .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2011, 19 (07) :807-812

[65] An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance [J].

Ye, Jie ;

Wang, Xin ;

Hu, Tixu ;

Zhang, Fengxia ;

Wang, Bing ;

Li, Changxin ;

Yang, Tianxia ;

Li, Hanxia ;

Lu, Yongen ;

Giovannoni, James J. ;

Zhang, Yuyang ;

Ye, Zhibiao .

PLANT CELL, 2017, 29 (09) :2249-2268

[66] Progress and prospects in plant genome editing [J].

Yin, Kangquan ;

Gao, Caixia ;

Qiu, Jin-Long .

NATURE PLANTS, 2017, 3 (08)

[67] Genome-Wide Association Mapping for Tomato Volatiles Positively Contributing to Tomato Flavor [J].

Zhang, Jing ;

Zhao, Jiantao ;

Xu, Yao ;

Liang, Jing ;

Chang, Peipei ;

Yan, Fei ;

Li, Mingjun ;

Liang, Yan ;

Zou, Zhirong .

FRONTIERS IN PLANT SCIENCE, 2015, 6 :1-13

[68]

Zhao JG, 2016, FRONT PLANT SCI, V7, DOI [10.3339/fpls.2016.01213, 10.3389/fpls.2016.01213]

[69] Rewiring of the Fruit Metabolome in Tomato Breeding [J].

Zhu, Guangtao ;

Wang, Shouchuang ;

Huang, Zejun ;

Zhang, Shuaibin ;

Liao, Qinggang ;

Zhang, Chunzhi ;

Lin, Tao ;

Qin, Mao ;

Peng, Meng ;

Yang, Chenkun ;

Cao, Xue ;

Han, Xu ;

Wang, Xiaoxuan ;

van der Knaap, Esther ;

Zhang, Zhonghua ;

Cui, Xia ;

Klee, Harry ;

Fernie, Alisdair R. ;

Luo, Jie ;

Huang, Sanwen .

CELL, 2018, 172 (1-2) :249-+

[70] De novo domestication of wild tomato using genome editing [J].

Zsogon, Agustin ;

Cermak, Tomas ;

Naves, Emmanuel Rezende ;

Notini, Marcela Morato ;

Edel, Kai H. ;

Weinl, Stefan ;

Freschi, Luciano ;

Voytas, Daniel F. ;

Kudla, Jorg ;

Pereira Peres, Lazar Eustiquio .

NATURE BIOTECHNOLOGY, 2018, 36 (12) :1211-+

← 1 2 3 4 5 6 7 →