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|Table of Contents|

基于RAD-seq技术的鹅掌楸基因组SNP标记开发(PDF)

《南京林业大学学报(自然科学版)》[ISSN:1000-2006/CN:32-1161/S]

Issue:
2019年04期
Page:
1-7
Column:
研究论文
publishdate:
2019-07-24

Article Info:/Info

Title:
Development of genomic SNP markers based on RAD-seq and genome data in Liriodendron
Article ID:
1000-2006(2019)04-0001-07
Author(s):
LU Ye12LONG Xiaofei12WANG Pengkai3CHEN Jinhui12SHI Jisen12*
(1. Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; 2. Co-Innovation Center for the Sustainable Forestry in Southern China,Nanjing Forestry University,Nanjing 210037,China; 3. Suzhou Polytechnic Institute of Agriculture, Suzhou 215008,China)
Keywords:
Liriodendron tulipifera Linn. Liriodendron chinense(Hemsl.)Sargent RAD-seq SNP marker genetic linkage map
Classification number :
Q755
DOI:
10. 3969/ j. issn. 1000-2006. 201806010
Document Code:
A
Abstract:
【Objective】 The large-scale development of reliable SNP markers is the key to obtaining molecular markers for the construction of high-density genetic linkage maps and for innovative selection and breeding strategies based on genomic information in Liriodendron. 【Method】One hundred and ninety-eight F1 trees were selected as the mapping population, which was obtained by intraspecific cross between the NK(♀)(Liriodendron tulipifera Linn.)and LS(♂)[L. chinense(Hemsl.)Sargent] genotypes. Genomic DNA of 200 individuals, including 2 parents and 198 offspring, was extracted and digested using the restriction endonuclease EcoR I. RAD libraries were constructed using genomic DNA from both parents and F1 trees. The read length of paired-end sequencing is 91 bp. In total, 387.21 Gb of data were obtained, with an average sequencing depth of 2× in the parents RAD libraries and 0.8× in their progeny RAD libraries, and the average production was 1.94 Gb. RAD-reads from each sample were analyzed using Stacks software. The distribution of candidate loci was tested by chi-squared test and the deletion rate was evaluated. Then each RAD-tag sequence containing genetic markers,whose segregation ratios were consistent with the expected Mendelian inheritance rations, was aligned to the reference genome of L. chinense. In the end, we selected 27 pairs of SNP markers then designed primers for amplification within random 16 F1 by PCR in order to validate the accuracy of the candidate SNPs.【Result】A total of 22 019 SNPs were observed in the candidate population, and 4 233 markers conformed to Mendelian inheritance. Finally, 3 501 candidate SNP markers were identified. In the validation experiment, 293 SNPs were successfully sequenced and all of these were identified as SNP loci. A total of 194(66.2%)SNPs were validated in variation types.【Conclusion】RAD-seq is a fast and effective technique for the large-scale development of SNPs and construction of genetic linkage maps in Liriodendron and other taxa.

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Last Update: 2019-07-22