Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

Area of Science:

• Genomics
• Population Genetics
• Bioinformatics

Background:

• Restriction site-associated DNA sequencing (RAD-Seq) is a valuable tool for population genomics, particularly in species lacking a reference genome.
• Its application in under-investigated species with low-to-medium sequencing depth requires further validation.

Purpose of the Study:

• To develop a Bayesian method for genotype calling in bottle gourd (Lagenaria siceraria) to construct a high-density genetic map.
• To assess the utility of RAD-Seq for population genomic studies in non-model organisms with limited sequencing data.
• To identify genetic loci associated with fruit shape variation in bottle gourd.

Main Methods:

• Utilized low-depth genome shotgun sequencing for scaffold assembly and anchoring.
• Employed RAD-Seq genotyping on a natural population of 80 bottle gourd accessions.
• Developed a Bayesian genotype calling method and performed comparative genomic analysis.

Main Results:

• Assembled approximately 50% of the bottle gourd genome, anchoring 922 scaffolds.
• Identified 3226 single nucleotide polymorphisms (SNPs) and revealed two sub-gene pools associated with fruit shape.
• Detected regions of elevated F(ST) and reduced heterozygosity/increased linkage disequilibrium (LD) on LG7, suggesting selection.
• Identified a candidate locus (LX3405) and its ortholog to a known fruit shape gene (OVATE) in tomato.

Conclusions:

• RAD-Seq is a promising approach for population genomics in non-model species, even with low-to-medium sequencing efforts.
• The developed genomic resources are valuable for cucurbit genome research.
• This study provides insights into the genetic basis of fruit shape variation in bottle gourd.