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Bulletin of Botanical Research ›› 2022, Vol. 42 ›› Issue (3): 373-382.doi: 10.7525/j.issn.1673-5102.2022.03.007

• Genetic and Breeding • Previous Articles     Next Articles

Genetic Structure Analysis of Picea crassifolia Based on Genome-wide SNP Molecular Markers

Hongbin ZHANG1,2, Dong LÜ1,2, Ming ZHAO1,2, Hu ZHAO1,3, Xingpeng ZHAO1,2, Wei LI2,3()   

  1. 1.Academy of Water Resources Conservation Forest of Qilian Mountains,Zhangye 734000
    2.National and Local Joint Engineering Research Center for the Breeding and Promotion of Endemic Plants of Qilian Mountains,Zhangye 734000
    3.School of Biological Sciences and Biotechnology,Beijing Forestry University,Beijing 100083
  • Received:2021-11-03 Online:2022-05-20 Published:2022-05-20
  • Contact: Wei LI E-mail:bjfuliwei@bju.edu.cn
  • About author:ZHANG Hongbin(1966—),male,master,senior engineer,mainly engaged in forest genetics and breeding and improved seed breeding.
  • Supported by:
    National Natural Science Foundation of China(31860221);Natural science foundation of Gansu Province(18JR3RG424)


A total of 106 clones of Picea crassifolia in Longqu P. crassifolia Clone Seed Orchard in Zhangye were used as materials, and the genomic DNA of P. crassifolia was extracted by improved CTAB method, the SLAF library was constructed and sequenced with high flux, and then the SLAF sequencing data were analyzed and SNP sites were screened, and the clustering of samples was obtained based on adjacency analysis respectively. The results showed that the efficiency of two terminal alignment was 95.33%, indicated that the SLAF database was successfully established. The Q30 of the sequence measured and the sequencing quality was high, but the error rate of base sequencing was low. A total of 4 058 883 SLAF tags were developed, and the average sequencing depth of the tags was 21.21×. A total of 12 275 765 P. crassifolia SNP markers were developed, and the number of SNPs in each P. crassifolia sample ranged from 1 890 934-4 487 841. Using the developed high quality SNP markers of P. crassifolia, 106 phylogenetic trees of P. crassifolia were constructed. It was found that P. crassifolia from different provenances were evenly distributed in each group, and P. crassifolia from different provenances mostly were clustered into one class. By SNP markers and principal component analysis, these clones were more likely to be derived from the same ancestor, indicated that the genetic relationship between clones was similar. It provids basic data for the analysis of genetic diversity and the construction of genetic map in the future, and also provids a basis for the elite seeds selection in P. crassifolia primary seed orchard, and lays a foundation for the construction of high generation seed orchard.

Key words: Picea crassifolia, DNA extraction, SLAF label, genetic structure analysis

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