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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #386817

Research Project: Genetics, Epigenetics, Genomics, and Biotechnology for Fruit and Vegetable Quality

Location: Plant, Soil and Nutrition Research

Title: Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato

item YE, JIE - Boyce Thompson Institute
item WANG, XIN - Huazhong Agricultural University
item WANG, WENQIAN - Boyce Thompson Institute
item YU, HUIYANG - Huazhong Agricultural University
item AI, GUO - Huazhong Agricultural University
item LI, CHANGXING - Huazhong Agricultural University
item SUN, PENGYA - Huazhong Agricultural University
item WANG, XIANYU - Guangxi University
item LI, HANXIA - Huazhong Agricultural University
item OUYANG, BO - Huazhong Agricultural University
item ZHANG, JUNHONG - Huazhong Agricultural University
item ZHANG, YUYANG - Huazhong Agricultural University
item HAN, HEYOU - Huazhong Agricultural University
item Giovannoni, James
item FEI, ZHANGJUN - Boyce Thompson Institute
item YE, ZHIBIAO - Huazhong Agricultural University

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2021
Publication Date: 6/17/2021
Citation: Ye, J., Wang, X., Wang, W., Yu, H., Ai, G., Li, C., Sun, P., Wang, X., Li, H., Ouyang, B., Zhang, J., Zhang, Y., Han, H., Giovannoni, J.J., Fei, Z., Ye, Z. 2021. Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiology. 2021:00:1-15.

Interpretive Summary: Tomato is considered the leading fruit crop, with a global production of 182.3 million tons in 2018, and has served as a model system for fleshy fruit biology. Tomatoes originated in South America with a long history of “wild” tomato distribution. The modern cultivated tomato could be improved with more information on genetic diversity in existing accessions and as derived from its wild ancestors. Here we provide phenotypic and genetic insights into the variation of yield-related traits in tomato. This information provides a powerful resource for genetic improvement of tomato and other realted crops. Genes and the possible causative DNA variation identified here could be used as potential targets for marker-assisted breeding and/or engineering of tomato with enhanced yield and stress tolerance.

Technical Abstract: Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ~4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of ~8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, Sl-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.