Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.)

Abstract

Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.

Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd ( Momordica charantia )

“…Track A denotes the gene density; tracks B to G show the two, three, four, five, six, and seven allele sites, respectively. The unassembled scaffolds or contigs were assigned to MC00 and the data of gene density was cited from a previous report [27]. A to F indicate the two, three, four, five, six, and seven allele sites; "All" indicates the total number of InDels.…”

“…Genome-wide SSRs markers have been developed for bitter gourd based on the recently published whole genome sequence [25][26][27]; however, no work has been done on InDel identification and marker development to date. In this study, using the Dali-11 genome as a reference, we identified the genome-wide InDels from resequencing data of 61 Chinese bitter gourd accessions [27]. Based on the polymorphic information content (PIC), we selected and designed a set of highly informative, unique InDel markers.…”

Bitter gourd from Africa expanded to Southeast Asia and was domesticated there: A new insight from parallel studies

“…The initial domestication was dated to 6,000 y ago, followed by the separation of further cultivars 800 y ago. A parallel study by Cui et al ( 2 ) (with partly overlapping authorship) instead inferred that wild bitter gourds and the lineage that gave rise to var. muricata and var.…”

“…No material is illustrated or vouchered in an herbarium, and some accessions (e.g., THMC170) are labeled as wild in the phylogenies but as cultivar in table S5. Cui et al ( 2 ) included 187 accessions from Asia, Africa, and South America, and rooted their phylogeny on two African species. Including African material was important because M. charantia occurs wild in Africa, Madagascar, and India (and naturalized in many tropical regions; refs.…”

“…The studies use similar methods to infer divergence times, with a mutation rate per generation of either 2 × 10 −8 ( 1 ) or 1 × 10 −8 ( 2 ). The specific method used in ref.…”