Identification of genes related with jujube fruit size based on selective sweep analysis

ObjectiveThe purpose of this study was to compare the differences in genetic diversity of jujube (Ziziphus jujuba), and to detect the selection sweep regions between the large fruit and small fruit groups. We hope to detect the genomic selection regions related with fruit size, laying a foundation for the analysis of the molecular mechanism of fruit size regulation.

MethodThe single nucleotide polymorphisms (SNPs) were called based on the genotyping-by-sequencing data of 37 jujube accessions, including 12 large fruit accessions and 25 small fruit accessions, and then the principal component analysis and genetic diversity analysis were carried out to analyze the genetic relationship of the jujube accessions. The genetic differentiation coefficient (Fst) and the nucleotide diversity (π) were calculated to detect the selection signals. The important genes in these selected regions were analyzed by GO and KEGG analysis. The relative expression levels of the potential genes related with fruit size were further analyzed in Z. jujuba ‘Tongbaidazao’ and Z. jujuba var. spinosa at six stages of fruit development.

ResultA total of 130 077 high-quality SNPs were obtained. The genetic diversity of the large fruit group (π: 0.32) was lower than that of the small fruit group (π: 0.33). We detected 83 and 149 sweep regions for large fruit and small fruit groups, respectively. Furthermore, we identified six candidate genes (LOC107404981, LOC107406728, LOC107424132, LOC107426306, LOC107418232, LOC107432595) involved in the regulation of cell cycle or hormone synthesis pathways. qRT-PCR showed that the expression of LOC107424132, LOC107426306, LOC107418232 and LOC107432595 increased at 75 days after flowering, while the expression of candidate genes LOC107404981 and LOC107406728 increased significantly at 45 days and 75 days after flowering, in agreement with the development curve of fruit size. We further found their differential expression between a large jujube cultivar and a sour jujube accession.

CouclusionLOC107404981 and LOC107406728 were possibly involved in the molecular regulation of jujube fruit size, and further researches are expected to reveal specific molecular functions.