title: Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis.
abstract: Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species.
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China.
authors.forename: Shufen
authors.initials: S
authors.lastname: Li
authors.affiliation: School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, PR China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China.
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Food Corps, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, PR China.
authors.forename: Lianjun
authors.initials: L
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China.
authors.forename: Jinhong
authors.initials: J
authors.lastname: Yuan
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China.
authors.forename: Chuanliang
authors.initials: C
authors.lastname: Deng
authors.affiliation: College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China. Electronic address: gaowujun1@163.com.
authors.forename: Wujun
authors.initials: W
authors.lastname: Gao
mesh_terms: D027761:Asparagus Plant / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D017931:DNA Primers / Q000378:metabolism; D056426:Genetic Loci; D005819:Genetic Markers; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D059372:Nucleotide Motifs / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results
chemical_list: D017931:DNA Primers; D005819:Genetic Markers
keywords: Asparagus officinalis; Genetic diversity; Genomic SSRs; Microsatellites; Motif