Genomics and Marker-Assisted Improvement of Vegetable Crops

Abstract

Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the 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 application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on 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 present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.

Understanding Molecular Plant–Nematode Interactions to Develop Alternative Approaches for Nematode Control

“…A striking example is Mi-1 homologs that can grant resistance against a broad range of pests and pathogens, comprising the most common root-knot nematodes (Meloidogyne javanica, M. incognita, and M. arenaria), insects, i.e., potato aphids (Macrosiphum euphorbiae), and sweet potato whitefly (Bemisia tabaci), and oomycetes (Phytophthora infestans) in tomato plants [9,43]. Thus, various approaches relying on molecular markers for PPN resistance such as amplified fragment length polymorphisms (AFLPs), random amplified polymorphic DNA (RAPDs), restriction amplified length polymorphisms (RALPs), cleaved amplified polymorphic sequence (CAPS), reverse-transcription polymerase chain reaction (RT-PCR), single nucleotide polymorphisms (SNPs), sequenced characterized amplified regions (SCAR), sequence tagged site (STS), and simple sequence repeats (SSRs) are being developed [88,89]. They can be used to select a broad range of economically important plant species/cultivars for resistance against serious nematode pests (Table 1).…”

Defense Strategies: The Role of Transcription Factors in Tomato–Pathogen Interaction

“…With diverse germplasms available across the world, breeding programs have made great strides in tomato improvement, with many morphological distinct cultivars developed from the single species of S. lycopersicum . However, the cultivated S. lycopersicum species was estimated to contain only about 5% of the total genetic variation existing in all tomato species, which occurred during its domestication and early breeding [ 23 ]. Unfortunately, resistance to important traits such as biotic and abiotic factors have been impaired during the process of domestication.…”

Molecular Relationships and Genetic Diversity Analysis of Venetian Radicchio (Leaf Chicory, Cichorium intybus subsp. intybus var. sylvestre, 2n = 2x = 18) Biotypes

“…Chicory (Cichorium intybus L., 2n = 2x = 18) is among the most popular leafy vegetables in the world [1]. This species, according to Funk et al [2] and others following taxonomic reclassifications [3], belongs to the tribe Cichorieae of the subfamily Chicorioideae of the family Compositae (Asteraceae [4]), instead of Lactuceae, together with other related species and genera [5].…”

“…Furthermore, hybridization among plants is promoted by floral morphological barriers that hamper selfing and physiological mechanisms that boost germination and growth of pollen grains and tubes in case of outcrossing [5,7]. Within leaf chicory, in Italy commonly called "radicchio", and in particular "radicchio Veneto" (Venetian radicchio, in English) in the north-eastern regions with specific reference to some typical red-leaved biotypes, cultivated populations of radicchio adopted for large-scale farming systems are currently represented by commercial seeds of open-pollinated (OP) varieties, synthetic varieties and F 1 hybrids that are available on the global chicory market [1]. However, a great proportion of radicchio is planted in many small farming units, using seeds of local varieties selected and maintained through mass selection by individual farmers [8,10].…”