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Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides.

Jing Tan1, Jun-Jie Guo2, Ming-Yu Yin3

  • 1Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China. planttj@126.com.

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|November 16, 2018
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Summary

This study developed new simple sequence repeat (SSR) markers for Betula alnoides using next-generation sequencing. These SSR markers are valuable for studying population genetics and advancing molecular breeding in this important tree species.

Keywords:
Betula alnoidesnext generation sequencing (NGS)polymorphismsimple sequence repeat (SSR)transferability

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Area of Science:

  • Genetics
  • Molecular Biology
  • Forestry

Background:

  • Betula alnoides is a fast-growing, valuable indigenous tree species in tropical and subtropical Asia.
  • The species is predominantly tetraploid in China, highlighting the need for genetic research.

Purpose of the Study:

  • To develop novel simple sequence repeat (SSR) markers for Betula alnoides using next-generation sequencing (NGS).
  • To assess the genetic diversity and polymorphism of B. alnoides using the developed SSR markers.
  • To evaluate the cross-species transferability of these SSR markers to related Betula species.

Main Methods:

  • Next-generation sequencing (NGS) was employed to identify SSR loci in Betula alnoides.
  • Primer sets were designed for putative SSR regions, and 900 were randomly selected for amplification and polymorphism analysis.
  • Genetic diversity was quantified using parameters such as the number of alleles, observed and expected heterozygosities, and Shannon-Wiener diversity index.
  • Cross-species transferability was tested on six related Betula species.

Main Results:

  • NGS identified 164,357 candidate SSR loci from 106,452 clean reads.
  • Mononucleotide repeats were most abundant (77.05%), followed by dinucleotide (10.18%).
  • Out of 900 tested primer sets, 310 polymorphic SSR markers were identified.
  • The developed markers revealed significant genetic diversity within B. alnoides populations (mean alleles=5.14, mean H_O=0.64, mean H_E=0.57, mean I=1.12).
  • Successful cross-species amplification ranged from 48.96% to 84.38% for tested Betula species.

Conclusions:

  • The study successfully developed a substantial set of polymorphic SSR markers for Betula alnoides.
  • These SSR markers provide valuable tools for population genetics studies and molecular marker-assisted breeding.
  • The markers demonstrate potential for genome-wide association studies and conservation efforts in Betula species.