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| Analysis of the SSR Loci and Development of Molecular Markers in Spinacia oleracea Transcriptome |
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Abstract Single sequence repeat (SSR) has the advantages of high polymorphism and comparability, great reproducibility and co-dominance, and has been widely used in genetics and breeding of vegetable crops. In this study, the SSR loci information of spinach (Spinacia oleracea) was analyzed, the SSR molecular markers were developed and genetic diversity of different spinach materials were analyzed. The study used the high generation inbred lines 1012 as the test material, the spinach tissues of flowers, roots, stems and leaves were collected at the flowering stage, and the Illumina HiSeqTM 2500 technique was used to sequence the genes expression. A total of 44 796 unigenes were screened by using MISA software from Spinacia oleracea transcriptome, 2 045 SSR loci occurred in 1 940 unigenes, 1 835 unigenes contained a single SSR loci, 105 unigenes contained 2 or more than 2 SSR loci, and the frequency of these SSRs was 4.33%, and the mean distance was 19.81 kb. Among all SSR loci of Spinacia oleracea, mononucleotide, trinucleotide and tetranucleotide repeat were major types, accounting for 19%, 65% and 7% of the total SSR, respectively, and the repeat types of dinucleotide, pentanucleotide and hexanucleotide were lesser, and the distribution frequency of these types were 0.18%, 0.10% and 0.17%, accounting for 4%, 2% and 3% of the total SSR, respectively. The average repeat length was 21 bp, and the main repeat length was 18~24 bp, accounting for 93.55% of the total SSR, the secondly repeat length was 25~30 bp, accounting for 4.11% of the total SSR，and number of SSR repeat length at 31~39 bp and ≥40 bp were fewer. The main number of repeats was 6 and 7, accounting for 31.42% and 31.05%, the secondly number of repeats were ＞12 and 5, accounting for 19.17% and 8.41%, respectively, the number of repeats was 8~12. The mononucleotide repeat motif of A/T was the predominant repeat types, dinucleotide repeat motifs of GA/TC and AG/CT were the predominant repeat types, trinucleotide repeat motifs of CAA/TTG, GTT/AAC, GAA/TTC, TGT/ACA and GAT/ATC were the predominant repeat types. The repeat motifs of tetranucleotide, pentanucleotide and hexanucleotide were dispersed, each repeat motifs were relatively lower. All 218 primers of 2 199 SSR primers were selected randomly for PCR amplification using 9 Spinacia oleracea materials with different sources, including 38 SSR markers which performed polymorphical bands, accounting for 17.43% of the total test primers. The 9 materials were divided into 3 major groups by UPGMA, and the first major group included 4 materials, which were 11231, 1408, 1439 and 13190, the second major group included 2 materials, 1012 and 09248, and the third major group included 3 materials, 0928, 8301 and 1723. The SSR information and obtaining abundant polymorphisms SSR markers were studyed, which can be used for the genetic diversity, genetic mapping construction and molecular marker-assisted breeding in Spinacia oleracea.
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Received: 27 May 2016
Published: 01 October 2016
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ZHAO Zhi-Dong, TIAN Hong-Shan, JIANG Yan-Yan, SHI Bin-Gang, LIU Xiu, LI Xu-Peng, WANG Deng-Zhe, CHEN Jin-Lin, HU Jiang. Polymorphisms of ACSL1 Gene Promoter and Their Association Analysis with Milk Quality Traits in Yak (Bos grunniens)[J]. 农业生物技术学报, 2019, 27(9): 1596-1603. |
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