Rewiring of the Fruit Metabolome in Tomato Breeding

doi:10.1016/j.cell.2017.12.019

. 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

Guangtao Zhu¹, Shouchuang Wang², Zejun Huang³, Shuaibin Zhang³, Qinggang Liao¹, Chunzhi Zhang¹, Tao Lin¹, Mao Qin¹, Meng Peng², Chenkun Yang², Xue Cao³, Xu Han¹, Xiaoxuan Wang³, Esther van der Knaap⁴, Zhonghua Zhang³, Xia Cui³, Harry Klee⁵, Alisdair R Fernie⁶, Jie Luo⁷, Sanwen Huang⁸

Affiliations

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.

PMID: 29328914
DOI: 10.1016/j.cell.2017.12.019

Free article

Rewiring of the Fruit Metabolome in Tomato Breeding

Guangtao Zhu et al. Cell. 2018.

Free article

. 2018 Jan 11;172(1-2):249-261.e12.

doi: 10.1016/j.cell.2017.12.019.

Authors

Affiliations

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.

PMID: 29328914
DOI: 10.1016/j.cell.2017.12.019

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.

PubMed Disclaimer

Comment in

Tomato Multiomics Reveals Consequences of Crop Domestication and Improvement.
Giovannoni J. Giovannoni J. Cell. 2018 Jan 11;172(1-2):6-8. doi: 10.1016/j.cell.2017.12.036. Cell. 2018. PMID: 29328921

Cited by

Volatile metabolomics and transcriptomics analyses provide insights into the mechanism of volatile changes during fruit development of 'Ehime 38' (Citrus reticulata) and its bud mutant.
He J, Qin Z, Liu K, Li X, Kou Y, Jin Z, He R, Hong M, Xiong B, Liao L, Sun G, He S, Zhang M, Liang D, Lv X, Wang X, Wang Z. He J, et al. Front Plant Sci. 2024 Jun 26;15:1430204. doi: 10.3389/fpls.2024.1430204. eCollection 2024. Front Plant Sci. 2024. PMID: 38984161 Free PMC article.
Regulation of fruit ripening by the brassinosteroid biosynthetic gene SlCYP90B3 via an ethylene-dependent pathway in tomato.
Hu S, Liu L, Li S, Shao Z, Meng F, Liu H, Duan W, Liang D, Zhu C, Xu T, Wang Q. Hu S, et al. Hortic Res. 2020 Oct 1;7:163. doi: 10.1038/s41438-020-00383-0. eCollection 2020. Hortic Res. 2020. PMID: 33082970 Free PMC article.
Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics.
Zhou Y, Shao L, Zhu J, Li H, Duan H. Zhou Y, et al. Sci Rep. 2021 Jun 1;11(1):11460. doi: 10.1038/s41598-021-90961-6. Sci Rep. 2021. PMID: 34075137 Free PMC article.
Genetic mapping and molecular marker development for white flesh color in tomato.
Liu J, Fang X, Yu F, Zhang C, Fan P, Wang N, Shao Q, Gan N, Lv X, Ouyang B, Zhang M, Wu X, Liao N. Liu J, et al. Front Plant Sci. 2024 Sep 3;15:1459013. doi: 10.3389/fpls.2024.1459013. eCollection 2024. Front Plant Sci. 2024. PMID: 39290736 Free PMC article.
Multi-layer molecular analysis reveals distinctive metabolomic and transcriptomic profiles of different sweet corn varieties.
Li K, Zeng J, Zhang N, Yu Y, Zhu W, Li G, Hu J. Li K, et al. Front Plant Sci. 2024 Aug 19;15:1453031. doi: 10.3389/fpls.2024.1453031. eCollection 2024. Front Plant Sci. 2024. PMID: 39224849 Free PMC article.

See all "Cited by" articles

Publication types

Actions
Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

LinkOut - more resources

Full Text Sources
- Elsevier Science
Other Literature Sources

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Rewiring of the Fruit Metabolome in Tomato Breeding

Affiliations

Rewiring of the Fruit Metabolome in Tomato Breeding

Authors

Affiliations

Abstract

Comment in

Similar articles

Cited by

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources