Genome-wide analysis of microsatellite and sex-linked marker identification in Gleditsia sinensis

• Published in: BMC plant biology Vol. 20; no. 1; p. 338
• Main Authors: Li, Jianjun, Ye, Chenglin
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 17-07-2020; BioMed Central; BMC
• Subjects: Amplification; Analysis; Cancer; Clustering; DNA Primers - genetics; DNA sequencing; Females; Flowering; Flowers & plants; Gene pool; Gene sequencing; Genetic Markers - genetics; Genome-Wide Association Study; Genomes; Genomics; Gleditsia; Gleditsia - genetics; Gleditsia sinensis lam; Males; Markers; Microsatellite Repeats - genetics; Microsatellites; Next-generation sequencing; Nucleotides; Plants (botany); Polymorphism; Primers; Sex; Sex identification; Sex linkage; SSR; Trees; Whole genome sequencing; Gleditsia sinensis lam; SSR; Sex identification
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-020-02551-9

Gleditsia sinensis Lam. (Leguminosae), a dioecious perennial arbor, demonstrates important medicinal properties and economic value. These properties can be harnessed depending on the sex of the plant. However, the sex of the plants is difficult to identify accurately through morphological methods before the flowering.
We used bulked segregant analysis to screen sex-specific simple sequence repeat (SSR) markers in G. sinensis. Five male and five female plants were pooled to form the male and female bulks, respectively, and subjected to whole-genome sequencing. After high-throughput sequencing, 5,350,359 sequences were obtained, in which 2,065,210 SSRs were searched. Among them, the number of duplicated SSRs was the highest. The male plants could reach 857,874, which accounted for 60.86% of the total number of male plants. The female plants could reach 1,447,603, which accounted for 56.25% of the total model of the female plants. Among all the nucleotide repeat types, the A/T-rich motif was the most abundant. A total of 309,516 female strain-specific SSRs were selected by clustering. After designing the primers, the male and female gene pools were amplified, and five pairs of primers (i.e., 27, 34, 36, 39, and 41) were found to amplify the differential bands in the male and female gene pools. Using the five pairs of primers, we performed PCR verification on 10 individuals of known sex, which constructed the gene pool. The female plants amplified a single fragment of lengths (i.e., 186, 305, 266, 203, and 260 bp) and no male plant strip, thereby completing the identification of the male and female sexes of the G. sinensis.
This study provides accurate sex identification strategies between female and male plants, thus improving the utilization rate of G. sinensis resources.