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Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla).

Hao W, Wang S, Liu H, Zhou B, Wang X, Jiang T - PLoS ONE (2015)

Bottom Line: A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus.The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66.The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.

ABSTRACT
In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

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The unweighted pair group method average (UPGMA) based dendrogram of 41 white birch genotypes from six geographical locations, based on their allelic constitution at 111 SSR loci. H1-H3, Huanren provenance, China; L1-L4, Liangshui provenance, China; X1-X7, Xiaobeihu provenance, China; Q1-Q7, Qingyuan provenance, China; M1-M15, Maoershan provenance, China; F1-F5, Finland provenance, Finland.
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pone.0125235.g003: The unweighted pair group method average (UPGMA) based dendrogram of 41 white birch genotypes from six geographical locations, based on their allelic constitution at 111 SSR loci. H1-H3, Huanren provenance, China; L1-L4, Liangshui provenance, China; X1-X7, Xiaobeihu provenance, China; Q1-Q7, Qingyuan provenance, China; M1-M15, Maoershan provenance, China; F1-F5, Finland provenance, Finland.

Mentions: Genetic diversity is a result of gene evolution in plant species [27] and becomes a foundation of the genetic improvement of species. Analyses of genetic diversity by using molecular markers could provide better understanding of genetic background of white birch cultivars. The results of the present study indicated that the white birch trees from six geographical locations had low to moderate similarity (0.025–0.610) and could be further separated into four clusters at a similarity coefficient of 0.22 (Fig 3). Genotypes from Huanren and Liangshui were closely related and grouped into the cluster I, and the genotypes from Xiaobeihu and Qingyuan into cluster II. Genotypes from Finland, and Maoershan were apparently different from each other and from the other groups as well, and grouped into the clusters III and IV respectively. The clusters of genotypes were apparently agreed with their provenances, suggested that the SSR primers used in this study can effectively distinguish white birch germplasm. The genetic relationships between these genotypes might provide useful information for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.


Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla).

Hao W, Wang S, Liu H, Zhou B, Wang X, Jiang T - PLoS ONE (2015)

The unweighted pair group method average (UPGMA) based dendrogram of 41 white birch genotypes from six geographical locations, based on their allelic constitution at 111 SSR loci. H1-H3, Huanren provenance, China; L1-L4, Liangshui provenance, China; X1-X7, Xiaobeihu provenance, China; Q1-Q7, Qingyuan provenance, China; M1-M15, Maoershan provenance, China; F1-F5, Finland provenance, Finland.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414481&req=5

pone.0125235.g003: The unweighted pair group method average (UPGMA) based dendrogram of 41 white birch genotypes from six geographical locations, based on their allelic constitution at 111 SSR loci. H1-H3, Huanren provenance, China; L1-L4, Liangshui provenance, China; X1-X7, Xiaobeihu provenance, China; Q1-Q7, Qingyuan provenance, China; M1-M15, Maoershan provenance, China; F1-F5, Finland provenance, Finland.
Mentions: Genetic diversity is a result of gene evolution in plant species [27] and becomes a foundation of the genetic improvement of species. Analyses of genetic diversity by using molecular markers could provide better understanding of genetic background of white birch cultivars. The results of the present study indicated that the white birch trees from six geographical locations had low to moderate similarity (0.025–0.610) and could be further separated into four clusters at a similarity coefficient of 0.22 (Fig 3). Genotypes from Huanren and Liangshui were closely related and grouped into the cluster I, and the genotypes from Xiaobeihu and Qingyuan into cluster II. Genotypes from Finland, and Maoershan were apparently different from each other and from the other groups as well, and grouped into the clusters III and IV respectively. The clusters of genotypes were apparently agreed with their provenances, suggested that the SSR primers used in this study can effectively distinguish white birch germplasm. The genetic relationships between these genotypes might provide useful information for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

Bottom Line: A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus.The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66.The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.

ABSTRACT
In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

Show MeSH