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Journal of Integrative Agriculture  2020, Vol. 19 Issue (1): 120-132    DOI: 10.1016/S2095-3119(19)62824-8
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Domestication and breeding changed tomato fruit transcriptome 
LIU Dan1, 2*, YANG Liang2, 4*, ZHANG Jin-zhe3, ZHU Guang-tao5, LÜ Hong-jun2, 6, LÜ Ya-qing2, WANG Yan-ling2, CAO Xue1, SUN Tian-shu3, HUANG San-wen2, WU Yao-yao 
1 College of Horticulture, Northwest A&F University, Yangling 712100, P.R.China
2 Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, P.R.China
3 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
4 Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, P.R.China
5 The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming 650500, P.R.China
6 Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory for Biology of Greenhouse Vegetables/Shandong Branch of National Improvement Center for Vegetables, Jinan 250100, P.R.China
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Tomato (Solanum lycopersicum) stress resistance and fruit total soluble solid (TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring.  However, the single tomato reference genome impedes characterization of whole-transcriptome variation during domestication and breeding at the population level.  Here, we constructed a pan-transcriptome of orange-stage tomato fruit, and investigated global expression presence/absence variation (ePAV) and differentially expressed genes (DEGs) based on RNA sequencing (RNA-seq) data from 399 tomato accessions.  A total of 7 181 genes absent from the reference genome were identified, 6 122 of which were ePAV genes during tomato domestication and breeding including resistance genes such as late blight resistance gene PIM_DN29746_c0_g3_i1 and peroxidase P7-like gene PIM_DN30274_c0_g2_i1.  In addition, 3 629 genes were significantly differentially expressed during tomato selection, among which 19 genes were associated with the reduced fruit TSS content of modern tomato cultivars, including LIN5, TIV1, and seven novel sugar transporter genes.  Our results indicate that natural and artificial selection greatly shaped the tomato transcriptome, thereby altering the fruit TSS content and resistance to abiotic and biotic stresses.
Keywords:  tomato        pan-transcriptome        ePAV        DEG        domestication        breeding  
Received: 27 March 2019   Accepted:
Fund: The authors are grateful to Prof. Zhang Zhonghua (Qingdao Agricultural University, China) for discussion and project coordination; Prof. Li Qing (The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences) for her revision of the manuscript, Prof. Zhu Xijian and Prof.Jiang Jibin (Yunnan Normal University, China) and Prof. Feng Shuangshuang (Nanjing Agricultural University, China) for greenhouse assistance. This work was supported by the Agricultural Science and Technology Innovation Program (ASTIP-CAAS), the National Natural Science Foundation of China (31601360) and the 13th Five-Year Plan Vegetable Breeding Program of Sichuan Province, China (2016NYZ0033).
Corresponding Authors:  Correspondence HUANG San-wen, E-mail:; WU Yao-yao, E-mail:   
About author:  * These authors contributed equally to this study.

Cite this article: 

LIU Dan, YANG Liang, ZHANG Jin-zhe, ZHU Guang-tao, Lü Hong-jun, Lü Ya-qing, WANG Yan-ling, CAO Xue, SUN Tian-shu, HUANG San-wen, WU Yao-yao. 2020. Domestication and breeding changed tomato fruit transcriptome . Journal of Integrative Agriculture, 19(1): 120-132.

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