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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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An example of SSR variation at the BP-293 locus across 41 white birch genotypes.M, DL2000 DNA ladder Marker; 1–41, each represents one of the 41 white birch plants.
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pone.0125235.g001: An example of SSR variation at the BP-293 locus across 41 white birch genotypes.M, DL2000 DNA ladder Marker; 1–41, each represents one of the 41 white birch plants.

Mentions: High-throughput Solexa sequencing technology has provided an efficient tool to develop SSR markers. In the present study, 544 SSR primer pairs were designed from the white birch genomes (S2 Table) and tested polymorphism among five white birch genotypes. Of them, 215 showed polymorphisms with visible bands, indicating that 39.5% of SSR loci could be used for white birch genotyping. It also suggests that development of SSR markers from the high-throughput whole genome sequences is more efficient than from genomic DNA library and EST sequences, because the SSR markers from whole genome sequences are more wide distributed and then show higher rates of polymorphism. Of the 215 polymorphic loci, 111 solid loci were selected to genotype the 41 white birch genotypes (Table 1). As results, a total of 717 alleles were visualized across these 41 genotypes. The SSR allele numbers varied by loci ranged from 2 (Loci BP-016, BP-022, BP-080, BP-121, and BP-301) to 12 (BP-210). Fig 1 showed the PCR amplification profile of the locus BP-293 across the 41 white birch genotypes.


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)

An example of SSR variation at the BP-293 locus across 41 white birch genotypes.M, DL2000 DNA ladder Marker; 1–41, each represents one of the 41 white birch plants.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0125235.g001: An example of SSR variation at the BP-293 locus across 41 white birch genotypes.M, DL2000 DNA ladder Marker; 1–41, each represents one of the 41 white birch plants.
Mentions: High-throughput Solexa sequencing technology has provided an efficient tool to develop SSR markers. In the present study, 544 SSR primer pairs were designed from the white birch genomes (S2 Table) and tested polymorphism among five white birch genotypes. Of them, 215 showed polymorphisms with visible bands, indicating that 39.5% of SSR loci could be used for white birch genotyping. It also suggests that development of SSR markers from the high-throughput whole genome sequences is more efficient than from genomic DNA library and EST sequences, because the SSR markers from whole genome sequences are more wide distributed and then show higher rates of polymorphism. Of the 215 polymorphic loci, 111 solid loci were selected to genotype the 41 white birch genotypes (Table 1). As results, a total of 717 alleles were visualized across these 41 genotypes. The SSR allele numbers varied by loci ranged from 2 (Loci BP-016, BP-022, BP-080, BP-121, and BP-301) to 12 (BP-210). Fig 1 showed the PCR amplification profile of the locus BP-293 across the 41 white birch genotypes.

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