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Citation:

Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

  • Received Date: 2014-06-27
  • Two samples of Populus cathayana from Yushu were sequenced with high-throughput sequencing technology (Illumina HiSeqTM 2000). A total of 7076 sequences were hunted for microsatellites analysis, including 525 compound microsatellite sequences. The results showed that the mononucleotide repeats were the highest (33.96%), followed by trinucleotide repeats (31.00%) and dinucleotide repeats 27.69%. The tetranucleotide, pentanucleotide and hexanucleotide repeats were all less than 8%. Among the dinnucleotide repeats, the AG repeats were with highest frequency followed by GA, CT and TC respectively. Similarly in trinucleotide repeats, the AAG repeats were the highest followed by GAA, TTC, AGA, GAG, CAG, TCT and TGG. In the single nucleotide polymorphism, the transition types were higher than transversion in both samples. In sample L1A, the transition types of SNPs were 61.06% while the transversion types were 38.94%. In sample L2A, the transition types were 61.27%, while the transversion types were 38.73%. Among the transitions of two samples, C-T occurrences frequencies were the most, 30.75% and 30.66% respectively. A-G occurrences frequencies were similar to C-T, list to the second (30.31% and 30.62%). In both samples, the single nucleotide polymorphism trends were similar. The ratios of the same single nucleotide polymorphism in both samples were 2∶ 1. The results of analysis indicated that the SNP was a more reliable maker in geneticdiversity than SSR.
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Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

  • 1. Key laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
  • 2. University of Chinese Academy of Sciences, Beijing 100039, China
  • 3. School of Life Sciences, Southwest University, Chongqing 400715, China

Abstract: Two samples of Populus cathayana from Yushu were sequenced with high-throughput sequencing technology (Illumina HiSeqTM 2000). A total of 7076 sequences were hunted for microsatellites analysis, including 525 compound microsatellite sequences. The results showed that the mononucleotide repeats were the highest (33.96%), followed by trinucleotide repeats (31.00%) and dinucleotide repeats 27.69%. The tetranucleotide, pentanucleotide and hexanucleotide repeats were all less than 8%. Among the dinnucleotide repeats, the AG repeats were with highest frequency followed by GA, CT and TC respectively. Similarly in trinucleotide repeats, the AAG repeats were the highest followed by GAA, TTC, AGA, GAG, CAG, TCT and TGG. In the single nucleotide polymorphism, the transition types were higher than transversion in both samples. In sample L1A, the transition types of SNPs were 61.06% while the transversion types were 38.94%. In sample L2A, the transition types were 61.27%, while the transversion types were 38.73%. Among the transitions of two samples, C-T occurrences frequencies were the most, 30.75% and 30.66% respectively. A-G occurrences frequencies were similar to C-T, list to the second (30.31% and 30.62%). In both samples, the single nucleotide polymorphism trends were similar. The ratios of the same single nucleotide polymorphism in both samples were 2∶ 1. The results of analysis indicated that the SNP was a more reliable maker in geneticdiversity than SSR.

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