Chagné David, Gasic Ksenija, Crowhurst Ross N, Han Yuepeng, Bassett Heather C, Bowatte Deepa R, Lawrence Timothy J, Rikkerink Erik H A, Gardiner Susan E, Korban Schuyler S
The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, Palmerston North 4442, New Zealand.
Genomics. 2008 Nov;92(5):353-8. doi: 10.1016/j.ygeno.2008.07.008. Epub 2008 Sep 14.
Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.
与基因编码区相关的分子标记是连接功能基因组学和结构基因组学的有用工具。由于单核苷酸多态性（SNP）在植物基因组中含量丰富，几乎存在于所有基因组区域，包括大多数编码序列。本研究的目的是利用苹果丰富的基因组学资源，包括大量的表达序列标签（EST），开发一套苹果SNP。利用生物信息学工具，在一个由多种苹果种质开发的约350,000个序列的EST数据库中搜索SNP。结果共鉴定出71,482个推定SNP。由于据报道苹果基因组是一个古老的多倍体，因此尝试验证在计算机上检测到的那些SNP是归因于等位基因多态性还是基因复制或旁系同源或同源序列变异。为此，设计了一组464对PCR引物，使用两个植物亚组进行PCR扩增，并对PCR产物进行测序。然后将从这些序列中检索到的SNP定位到苹果遗传图谱上，包括新构建的皇家嘎啦×A689 - 24杂交组合和马林9×健壮5的图谱，使用bin定位策略进行图谱构建。使用高分辨率熔解（HRM）技术进行SNP基因分型。共成功定位了93个包含210个编码SNP的新标记。这套新的苹果SNP标记为利用数量性状位点（QTL）或连锁不平衡分析理解重要园艺性状的遗传控制提供了新机会。这些标记也可作为有用的标记用于比对物理图谱和遗传图谱，以及作为蔷薇科潜在的可转移标记。
