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Cell. 2018 Jan 11;172(1-2):249-261.e12. doi: 10.1016/j.cell.2017.12.019.

Rewiring of the Fruit Metabolome in Tomato Breeding.

Author information

1
Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China.
2
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, 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
Department of Horticulture, University of Georgia, Athens, GA 30602, USA.
5
Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL 32611, USA.
6
Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, Plovdiv 4000, Bulgaria.
7
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, Hainan 572208, China. Electronic address: jie.luo@mail.hzau.edu.cn.
8
Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China; 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. Electronic address: huangsanwen@caas.cn.

Abstract

Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.

KEYWORDS:

domestication; flavonoid; fruit weight; genome; linkage drag; metabolome; multi-omics; steroidal glycoalkaloid; tomato; transcriptome

PMID:
29328914
DOI:
10.1016/j.cell.2017.12.019
[Indexed for MEDLINE]
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