Transcriptomic SSR Marker Development and Genetic Diversity Analysis in Celery (Apium graveolens)
CHEN Chang-Long1, DONG Yan2, TIAN Yu1, SHI Miao-Han1,2, GE Xiu-Xiu3, XIE Hua1*
1 Beijing Agro-Biotechnology Research Center/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; 2 Chengde Academy of Agriculture and Forestry Sciences, Chengde 067000, China; 3 College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102206, China
Abstract：Celery (Apium graveolens) is one of the most economically important leafy vegetables worldwide. Current celery genetic research requires some valuable molecular markers. A total of 4 034 SSR loci were identified in 39 619 unigenes assembled from 3 sets of high quality reads of celery transcriptome data in GenBank. Of these, di-nucleotide repeat motifs were found to be the most abundant, which accounted for 43.9% (1772), followed by mono- (26.7%, 1078) and tri- (21.0%, 846) nucleotide repeat motifs. Tetra-, penta-, and hexa- nucleotide repeats accounted for 1.3% (52) and the other was compound type (7.1%, 286). A set of 39 pairs of primers from the designed 375 SSR primers were successfully validated to yield clear and stable high quality specific PCR products in 5 selected representative celery accessions from different sources. Using fluorenscently labelled PCR and multiplex capillary electrophoresis, all the 39 markers detected 110 alleles in 76 celery accessions, ranging from 2~4 with an average number of 2.821 alleles and 2~9 genotypes with an average of 4.308 per locus. Average polymorphism information content (PIC) and discrimination power (PD) were 0.256 (0.013~0.581) and 0.379 (0.026~0.764) for per locus, respectively. Genetic diversity analysis of the 76 celery accessions indicated that for local celery and celery, the average numbers of alleles were 2.641 and 2.436, the average Nei's indices were 0.347 and 0.194 and the average Shannon's indices were 0.589 and 0.351, suggesting greater genetic diversity in local celery than that in celery. Analysis of molecular variance (AMOVA) of A. graveolens showed that 61.72% of genetic variation was within celery individuals, 22.07% among individuals within local celery or celery population, and 16.22% between local celery and celery populations. The cluster results of PCA (principal component analysis) and UPGMA (unweighted pair-group method with arithmetic means) dendrogram separated the 76 celery cultivars into 2 groups mainly corresponding to celery and local celery, respectively. However, compared to celery, local celery formed a more discrete cluster, which indicated local celery probably had more complex genetic background. The study could enrich SSR markers and provide multiplex capillary electrophoresis detection system based on fluorescence labeling for genetic diversity analysis and identification of a large number of celery germplasm resources.
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