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Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers

Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR m... Full description

Journal Title: Plant molecular biology reporter 2019-05-18, Vol.37 (3), p.204-213
Main Author: Yan, Lin
Other Authors: Ogutu, Collins , Huang, Lifang , Wang, Xiaoyang , Zhou, Hua , Lv, Yulan , Long, Yuzhou , Dong, Yunping , Han, Yuepeng
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: New York: Springer US
ID: ISSN: 0735-9640
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recordid: cdi_proquest_journals_2226908800
title: Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers
format: Article
creator:
  • Yan, Lin
  • Ogutu, Collins
  • Huang, Lifang
  • Wang, Xiaoyang
  • Zhou, Hua
  • Lv, Yulan
  • Long, Yuzhou
  • Dong, Yunping
  • Han, Yuepeng
subjects:
  • Alleles
  • Analysis
  • Beverages
  • Bioinformatics
  • Biological diversity
  • Biomedical and Life Sciences
  • Breeding
  • Ceratina liberica
  • Clustering
  • Coffea arabica
  • Coffee
  • Collections
  • Differentiation
  • Gene mapping
  • Genetic distance
  • Genetic diversity
  • Genetic research
  • Genetics
  • Germplasm
  • Heterozygosity
  • Life Sciences
  • Linkage disequilibrium
  • Mapping
  • Markers
  • Metabolomics
  • Original Paper
  • Outliers (statistics)
  • Plant Breeding/Biotechnology
  • Plant Sciences
  • Population genetics
  • Population structure
  • Positive selection
  • Proteomics
  • Strategic planning (Business)
  • Subgroups
ispartof: Plant molecular biology reporter, 2019-05-18, Vol.37 (3), p.204-213
description: Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity ( H e ) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora , with F st values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the F st value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise ( F st ) index and Nei’s standard genetic distance tests. The F st outlier test for deviation from expected distribution between F st and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.
language: eng
source:
identifier: ISSN: 0735-9640
fulltext: no_fulltext
issn:
  • 0735-9640
  • 1572-9818
url: Link


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titleGenetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers
creatorYan, Lin ; Ogutu, Collins ; Huang, Lifang ; Wang, Xiaoyang ; Zhou, Hua ; Lv, Yulan ; Long, Yuzhou ; Dong, Yunping ; Han, Yuepeng
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descriptionPopulation genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity ( H e ) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora , with F st values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the F st value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise ( F st ) index and Nei’s standard genetic distance tests. The F st outlier test for deviation from expected distribution between F st and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.
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subjectAlleles ; Analysis ; Beverages ; Bioinformatics ; Biological diversity ; Biomedical and Life Sciences ; Breeding ; Ceratina liberica ; Clustering ; Coffea arabica ; Coffee ; Collections ; Differentiation ; Gene mapping ; Genetic distance ; Genetic diversity ; Genetic research ; Genetics ; Germplasm ; Heterozygosity ; Life Sciences ; Linkage disequilibrium ; Mapping ; Markers ; Metabolomics ; Original Paper ; Outliers (statistics) ; Plant Breeding/Biotechnology ; Plant Sciences ; Population genetics ; Population structure ; Positive selection ; Proteomics ; Strategic planning (Business) ; Subgroups
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descriptionPopulation genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity ( H e ) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora , with F st values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the F st value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise ( F st ) index and Nei’s standard genetic distance tests. The F st outlier test for deviation from expected distribution between F st and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.
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abstractPopulation genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding strategies. Here, we report population structure patterns and genetic differentiation of coffee germplasm collections in China using 19 ISSR markers. A total of 129 unique alleles were detected, with an average of 6.8 alleles per ISSR. The estimated average Nei’s gene diversity ( H e ) index for all tested accessions was 0.49. A clustering pattern correlating with predefined species origin, rather than isolation by distance, was observed for all the tested accessions. C. arabica is highly differentiated from C. liberica and C. canephora , with F st values of 0.33 and 0.21, respectively. By contrast, C. liberica and C. excelsa Chevalier showed a close genetic association, with the F st value of 0.04. Significant differentiation was also detected within C. arabica accessions, which were separated in three genetic subgroups supported by pairwise ( F st ) index and Nei’s standard genetic distance tests. The F st outlier test for deviation from expected distribution between F st and expected heterozygosity identified five putative ISSRs under selection, with two, UBC864 and UBC842, showing signals of positive selection. Our study provides useful information for identifying core collections for genetics studies, breeding programs, and development of future germplasm management strategies.
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doi10.1007/s11105-019-01148-3
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