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Seonghyu Shin,Marcial Pastor-Corrales,Qijiang Song,Gaofeng Jia,Miok Woo,Perry Cregan 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Recently whole genome SNP genotyping has been used to do association analysis and to map a gene of interest. Here we report application of bulked segregant analysis(BSA) using Infinium HD assay with ‘BARC Bean6K_3’, a SNP genotyping beadchip containing 5,399 SNPs for common bean to locate a target gene. We used BSA using Infinium HD assay was performed to find the candidate region of a single dominant rust resistant gene in PI310762, a common bean cultivar. And SSR markers were identified and mapped on the candidate region using F2 population derived from the cross of susceptible Pinto114 x resistant PI310762. BSA revealed the candidate region of the resistant gene is on chromosome 4 where we developed nine SSR markers. Three SSR markers (beanssr1170, beanssr1168, and beanssr1167) of them appeared closely linked to the resistant gene which is located between beanssr1167 at 0.1cM and beanssr1170 at 0.5cM on chromosome 4. This study showed BSA using high-throughput whole genome SNP genotyping is a very fast and efficient method to locate a gene of interest on chromosome.
Van, K.,Hwang, E.-Y.,Kim, M. Y.,Park, H. J.,Lee, S.-H.,Cregan, P. B. American Genetic Association 2005 The Journal of heredity Vol.96 No.5
<P>Single nucleotide polymorphisms (SNPs) including insertion/deletions (indels) serve as useful and informative genetic markers. The availability of high-throughput and inexpensive SNP typing systems has increased interest in the development of SNP markers. After fragments of genes were amplified with primers derived from 110 soybean GenBank ESTs, sequencing data of PCR products from 15 soybean genotypes from Korea and the United States were analyzed by SeqScape software to find SNPs. Among 35 gene fragments with at least one SNP among the 15 genotypes, SNPs occurred at a frequency of 1 per 2,038 bp in 16,302 bp of coding sequence and 1 per 191 bp in 16,960 bp of noncoding regions. This corresponds to a nucleotide diversity (&thetas;) of 0.00017 and 0.00186, respectively. Of the 97 SNPs discovered, 78 or 80.4% were present in the six North American soybean mapping parents. The addition of “Hwaeomputkong,” which originated from Japan, increased the number to 92, or 94.8% of the total number of SNPs present among the 15 genotypes. Thus, Hwaeomputkong and the six North American mapping parents provide a diverse set of soybean genotypes that can be successfully used for SNP discovery in coding DNA and closely associated introns and untranslated regions.</P>