Development of a set of SNP markers present in expressed genes of the apple Export

@article{citeulike:3750214, abstract = {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\ \&\#xd7;\ A689-24 cross and a Malling 9\ \&\#xd7;\ 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.}, author = {Chagne, D. and Gasic, K. and Crowhurst, R. and Han, Y. and Bassett, H. and Bowatte, D. and Lawrence, T. and Rikkerink, E. and Gardiner, S. and Korban, S.}, citeulike-article-id = {3750214}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ygeno.2008.07.008}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0888754308001808}, doi = {10.1016/j.ygeno.2008.07.008}, issn = {08887543}, journal = {Genomics}, keywords = {apple, est, snp}, month = {November}, number = {5}, pages = {353--358}, posted-at = {2008-12-05 14:42:15}, priority = {2}, title = {Development of a set of SNP markers present in expressed genes of the apple}, url = {http://dx.doi.org/10.1016/j.ygeno.2008.07.008}, volume = {92}, year = {2008} }

TY - JOUR ID - citeulike:3750214 L3 - citeulike-article-id:3750214 N2 - 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 × A689-24 cross and a Malling 9 × 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. IS - 5 JF - Genomics SN - 08887543 EP - 358 TI - Development of a set of SNP markers present in expressed genes of the apple VL - 92 SP - 353 KW - apple KW - est KW - snp AU - Chagne, D AU - Gasic, K AU - Crowhurst, R AU - Han, Y AU - Bassett, H AU - Bowatte, D AU - Lawrence, T AU - Rikkerink, E AU - Gardiner, S AU - Korban, S PY - 2008/11// UR - http://dx.doi.org/10.1016/j.ygeno.2008.07.008 ER -