• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Journal of Life Science
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• v.25 no.9
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• pp.1059-1071
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• 2015

Watermelon and melon are economically important Cucurbitaceae crops. Recently, the development of molecular markers based on the construction of genetic linkage maps and detection of DNA sequence variants through next generation sequencing are essential as molecular breeding strategies for crop improvement that uses marker-assisted selection and backcrossing. In this paper, we intended to provide useful information for molecular breeding of watermelon and melon by analyzing the current status of international and domestic research efforts on genomics and molecular markers. Due to diverse genetic maps constructed and the reference genome sequencing completed in the past, DNA markers that are useful for selecting important traits including yield, fruit quality, and disease resistances have been reported and publicly available. To date, more than 16 genetic maps and loci and linked markers for more than 40 traits have reported for each watermelon and melon. Furthermore, the functional genes that are responsible for those traits are being continuously discovered by high-density genetic map and map-based cloning. In addition, whole genome resequencing of various germplasm is under progress based on the reference genome. Not only by the efforts for developing novel molecular markers, but application of public marker information currently available will greatly facilitate breeding process through genomics-assisted breeding.

• Korean Journal of Breeding Science
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• v.41 no.3
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• pp.236-243
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• 2009

This study was conducted to develop a japonica-type rice cultivar with brown planthopper (BPH) resistance using DNA markers. A doubled haploid (DH) population consisting of 120 pure-lines was established by anther culture of $F_1$ hybrids between 'Samgang', a Tongil type BPH resistance cultivar, and 'Nagdong', a japonica cultivar. To determine the map position of genes responsible for BPH resistance in rice, a genetic map was constructed based on 120 DH lines. A total of 162 molecular markers were classified into 12 linkage groups, covering 1,884 Kosami centimorgan (cM) with an average of 11.6 cM. Five QTLs (qBPR3, qBPR6, qBPR7, qBPR8, and qBPR12) associated with BPH resistance were identified and mapped on chromosomes 3, 6, 7, 8, and 12, respectively, using the genetic map constructed in this study. To analyze the relationship between BPH resistance and agronomic traits, a total of eight QTLs related to the agronomic traits were detected on 12 rice chromosomes. In an analysis of relationships, three QTLs (qBPR3, qBPR7, and qBPR8) showed a linkage with tested agronomic traits. A QTL (qBPR3) located on chromosome 3 (RM282-3023) was closely linked to culm length (qCL3). The QTL (qBPR8) for BPH resistance on the short arm of chromosome 8 also overlapped the region detected in culm length (qCL8).

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.2
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• pp.155-160
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• 2008

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

• Plant Biotechnology Reports
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• v.2 no.3
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• pp.191-198
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• 2008

Germplasm characterization and evolutionary process in viable populations are important links between the conservation and utilization of plant genetic resources. Here, an investigation is made, based on molecular and biochemical techniques for assessing and exploiting the genetic variability in germplasm characterization of taro, which would be useful in plant breeding and ex situ conservation of taro plant genetic resources. Geographical differentiation and phylogenetic relationships of Indian taro, Colocasia esculenta (L.) Schott, were analyzed by random amplified polymorphic DNA (RAPD) and isozyme of seven enzyme systems with specific reference to the Muktakeshi accession, which has been to be proved resistant to taro leaf blight caused by P. colocasiae. The significant differentiations in Indian taro cultivars were clearly demonstrated by RAPD and isozyme analysis. RAPD markers showed higher values for genetic differentiation among taro cultivars and lower coefficient of variation than those obtained from isozymes. Genetic differentiation was evident in the taro accessions collected from different regions of India. It appears that when taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred, possibly causing random differentiation among locally adapted taro populations. The selected primers will be useful for future genetic analysis and provide taro breeders with a genetic basis for selection of parents for crop improvement. Polymorphic markers identified in the DNA fingerprinting study will be useful for screening a segregating population, which is being generated in our laboratory aimed at developing a taro genetic linkage map.

• Journal of Forest and Environmental Science
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• v.11 no.1
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• pp.81-101
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• 1995

Random amplified polymorphic DNA (RAPD) technology, a recent approach in molecular genetics, is much usable to select the elite trees and to maximize the genetic gain in forest tree breeding program, providing a clue to determine the genetic marker-trait correlation. This review intorduces research on bark thickness and breeding strategy in Pinus elliottii, Pinus caribaea and their hybrid by Queensland Forest Service and ForBio Research Pty Ltd, University of Queensland, which employ RAPD technology. Genetic linkage map of $F_1$ hybrids includes 186 RAPD markers and 16 linkage groups (1641 cM long in total) and 6 quantitative trait loci are located putatively for bark thickness. Following recent research results and experiences in pine breeding programs, the forseeable stages in the application and development are proposed for marker assisted selectin; stage 1-determination of species specific markers for genes controlling traits of commercial interest, and stage 2-determination of marker-allele association for specific allelic variants within pure species. As pines inherit their megagametophytes from the seed parent and zygotic embryos from both male and female parents, the determination of marker-trait correlation is possible even in embryo stage, eventually making ways for the early selection of elite individuals.

• Mycobiology
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• v.45 no.2
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• Horticultural Science & Technology
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• v.31 no.4
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• pp.473-482
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• 2013

Molecular markers, as an efficient selection tool, have been and is being used for practical breeding program in chili pepper (Capsicum annuum L.). Recently, a lot of researches on inheritance and genetic analysis for quantitative traits including capsaicinoids, carotenoids, and sugar content in pepper are being performed worldwide. It has been also reported that QTL mapping is a necessary tool to develop molecular markers associated with the quantitative traits. In this study, we suggested a new method to construct a pepper genetic map using SNP (HRM) markers generated from NGS resequencing of female and male parents. Plant materials were C. annuum 'NB1' (female parent), C. chinense 'Jolokia' (male parent), and their $F_2$ population consisting of 94 progenies. Sequences of 4.6 Gbp and 6.2 Gbp were obtained from NGS resequencing of 'NB1' and 'Jolokia', respectively. Totally, 4.29 million SNPs between 'NB1' and 'Jolokia' were detected and the 1.76 million SNPs were clearly identified. Among them, total 145 SNP (HRM) primer pairs covering pepper genetic map were selected, and the 116 SNP (HRM) markers of them were located on this map. Total distance of the map, which consisted of 12 linkage groups and matched with basic chromosome numbers of pepper, was 1,167.9 cM. According to the mapping result, we concluded that our mapping method was suitable to construct a pepper genetic map fast and accurately. In addition, the genetic map could be directly used for QTL analysis of traits different between both parents.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.145-145
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• 2017

Foxglove aphid, Aulacorthum solani (Kaltenbach), is a Hemipteran insect that infected a wide variety of plants worldwide and caused serious yield losses in crops. The objective of this study was to identify the putative genes to foxglove aphid resistance in wild soybean, PI 366121 (Glycine soja Sieb. and Zucc.). One hundred and forty-one F4:8 recombinant inbred lines developed from a cross between susceptible variety, Williams 82 and foxglove aphid resistance wild soybean, PI 366121 were used. The two type of resistance response, antibiosis and antixenosis resistance were evaluated through choice and no-choice test, graded by the degree of total plant damage and primary infestation leaf damage; a genome-wide molecular linkage map was constructed with 29,898 single-nucleotide polymorphism markers utilizing a Axiom(R) 180K soyaSNP array. Using inclusive composite interval mapping analysis for foxglove aphid resistance, one major candidate QTL on chromosome 7 was identified. The major QTL on chromosome 7 showed both antixenosis and antibiosis resistance responses. The newly identified major QTL was consistent with previously reported QTL, Raso2, which showed around 5 times narrow down interval range with 8 candidate genes. Furthermore, total 1,115 soybean varieties including Glycine soja and Glycine max were exposed to germplasm screening, and 31 varieties, which showed significant antibiosis type foxglove aphid resistance were identified. This result could be useful in breeding for new foxglove aphid resistant soybean cultivars and developing novel insecticides.

• BMB Reports
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• v.41 no.6
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• pp.466-471
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• 2008

Three isoforms of pig PDE4B were cloned and classified as two forms: PDE4B1 and PDE4B3, which contain UCR1 and UCR2; and PDE4B2, which contains only UCR2. The amino acid sequences of each isoform showed good conservation in human and rat. PDE4B2 is expressed in a wide range of tissues, but PDE4B1 and PDE4B3 are not. Using an informative SNP for the Iberian x Landrace intercross detected from intron 12, a linkage map was constructed. The location of PDE4B was estimated at 123.6 cM outside of the QTL-CI (124-128 cM) for IMF. However, the QTL-CI for IMF was reconfirmed with high significance, and its position was narrowed down to an interval of 4 cM (the region defined by markers PDE4B and SW1881). Using radiation hybrid mapping, LEPR, LEPROT, DNAJC6, AK3L1 and AK3L2 were selected as positional and/or functional candidates related to the QTL.