scholarly journals Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0247815
Author(s):  
Bo-Hye Nam ◽  
Hyaekang Kim ◽  
Donghyeok Seol ◽  
Heebal Kim ◽  
Eun Soo Noh ◽  
...  
Keyword(s):  
Population Structure ◽  
Genotyping By Sequencing ◽  
Population Genetic Study ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Pacific Abalone ◽  
Genome Region ◽  
Population Structures ◽  
Haliotis Discus ◽  
Abalone Haliotis Discus

Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.

Identification of growth-related SNPs and genes in the genome of the Pacific abalone (Haliotis discus hannai) using GWAS

Aquaculture ◽  
2021 ◽  
Vol 541 ◽  
pp. 736820
Author(s):  
Wenzhu Peng ◽  
Feng Yu ◽  
Yiyu Wu ◽  
Yifang Zhang ◽  
Chengkuan Lu ◽  
...  
Keyword(s):  
Haliotis Discus Hannai ◽  
Pacific Abalone ◽  
The Pacific ◽  
Haliotis Discus ◽  
Abalone Haliotis Discus

scholarly journals Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Guang Yao Fan ◽  
Yi Ye ◽  
Yi Ping Hou
Keyword(s):  
Population Structure ◽  
X Chromosome ◽  
Cost Effective ◽  
Genetic Distances ◽  
Ancestry Informative Marker ◽  
Genetic Population ◽  
Single Nucleotide ◽  
Chinese Populations ◽  
Population Structures ◽  
Biogeographical Ancestry

Abstract Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.

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