We have used bulked segregant analysis to screen the strain-specific DNA marker associated thermophilic strain of Pleurotus eryngii. Bulked genomic DNAs of Pleurotus eryngii were amplified by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S primers to screen the strain-specific DNA marker. A unique DNA fragment of 550 bp was amplified with OP-S07 primer from the thermophilic strain and sequenced. A sequence characterized amplified region (SCAR) marker was designed on the basis of the determined sequence and named as OP-S07-1. The PCR analysis with the OP-S07-1 primer showed that this SCAR marker clearly distinguish the thermophilic strains from the control strains.

We have used bulked segregant analysis to screen the strain-specific DNA marker associated psychrophilic strain of Pleurotus eryngii. Bulked genomic DNAs of Pleurotus eryngii were amplified by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S primers to screen the strain-specific DNA marker. A unique DNA fragment of 490 bp was amplified with OP-L18 primer from the psychrophilic strain and sequenced. A sequence characterized amplified region (SCAR) marker was designed on the basis of the determined sequence and named as OP-L18-1. The PCR analysis with the OP-L18-1 primer showed that this SCAR marker clearly distinguish the psychrophilic strains from the control strains.

We have used bulked segregant analysis to screen the strain-specific DNA marker associated thermophilic strain of Pleurotus eryngii. Bulked genomic DNAs of Pleurotus eryngii were amplified by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S primers to screen the strain-specific DNA marker. A unique DNA fragment of 500 bp was amplified with OP-A11 primer from the psychrophilic strain and sequenced. A sequence characterized amplified region (SCAR) marker was designed on the basis of the determined sequence and named as OP-A11-1. The PCR analysis with the OP-A11-1 primer showed that this SCAR marker clearly distinguish the psychrophilic strains from the control strains.

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.

For developing molecular markers linked to white rust resistance in chrysanthemum, RAPD and AFLP were carried out in ‘Puma White’ x ‘Dancer’ mapping population through Bulked Segregant Analysis (BSA) methods. 10 resistant and 10 susceptible individuals were selected and bulked. And then, these bulks were screened using 280 RAPD primers (10 mer) with two parents. As a result of BSA-RAPD, 25 Dancer/R-bulk specific bands in 21 primers and 22 Puma White/S-bulk specific bands in 18 primers were selected. These resistant or susceptible specific bands were screened in 10 resistant and 10 susceptible individuals. Except OPI-13520, all bands were confirmed as false positive. OPI-13520 band presumed as closely linked marker to white rust disease resistance was tested in whole population. Among 187 progenies, just six off-springs did not correspond with phenotypic data. Based on expected phenotypic segregation ratios in the pseudo F1 progenies, it was assumed that a duplex type of white rust resistance in ‘Dancer’ (RRrrrr) were in combination with a duplex type of OPI-13520 marker. As a result of x2-test of independence between resistance gene and OPI-13520 marker, x2 score is 76.08 and probability is 2.13x10-16. And resistance gene and OPI-13520 marker were assumed to be linked in coupling phase. The value of recombination fraction obtained by successive trials and second derivative of log likelihood was 0.03832±0.0271.

Co-segregation of male fertility with DNA markers selected by RAPD analysis as being potentially linked to the restorer gene (Rf) for Cytoplasmic male sterility (CMS) was analyzed using segregating F2 population. One RAPD marker directly linked to the Rf locus was identified. Amplification of OPT-02/570 using the STS primers generated a monomorphic band of each fertile plants randomly selected F2 progenies. From these results, this specific marker would be strongly linked to be restoring gene. The use of STS marker is effective in overcoming the reliability of the RAPD phenotype and improving their utility for MAS, co-dominant STS markers are especially very useful.