Impact of fruit shape selection on genetic structure and diversity uncovered from genome-wide perfect SNPs genotyping in eggplant

Abstract

The recently constructed eggplant genome provides an opportunity for genome-wide marker exploration to be used for variety identification and genetic analysis. SNPs with high density across the genome and genetic stability are suitable for DNA fingerprint and genetic analysis. In this study, we used the eggplant reference genome of line 63/7 and resequencing data of 45 unique lines to select 219 genome-wide perfect SNPs in the eggplant. The high-throughput SNP genotyping technique target SNP-seq was used to successfully validate the 219 SNPs across 377 eggplant varieties to establish the unique DNA fingerprint for each variety. In addition, we chose 36 SNPs as a core SNP set with the ability to differentiate 95% of 377 eggplant varieties. Model-based structure and principal component analysis suggested three major population groups and indicated a significant impact of long-term selection for fruit shape in eggplant varieties. Further genetic diversity analysis within the three population groups showed a considerably narrow genetic background in round- and oval-fruited eggplants. This could be a result of limited choices of varieties used for breeding of round- and oval-fruited eggplants in Asia, indicated by its low observed heterozygosity (Ho) value (0.152) and high inbreeding coefficient (0.442). Finally, a genome-wide association study based on the 219 SNPs identified five associated SNPs located near the SUN and OVATE homologs, which had conserved function in controlling the fruit shape. This study signals a risk of genetic erosion in the round- and oval-fruited eggplants and provides valuable information for future variety management and breeding programs.