Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

被引：270

作者：

Aflitos, Saulo ^{[1
,2
,3
]}

Schijlen, Elio

de Jong, Hans ^{[3
,4
]}

de Ridder, Dick ^{[2
,3
]}

Smit, Sandra

Finkers, Richard ^{[3
,5
]}

Wang, Jun ^{[6
]}

Zhang, Gengyun ^{[7
]}

Li, Ning ^{[8
]}

Mao, Likai ^{[6
]}

Bakker, Freek ^{[9
]}

Dirks, Rob ^{[10
]}

Breit, Timo ^{[11
]}

Gravendeel, Barbara ^{[12
]}

Huits, Henk ^{[13
]}

Struss, Darush ^{[14
]}

Swanson-Wagner, Ruth ^{[15
]}

van Leeuwen, Hans ^{[16
]}

van Ham, Roeland C. H. J. ^{[17
]}

Fito, Laia ^{[18
]}

Guignier, Laetitia ^{[19
]}

Sevilla, Myrna ^{[20
]}

Ellul, Philippe ^{[21
]}

Ganko, Eric ^{[22
]}

Kapur, Arvind ^{[23
]}

Reclus, Emannuel ^{[24
]}

de Geus, Bernard ^{[25
]}

van de Geest, Henri ^{[1
]}

te Lintel Hekkert, Bas ^{[1
]}

van Haarst, Jan ^{[1
]}

Smits, Lars ^{[1
]}

Koops, Andries ^{[1
]}

Sanchez-Perez, Gabino ^{[1
]}

van Heusden, Adriaan W. ^{[3
,4
]}

Visser, Richard ^{[3
,4
]}

Quan, Zhiwu ^{[6
]}

Min, Jiumeng ^{[8
]}

Liao, Li ^{[8
]}

Wang, Xiaoli ^{[8
]}

Wang, Guangbiao ^{[8
]}

Yue, Zhen ^{[8
]}

Yang, Xinhua ^{[8
]}

Xu, Na ^{[8
]}

Schranz, Eric ^{[9
]}

Smets, Erik

Vos, Rutger ^{[10
]}

Rauwerda, Johan ^{[11
]}

Ursem, Remco ^{[12
]}

Schuit, Cees ^{[13
]}

Kerns, Mike ^{[15
]}

机构：

[1] Plant Res Int, Cluster Appl Bioinformat, Business Unit Biosci, NL-6708 PB Wageningen, Netherlands

[2] Wageningen Univ, Dept Plant Sci, NL-6708 PB Wageningen, Netherlands

[3] Res Ctr, NL-6708 PB Wageningen, Netherlands

[4] Wageningen Univ, Genet Lab, NL-6708 PB Wageningen, Netherlands

[5] Wageningen Univ, Lab Plant Breeding, NL-6708 PB Wageningen, Netherlands

[6] Beijing Genom Inst, Shenzhen 518083, Peoples R China

[7] Beijing Genom Inst, State Key Lab Agr Gen, Shenzhen 518083, Peoples R China

[8] BGI Europe, DK-2200 Copenhagen, Denmark

[9] Wageningen Univ, Biosystemat Grp, NL-6708 PB Wageningen, Netherlands

[10] Rijk Zwaan Breeding, Dept R&D Bioinformat, NL-2678 ZG De Lier, Netherlands

[11] Univ Amsterdam, Fac Sci, Swammerdam Inst Life Sci, RNA Biol & Appl Bioinformat, NL-1098 XH Amsterdam, Netherlands

[12] Netherlands Biodivers Ctr Nat, NL-2333 CR Leiden, Netherlands

[13] Bejo Zaden BV, Res Ctr, NL-1749 CZ Warmenhuizen, Netherlands

[14] Hortigenet Res, East West Seed, Chiang Mai 50290, Thailand

[15] Monsanto Holland BV, NL-2660 BB Bergschenhoek, Netherlands

[16] Nunhems Netherlands BV, NL-6080 AA Haelen, Netherlands

[17] Keygene NV, NL-6700 AE Wageningen, Netherlands

[18] Semillas Fito, Ctr Biotechnol, Cabrera De Mar 08349, Spain

[19] Gautier Semences, F-13630 Eyragues, France

[20] BHN Res, Immokalee, FL 34143 USA

[21] Consultat Grp Int Agr Res, F-34394 Montpellier, France

[22] Syngenta Biotechnol Inc, Res Triangle Pk, NC 27709 USA

[23] Rasi Seeds, Salem, Tamil Nadu, India

[24] ADNid Cap Alpha, F-34830 Clapiers, France

[25] Technol Top Inst Groene Genet, NL-2805 PC Gouda, Netherlands

来源：

PLANT JOURNAL | 2014年 / 80卷 / 01期

关键词：

Solanum genetic diversity; comparative sequence analysis; phylogenomics; introgression; chromosome evolution; Solanum lycopersicum; Solanum pennellii; Solanum arcanum; Solanum habrochaites; heterozygosity; SINGLE-NUCLEOTIDE POLYMORPHISMS; WILD TOMATOES; READ ALIGNMENT; FRUIT SIZE; EVOLUTION; PLANT; DOMESTICATION; SOLANACEAE; NUMBER;

D O I：

10.1111/tpj.12616

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.

引用

页码：136 / 148

页数：13

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