...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>BMC Genomics >The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce
【24h】

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

机译：北方黑云杉使用候选SNP方法的适应性状的基因组结构和关联遗传

获取原文
   

获取外文期刊封面封底 >>

       
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Background The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing. Results A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years. Conclusions The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.
机译：背景技术在非模型植物中，对适应性状的基因组结构了解甚少。可以使用各种方法来弥合这种差距，包括在系谱中绘制定量性状基因座（QTL）以及在非结构化人群中进行遗传关联研究。在这里，我们介绍黑云杉（是北美北方森林中分布广泛的针叶树）的适应性状的基因组结构的结果。作为常用候选基因方法的替代方法，已开发了一种候选SNP方法用于关联测试。结果使用包含231个基因位点的遗传图谱来鉴定QTL，该QTL与花蕾时机和多年和地点评估的树高有关。确定了22个独特的基因组区域，包括20个与花蕾时机相关的区域和6个与树高相关的区域。使用434个基因的DNA池测序从离群值检测和适应性状的大量分离子分析结果中，鉴定出52个候选SNP，随后在遗传协会研究中测试了多年和地点评估的花序时间和树高。总共34个（65％）SNP与花蕾时机或树高或两者均显着相关。尽管单个SNP的解释方差（PVE）百分比很小，但站点之间和年份之间共享几个重要的SNP。结论花蕾时间和树高之间的基因组区域和重要的SNP共享表明多效性效应。多年以来，重要的QTL和SNP差异很大，这表明同一字符的不同基因集在树的生活史的不同阶段涉及。携带显着SNP和低PVE的基因的功能多样性进一步表明，大量的多态性与适应性遗传变异有关。因此，对于未驯化的物种（例如黑云杉），其自然种群具有较大的有效规模和较低的连锁不平衡度，因此，预测适应性的有效标记系统应需要调查大量的SNP。像本研究中开发的那样的候选SNP方法可能有助于减少这些数量。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号