Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Abstract

This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Evaluation of diversity, population structure and core collection of Thailand Luffa cylindrica germplasm accessions

“…The low genetic differentiation (F ST =0.076) between Cluster 1 and Cluster 2 indicated that the populations were less isolated, with an increased probability of crossing between the populations. The F ST of the L. cylindrica germplasm was lower when compared to the F ST of high subpopulation numbers of L. acutangula (Perez et al, 2021). It revealed more admixture between the two subpopulations of L. cylindrica than those subpopulations in ridge gourd.…”

“…The present results indicated low inbreeding coefficients in Cluster 1 (F IS = 0.064) and Cluster 2 (F IS = 0.185) and low global inbreeding (F IT = 0.205) in the whole germplasm, indicating that a low degree of inbreeding had occurred in the sponge gourd germplasm collection (Table 3). An overall lower global inbreeding (F IT = 0.057) and inbreeding coefficient (F IS = -0.092) have been reported in the high number of subpopulations in ridge gourd by Perez et al (2021), indicating a lower degree of inbreeding occurred in ridge gourd. All alleles contributed evenly to the diversity in the entire population (H = 5.537), as shown in Table 3.…”

“…Such may be the case in the L. cylindrica germplasm, where there is more gene flow than artificial selection. Therefore, the exchange of genotypes across Thailand may occur moderately without selective agricultural pressure, in contrast to the highly structured commercial ridge gourd germplasm (Perez et al, 2021). Perhaps L. cylindrica has not been a major source of income for farmers.…”

Comparative Proteomic Analysis of Ridge Gourd Seed (Luffa acutangula (L.) Roxb.) during Artificial Aging

“…Ridge gourd is one of the cucurbit crops that contribute significantly to world food and nutrition security and is economically essential to smallholder farmers, who account for 83% of global cucurbit production . Thailand has been the leading exporter of ridge gourds among all Asian countries, with a particularly strong position in the competitive Western European market. , Moreover, the demand for ridge gourds in Asia is continuously increasing. , The cultivation demand is increasing due to the nutritional requirements of a growing population . To produce high-quality commercial ridge gourd fruit and seed in order to meet worldwide demand, a comprehensive study of the biological processes (BPs) of the ridge gourd seed is essential to enhance production efficiency and improve seed quality.…”

“…6 , 7 Moreover, the demand for ridge gourds in Asia is continuously increasing. 8 , 9 The cultivation demand is increasing due to the nutritional requirements of a growing population. 10 To produce high-quality commercial ridge gourd fruit and seed in order to meet worldwide demand, a comprehensive study of the biological processes (BPs) of the ridge gourd seed is essential to enhance production efficiency and improve seed quality.…”