Molecular confirmation of varietal status in bottle gourd (Lagenaria siceraria) using genotyping-by-sequencing

Abstract

Bottle gourd (<i>Lagenaria siceraria</i>) is an important food, medicinal and utilitarian crop with a large pan tropical distribution. The two morphologically different types in the <i>siceraria</i> subspecies are sufficiently different to be considered as varieties but they are assigned into different taxonomic ranks. The genotyping-by-sequencing (GBS) of 95 different accessions from the Nangui Abrogoua University collection used to confirm varietal status in bottle gourd have produced 22,575 single-nucleotide polymorphisms (SNPs). Cluster analyses conducted with 2,250 (9.96%) SNPs have distinctly separated hard-shelled from soft-shelled types. The analysis of 23 SNPs located in 11 genes coding for traits that differentiate the two types of gourd revealed that soft-shelled genes had about 21% fewer SNPs than those of hard-shelled that had more non-synonymous SNPs. Cluster analyses conducted with the 23 SNPs fitted well with the structure defined by the 2,250 SNPs, suggesting the implication of these SNPs in the varietal differentiation of bottle gourd. These changes along with the genetic relationships between the accessions provided a molecular proof supporting the status of two varieties. To prevent the confusions inherent to the use of synonyms and homonyms in bottle gourd, we suggest the terms "hard-shelled" and "soft-shelled" to designate respectively the varieties used as utensils and those grown for its edible seeds.

The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

“…USVL1VR-Ls as reference genome which resulted in a set of 12,766 filtered SNP markers. A recent GBS study used to confirm the varietal status of bottle gourd accessions pro-duced 22,575 SNPs [21], which was higher than the present study. Other high-throughput studies conducted in bottle gourd used restriction site-associated DNA sequencing (RAD-Seq), a form of GBS that generates low coverage genome sequencing in which reference genomes are not available [19,27].…”

“…Xu et al [19] using 3226 SNPs markers identified two distinct groups among Chinese bottle gourd accessions based on fruit shape rather than collection site. To date, molecular markers have been used to study population structure and genetic relationships of L. siceraria, such as inter-sequence simple repeats [20], SSRs [15,17], and SNPs [19,21]. Next-generation sequencing (NGS)-based SNPs are the most widely used molecular markers to study genome-wide association, population structure, genomic selection, and genetic diversity due to their genome-wide abundance, particularly when many markers are required [22,23].…”