|Table of Contents|

SNP Molecular Markers Development and Population Genetic Diversity Analysis of Liparis gigantea

《北方园艺》[ISSN:1001-0009/CN:23-1247/S]

Issue:
2023年21
Page:
101-108
Research Field:
Publishing date:

Info

Title:
SNP Molecular Markers Development and Population Genetic Diversity Analysis of Liparis gigantea
Author(s):
CUI Xueqiang; DENG Jieling; HUANG Changyan; ZHANG Zibin
(Flower Research Institute，Guangxi Academy of Agricultural Sciences，Nanning，Guangxi 530007)
Keywords:
Liparis gigantea; SLAF-seq; SNP marker; populations; genetic diversity
PACS:
S 682.31
DOI:
10.11937/bfyy.20231659
Abstract:
A total of 44 samples from 4 geographical populations of Liparis gigantea in Leye county，Guangxi were used as test materials.Specific site amplified fragment sequencing (SLAF-seq) was used to develop SNP markers for Liparis gigantea.The genetic diversity and genetic relationships among different geographical populations of Liparis gigantea were studied by using the developed markers，in order to provide reference for the development，utilization and wild population protection of Liparis gigantea.The results showed that a total of 152 Mb of Clean Reads data were obtained from the test samples.The Reads data of each sample ranged from 2 098 129 to 5 169 592.The average GC content and sequencing quality value (Q30) of samples was 35.67% and 94.19%.Through sequencing data analysis，a total of 1 428 438 SLAF tags and 210 148 polymorphic SLAF tags were obtained.The average sequencing depth of the tags was 13.12×.A total of 574 866 population SNP markers were developed.The number of SNP markers in each sample ranged from 232 156 to 420 019.The integrity ratio was 40.38% to 73.06%，and the hetloci ratio was 2.51% to 5.47%.The population SNPs were filtered，and a total of 52 450 highly consistent and effective SNP markers were obtained.Using relevant software to calculate the genetic diversity index.The average minimum allele frequency (MAF) was 0.314 6.The average observed heterozygosity (Ho) was 0.160 1.The average Nei′s gene diversity index (H) was 0.436 8.The average polymorphism information content (PIC) was 0.312 6.The average Shannon diversity information index (I) was 0.580 8，indicating that the genetic diversity among populations of Liparis gigantea was relatively rich.The phylogenetic tree was constructed by using the SNP markers obtained.The 44 Liparis gigantea resources were divided into 4 groups.Analysis revealed that the genetic diversity and clustering results of the population were correlated with their growth altitude.

References:

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Last Update: 2023-12-06