The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd ( Momordica charantia ), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.

Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as 'hidden hunger.' Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail.

Okra (Abelmoschus esculentus) is a heat tolerant vegetable crop with high economic and nutritional importance in parts of Asia, Africa, and America. The okra biodiversity held in gene bank collections could be mined for traits for breeding more stress tolerant and nutritional cultivars. An okra core collection of 166 accessions comprising A. esculentus, A. moschatus, A. caillei, and A. manihot has been assembled from the World Vegetable Center germplasm collection (840 accessions) based on diversity analysis with 20 microsatellite markers. A selection of A. esculentus accessions of the core collection (75 accessions) and 20 breeder-selected genotypes have been screened for variation of their response to flooding stress under field conditions using a high throughput phenotyping system. Growth increment per day and changes of physiological indices were measured before, during, and after application of 9 days of flooding stress. Several accessions showed only a small reduction in daily growth increment during flooding. Across the germplasm panel, maintained growth was correlated with maintained normalized differential vegetation index and was negatively correlated with plant senescence index. Accessions with maintained growth and health under flooding were selected for future further analysis and use in breeding.

Amaranth (Amaranthus spp.), is an underutilized crop increasing in popularity as a grain and as a leafy vegetable. It is rich in protein, minerals and vitamins, and adapts well to a range of production systems. Currently, the lack of improved varieties limits the use of the crop. Breeding improved varieties requires access to large collections of amaranth biodiversity stored in genebanks. The task of searching such vast collections for traits of interest can be eased by generating core collections, which display the diversity of large collections in a much smaller germplasm set. The World Vegetable Center amaranth collection contains around 1,000 accessions of 13 species; among them, there are 281 accessions of four species important for use as vegetable amaranth in Africa (A. cruentus, A. hypochondriacus, A. caudatus and A. dubius). Based on SNP marker genotype diversity, a core collection of 76 accessions, varieties and selections was assembled. To a large extent, it represents the diversity of the whole collection. The core collection was evaluated for yield and nutritional parameters during the cool and warm seasons in Tanzania and Taiwan and a pre-test for variation of drought tolerance in the core collection has been performed. Variety Madiira 2, an improved cultivar developed for vegetable production in Africa, outperformed all other tested varieties in terms of yield stability, but several core collection accessions had higher yield, lower wilting score, and higher nutrient content than Madiira 2. This indicates the core collection can be used for further improvement of amaranth varieties.