Ćalić Irina, Koch Jennifer, Carey David, Addo-Quaye Charles, Carlson John E, Neale David B
Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
USDA Forest Service, Northern Research Station, Forestry Sciences Laboratory, Delaware, OH, 43015, USA.
BMC Genomics. 2017 Jul 20;18(1):547. doi: 10.1186/s12864-017-3931-z.
The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees.
In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1.5 K - 50 K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher's exact test and logistic regression tests were performed to test associations between SNPs and phenotypes.
Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes a mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. Metallothioneins represent Cys-rich metal chelators able to coordinate metal atoms and may play an important role in the resistance mechanisms against beech scale insect.
The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs.
美国山毛榉树（Fagus grandifolia Ehrh.）原产于北美东部，具有重要的生态意义，并能提供高质量的木材产品。该树种易感染山毛榉树皮病（BBD），在北美面临着高死亡率。这种疾病是由毛毡山毛榉蚧虫（Cryptococcus fagisuga）、两种红球菌属真菌（N. faginata或N. ditissima）之一与美国山毛榉树相互作用引发的。
在这项病例对照全基因组关联研究（GWAS）中，我们使用Affymetrix Axiom 1.5K - 50K检测法对16K个高质量单核苷酸多态性（SNP）进行检测，以对514个个体的关联群体进行基因分型。我们还在一个由115个个体组成的全同胞家系中进行了连锁分析。采用Fisher精确检验和逻辑回归检验来检测SNP与表型之间的关联。
关联测试在第5号染色体（Chr）上发现了与一个单一基因（Mt）相关的四个高度显著的SNP，该基因编码欧洲山毛榉中一种类金属硫蛋白（金属离子结合）的mRNA。金属硫蛋白是富含半胱氨酸的金属螯合剂，能够配位金属原子，可能在抗山毛榉蚧虫的抗性机制中发挥重要作用。
GWAS研究确定了一个对山毛榉树皮病抗性有主要影响的单一位点。了解这个有助于抗性的基因位点可应用于育种、保护和恢复计划。
