• Molecules and Cells
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• v.21 no.1
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• pp.135-140
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• 2006

Cytoplasmic male sterility (CMS) in plants, which is due to failure to produce functional pollen, is a maternally inherited trait. Specific nuclear genes that suppress CMS, termed fertility restorer (Rf) genes, have been identified in several plants. In this study, Rfl-inked molecular markers in pepper (Capsicum annuum L.) were detected by bulked segregant analysis of eight amplified fragment length polymorphisms (AFLPs). Only AFRF8 was successfully converted to a cleaved amplified polymorphic sequence (CAPS) marker. This was named AFRF8CAPS and genotype determination using it agreed with that obtained with the original AFRF8. A linkage map with a total size of 54.1 cM was constructed with AFRF8CAPS and the seven AFLP markers using the Kosambi function. The AFRF8CAPS marker was shown to be closest to Rf with a genetic distance of 1.8 cM. These markers will be useful for fast and reliable detection of restorer lines during $F_1$ hybrid seed production and breeding programs in pepper.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.1
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• pp.124-132
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• 2023

This study aimed to cross between Korean and Japanese pure lines of Neopyropia strains to establish cross breeding technology and identify a superior variety that harbors the strength of both parents. Four crossing combinations were tried using three methods, resulting in 1,476 single conchocelis colonies. The three co-dominant Cleaved Amplified Polymorphic Sequence (CAPS) markers (EF-1α/Mse I, TOP2/Mse I, car A/ApaL I) were used to distinguish heterozygotic sporophytes and their maternal lines obtained from the inter and intraspecific cross-fertilization within the wild type of Neopyropia strains. Of the 1,476 colonies, 26.9% (218) were heterozygotes obtained from the nuclear CAPS markers. Their maternal line was clearly confirmed using organelle CAPS marker and chimeric thallus was obtained from crossing experiment of Japanese N. yezoensis (♀) and Korean N. yezoensis (♂). The use of CAPS markers improved the efficiency of crossbreeding by quickly screening heterozygotes and maternal lines in the conchocelis phase, which otherwise required pigmentation mutants as genetic markers.

• The Korean Journal of Mycology
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• v.49 no.1
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• pp.33-44
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• 2021

Lentinula edodes (Berk.) Pegler, the most produced mushroom in the world, is an edible mushroom with very high nutritional and pharmacological value. Currently, interest in the protection of genetic resources is increasing worldwide, and securing the distinction between new cultivars is very important. Therefore, the development of efficient molecular markers that can discriminate between L. edodes cultivars is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanbaekhyang and Sulbaekhyang). These markers were developed from whole genome sequencing data from L. edodes monokaryon strain B17 and resequencing data from 40 cultivars. A nucleotide deletion existed in scaffold 19 POS 214449 in Sanbaekhyang (GT→G), and a single nucleotide polymorphism changed in scaffold 7 POS 215801 in Sulbaekhyang (G→A). The restriction enzymes Hha I and HpyCH4IV distinguished Sanbaekhyang and Sulbaekhyang, respectively, from other cultivars. Thus, we developed two CAPS markers for the identification of the L. edodes cultivars Sanbaekhyang and Sulbaekhyang.

• Horticultural Science & Technology
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• v.30 no.1
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• pp.56-63
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• 2012

Tomato hypocotyl can generally be one of two colors, purple or green. Genetically, this trait is controlled by a single dominant gene. Hypocotyl tissue specific color expression is one of many visible genetic marker sources used to select tomato progeny. However, the visible marker does not show a clear distinction between homozygous genotype and heterozygous genotype from the breeding lines. Therefore, to identify a hypocotyl pigmentation related marker, we screened DNA polymorphisms in thirteen tomato lines showing purple or green hypocotyls. The markers used for screening consisted of primer set information obtained from anthocyanin related genes, conserved ortholog set II (COS II) marker sets localized near anthocyanin related genes, and restriction fragment length polymorphism (RFLP) markers localized near COS II markers, which produce polymorphisms between purple and green tomatoes. One primer from a RFLP fragment resulted in a polymorphism on agarose gel electrophoresis. From the RFLP fragment, a cleaved amplified polymorphic sequence (CAPS) marker was developed to distinguish between purple and green hypocotyls. The genotypes of 135 $F_2$ individuals were analyzed using the CAPS marker, and among them, 132 individuals corresponded to the phenotypes of hypocotyl pigmentation.

• Journal of Mushroom
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• v.8 no.1
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• pp.27-32
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• 2010

This study was carried out to analyze the genetic relationships among 22 strains of Sparassis crispa, which were collected from various regions of worldwide. The cleaved amplified polymorphic sequence were obtained from the ribosomal DNA ITS regions of each strain. Based on the sequence analysis, the presence of five different groups were observed. Most strains shared the high nucleotide sequence similarity (about 90%) to each other, except only one strain, KACC50866. Nucleotide sequence similarity of KACC50866 was below 10% to other strains, indicating the genetic relatedness of strain KACC50866 was low compared to other strains. More works such as mitochondria genome analysis should help to determine the precise genetic diversity of S. crispa strains.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.722-729
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• 2015

Powdery mildew (PM) caused by Podosphaera aphanis is a major disease that can result in significant yield losses in strawberry (Fragaria ${\times}$ ananassa Duchesne). For preventing PM, pesticides are usually applied in strawberry. In this study, molecular markers were developed to increase breeding efficiency of PM-resistance cultivars by marker-assisted selection (MAS). An $F_2$ population derived from a cross between PM-resistance 'Seolhyang' and PM-susceptibility 'Akihime' was evaluated for disease resistance to PM and RAPD (random amplification of polymorphic DNA)-BSA (bulked segregant analysis). Among 200 RAPD primers tested, OPE10 primer amplified a 311bp-band present in with 331bp. Sequence alignment performed for searching polymorphisms and six single nucleotide polymorphism (SNP) were found in amplified regions. To develop polymorphic marker for distinguishing between resistant and susceptible, RAPD was converted to cleaved amplified polymorphic sequence (CAPS) marker. Among restriction enzymes associated with six SNPs, Eae I (Y/GGCCR) was successfully digested to 231bp in susceptible. The results suggest that the selected CAPS marker could be used for increasing efficiency of selecting powdery mildew resistant strawberry in breeding system.

• The Korean Journal of Mycology
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• v.32 no.1
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• pp.1-7
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• 2004

To establish the phylogenetic relationships of Dictyophora spp., rDNA-ITS regions of 11 strains of veiled lady mushroom collected from various countries were amplified and sequenced. It was observed that the 11 strains were divided into four groups based on PCR band patterns of each ITS region cleaved by eight different restriction enzymes in cleaved amplified polymorphic sequence analysis (CAPS). The phylogenic relationship of each group by cleaved amplified polymorphic sequence (CAPS) analysis matches well with previously reported morphological phylogeny, such as 5 strains of D. indusiata, 4 strains of D. echinovolvata, and a strain of Phallus rugulosus. Sequence analysis using the cluster V methods showed more detail classification than CAPS analysis. The 5.8S region showed two point nucleotide base exchanges from G to A according to four groups, and four groups were subdivided by sequence variation of ITS I and ITS II regions. But sequence variation of Phallus rugulosus was not showed in full ITS region. This study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequence, are most useful in systematics and other mushroom study.

• The Korean Journal of Mycology
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• v.45 no.2
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• pp.114-120
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• 2017

Lentinula edodes is an edible mushroom that is mainly cultivated in Asian countries. Recently, new cultivars of this mushroom have been developed in Korea; variety protection is very important, so the development of efficient molecular markers that can distinguish each variety is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanmaru 1ho and Chunjang 3ho). These markers were developed from whole genomic sequencing data from L. edodes monokaryon strain B17 and resequencing data from 10 dikaryon strains. A single nucleotide polymorphism changed in scaffold 9 POS 1630048 in Sanmaru 1ho($G{\rightarrow}T$), and in scaffold 13 POS 920681 in Chunjang 3ho ($G{\rightarrow}A$). The restriction enzymes TspR I and Xho I distinguished Sanmaru 1ho and Chunjang 3ho, respectively, from other strains. Thus, we developed 2 CAPS markers for the identification of the L. edodes cultivars Sanmaru 1ho and Chunjang 3ho.

• The Korean Journal of Mycology
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• v.48 no.4
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• pp.389-396
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• 2020

Lentinula edodes is one of the most widely consumed edible mushrooms in Korea. Mating in L. edodes is regulated by a tetrapolar system, and two unlinked genetic loci, A and B, are known to be major determinants of the mating types, as reported in other heterothallic basidiomycetes. The A locus of L. edodes encodes a pair of homeodomain (HD) transcription factors. The highly variable N-termini of these HD transcription factors contribute to the diversity among the A mating types. In this study, we developed a cleaved amplified polymorphic sequence (CAPS) marker to discriminate 11 different A mating type alleles predominant among both cultivated and wild strains. Amplification of the variable region of the A locus followed by digestion with HaeIII and EcoRI restriction enzymes enabled successful discrimination among the 11 A mating type alleles. We also evaluated the applicability of this method in the identification of two A mating types of a dikaryotic strain.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.550-558
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• 2015

To analyze the linkage relationships among molecular markers recently reported to be linked to onion (Allium cepa L.) Ms, a restorer-of-fertility locus, in onion (Allium cepa L.), three single nucleotide polymorphism markers were converted into cleaved amplified polymorphic sequence (CAPS) markers based on onion transcriptome sequences and the rice genome database. Analysis of the recombinants selected from 4,273 segregating plants using CAPS and other linked markers demonstrated the jnurf13 and jnurf610 markers to perfectly co-segregate with the Ms locus. In contrast to jnurf13, the jnurf610 marker was not in perfect linkage disequilibrium with the Ms locus in diverse breeding lines. Thus, the jnurf13 marker and the marker for identification of cytoplasm types were utilized to enhance the efficiency of onion breeding through four applications. First, 89 maintainer lines containing the normal cytoplasm and homozygous recessive Ms genotypes were successfully identified from 100 breeding lines. Second, these two molecular markers were used to analyze the main sources of male-fertile contaminants frequently found in the male-sterile parental lines during F1 hybrid seed production. The majority of the contaminants contained heterozygous Ms genotypes, indicating that pollen grains harboring the dominant Ms genotype may have been introduced during propagation of the maintainer lines. Therefore, the genetic purity of the two maintainer lines was analyzed in the third application, and the results showed that both maintainer lines contained 13-21% off-types. Finally, the two markers were used to increase the seed yield potentials of two open-pollinated varieties containing sterile cytoplasms by removing the plants harboring homozygous recessive and heterozygous Ms genotypes.