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Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest trees

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Forestry Studies in China

Abstract

With completion of the Populus genome sequencing project and the availability of many expressed sequence tags (ESTs) databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms (SNPs), which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium (LD) rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.

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  1. Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, 100083, Beijing, P. R. China

    Zhang De-qiang & Zhang Zhi-yi

  2. Laboratory of Biotechnology, Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, P. R. China

    Zhang De-qiang

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  1. Zhang De-qiang
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Correspondence to Zhang Zhi-yi.

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[Supported by the National Natural Science Foundation of China (Grant No. 30471409) and the National “863” Project (Grant No. 2002AA241071)]

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Zhang, Dq., Zhang, Zy. Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest trees. For. Stud. China 7, 1–14 (2005). https://doi.org/10.1007/s11632-005-0024-x

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