A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia)

Abstract

Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line ‘K44’ and the monoecious line ‘Dali-11.’ This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of domestication

“…5a). QTL in the same region were also identified in another cross between Chinese accessions Dali-11 and K44 (Cui et al 2018). While increasing the proportion of female flowers is the focus of continuous breeding efforts in the accession level, in the population level this locus is expected to be under negative frequency dependent selection as either the fixation or loss of female-biased allele results in overall lower fitness.…”

“…For chromosome map development, two independent linkage maps were reconstructed using previously analyzed RAD-seq (Restriction-site Associated DNA Sequence) data of two F 2 populations (Urasaki et al 2017; Cui et al 2018). After imputing missing marker genotypes in F 2 populations, we identified 12 linkage groups from the OHB61-5 x OHB95-1A cross (Urasaki et al 2017) and 10 linkage groups from the K44 x Dali-11 cross (Cui et al 2018). The final set of 11 chromosomes were identified by comparison between the two linkage maps.…”

“…Restriction-site Associated DNA Sequence (RAD-seq) (Davey and Blaxter 2010) data were also obtained from two F2 crosses: 97 F2 individuals from a cross in Japan (Urasaki et al 2017) and 423 F2 individuals from a cross in China (Cui et al 2018). In order to solve the low coverage and high missing-data problem in RAD-seq data, we employed a window-based method to define marker genotypes (Lee et al 2017).…”

“…We also imputed the missing markers: If the upstream and downstream of a missing marker has the same allele, and this missing marker is within 10 cM of either two closest markers, we imputed it with the closest marker. Consequently, we identified 12 linkage groups from the Japanese cross (Urasaki et al 2017) and 10 linkage groups from the Chinese cross (Cui et al 2018). The final set of 11 linkage groups were identified by comparison between the two linkage maps.…”

Visiting Bitter Gourd (<em>Momordica charantia</em>) from a Breeding Perspective: A Review

“…Gynoecium is actually under the command of an individual recessive gene (gy 1)(Ram et al, 2006;Behera et al, 2009), whereas Ishida andIwamoto (2006) found that gynoecious se×e×pression in bitter gourd is partly dominant. 2 pairs of Genes described byCui et al, 2018 Moreover, the subsequent decades (including F1)…”