Genomics and marker assisted improvement of vegetable crops

Authors: Simko, Ivan; JIA, MENGYUAN - Pennsylvania State University; VENKATESH, JELLI - Seoul National University; KANG, BYOUNG-CHEORL - Seoul National University; Weng, Yiqun; BARCACCIA, GIANNI - Universita Di Padova; LANTERI, SERGIO - University Of Turin; BHATTARAI, GEHENDRA - University Of Arkansas; FOOLAD, MAJID - Pennsylvania State University

Submitted to: Critical Reviews in Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2021
Publication Date: 9/23/2021
Citation: Simko, I., Jia, M., Venkatesh, J., Kang, B., Weng, Y., Barcaccia, G., Lanteri, S., Bhattarai, G., Foolad, M.R. 2021. Genomics and marker-assisted improvement of vegetable crops. Critical Reviews in Plant Sciences. 40(4):303-365. https://doi.org/10.1080/07352689.2021.1941605.
DOI: https://doi.org/10.1080/07352689.2021.1941605

Interpretive Summary: Vegetables are an assorted group of crop species whose stems, leaves, fruits, flowers, roots, or seeds are an important part of human diet all over the world. They can be eaten raw or cooked and are usually low in carbohydrates and fats while being a good source of vitamins, minerals, and dietary fiber. Classical breeding approaches have been used to develop new vegetable cultivars with improved traits, such as resistance or tolerance to biotic and abiotic factors, high yield, and the content of compounds beneficial to human health. The technological progress since early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and to practical use of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies were used to identify chromosomal locations of loci associated with plant phenotypic variations important for crop improvement. This review gives up-to-date information about the status of genomics and marker assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop we provide the most recent information about genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and quantitative trait loci, status of marker-assisted selection and genomic selection, and discuss the expected future research and the application of novel techniques and approaches.

Technical Abstract: Vegetables are an integral part of human diet. Classical breeding approaches have been used to develop new vegetable cultivars with improved traits, such as resistance or tolerance to biotic and abiotic factors, high yield, and the content of compounds beneficial to human health. The technological progress since early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and to practical use of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies were used to identify chromosomal locations of loci associated with plant phenotypic variations important for crop improvement. This review gives up-to-date information about the status of genomics and marker assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop we provide the most recent information about genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and quantitative trait loci, status of marker-assisted selection and genomic selection, and discuss the expected future research and the application of novel techniques and approaches.