• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Reproductive and Developmental Biology
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• v.36 no.3
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• pp.183-188
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• 2012

The bovine fatty acid binding protein 4 and 5 (FABP4 and 5) is a major positional and physiological candidate gene for the bovine marbling and carcass weight. The aim of this study was to evaluate the association between economic traits of Korean cattle (Hanwoo) and genetic variation in fatty acid binding protein 4 and 5 (FABP4 and 5) genes within carcass/meat quality traits and the before/after of fatting in breed Hanwoo. Here, we characterized the nucleotide polymorphism of FABP4 and 5 in 86 cattle. We were detected the variability of three types (GG, AG, and AA) by PCR, and economic traits were analyzed by the mixed regression model implemented in the ASReml program. As the result of statistical and supersonic analysis, FABP4 gene was highly showed significant effect (p<0.006) on marbling score (MS), in contrast FABP5 gene was lowed (p<0.084) on MS before fatting. But, FABP4 gene was highly showed significant effect (p<0.0054) on MS, in contrast FABP5 gene lowest (p<0.0899) on MS in the after of fatting. Compare to supersonic result before fatting in FABP4 gene, it was detected type GG: (p<7.18), AG: (p<8.50), and AA: (p<10.50) (n=50), showed type GG: (p<4.88), AG: (p<2.33), and AA: (p<0.00) after weed out (n=20). Futhermore, it was detected type GG: (p<9.30), AG: (p<7.95), and AA: (p<7.40) (n=50) before fatting in the FABP5 gene. It was shown type GG: (p<2.67), AG: (p<3.50), and AA: (p<5.00) after weed out (n=50). Our results indicate that FABP4 and 5 gene transcription is regulated by the environment of feeding and management, and suggest that feeding and management could be potential key in determining FABP4 and 5 genes transcription for carcass/meat quality traits in breed Hanwoo.

• Horticultural Science & Technology
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• v.30 no.3
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• pp.278-285
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• 2012

Cymbidium goeringii is one of the most important and popular species in the orchid family in north-east Asia. In the present study, we prepared multiplex PCR system, and used it for the genotyping of eight simple sequence repeats (SSR) markers (CG409, CG415, CG709, CG722, CG787, CG1023, CG1210, and CG1281) in subject with 40 samples of cultivated varieties. All the analyzed samples showed different combined genotypes. The average combined power of discrimination was very high value of $7.14{\times}10^{-10}$, and observed heterozygosity (Ho = 0.466) was similar with two wild populations of C. goeringii, which may indicate no or little occurrence of genetic change after collection from wild habitats. The present study also developed a two-dimensional barcode to express information of genotype results of eight SSR markers (SSR DNA ID). The discrimination power of DNA ID between two individuals will be statistically more than 99.999999%. The SSR DNA ID and two-dimensional barcode may be very usefully applied for the discrimination and maintence of cultivars of C. goeringii.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.323-333
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• 2013

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright's F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

• Molecules and Cells
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• v.25 no.4
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• pp.467-478
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• 2008

Simple sequence repeats (SSRs) and interSSR (ISSR) marker systems were used in this study to reveal genetic changes induced by artificial selection for short/long larval duration in the tropical strain Nistari of the silkworm Bombyx mori. Artificial selection separated longer larval duration (LLD) ($29.428{\pm}0.723days$) and shorter larval duration (SLD) ($22.573{\pm}0.839days$) lines from a base, inbred population of Nistari (larval span of $23.143{\pm}0.35days$). SSR polymorphism was observed between the LLD and SLD lines at one microsatellite locus, Bmsat106 ($CA_7$) and at two loci of 1074 bp and 823 bp generated with the ISSR primer UBC873. Each of these loci was present only in the LLD line. The loci segregated in the third generation of selection and were fixed in opposite directions. In the $F_2$ generation of the $LLD{\times}SLD$ lines, the alleles of Bmsat106 and $UBC873_{1074bp}$ segregated in a 1:1 ratio and the loci were present only in the LLD individuals. $UBC873_{823bp}$ was homozygous. Single factor ANOVA showed a significant association between the segregating loci and longer larval duration. Together, the two alleles contributed to an 18% increase in larval duration. The nucleotide sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci had 67% A/T content and consisted of direct, reverse, complementary and palindromic repeats. The repeats appeared to be "nested" (59%) in larger repeats or as clustered elements adjacent to other repeats. Of 203 microsatellites identified, dinucleotides (67.8%) predominated and were rich in A/T and T/A motifs. The sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci showed similarity (E = 0.0) to contigs located in Scaffold 010774 and Scaffold 000139, respectively, of the B. mori genome. BLASTN analysis of the $UBC873_{1074bp}$ sequence showed significant homology of (nt.) 45-122 with upstream region of three exons from Bombyx. The complete sequence of this locus showed ~49% nucleotide conservation with transposon 412 of Drosophila melanogaster and the Ikirara insertions of Anopheles gambiae. The A + T richness and lack of coding potential of these small loci, and their absence in the SLD line, reflect the active process of genetic change associated with the switch to short larval duration as an adaptation to the tropics.

• Journal of Korean Society of Forest Science
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• v.104 no.4
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• pp.549-557
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• 2015

Novel cpSSR primers were developed based on the sequence information of the Pinus koraiensis chloroplast genome. A total of 30 cpSSR loci were detected in the chloroplast genome, and a total of 30 primer sets flanking those loci were designed. All primer sets were successfully amplified for chloroplast DNA in P. koraiensis. The cross-species transferability of the 30 primer sets was considerably high in P. pumila (100%) and P. paviflora (97%) belonging to the same Subgenus (Strobus) of P. koraiensis. Meanwhile, the transferability was relatively low (73%) in P. densiflora and P. sylvestris belonging to Subgenus Pinus. A total of 13 cpSSR loci out of the 30 loci were polymorphic in the Mt. Jumbong population of P. koraiensis. The mean of haploid diversity(H) was 0.512. The number of haplotypes(N) and the haplotype diversity($H_e$) were 25 and 0.992, respectively. Of the 25 haplotypes, 22 were unique in the analyzed population. The unique haplotypes differentiated 22 individuals (79%) from the total of 28 individuals. In conclusion, the novel cpSSR primers developed in this study would be applicable to other Pinus species, especially the subgenus Strobus, and provide a high level of polymorphism for the study of genetic variation of P. koraiensis.

• Journal of Life Science
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• v.20 no.7
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• pp.1086-1092
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• 2010

To estimate the genetic characteristics and cumulative power of discrimination (CPD) within Korean native commercial chicken, we used a total of 395 genomic DNAs from six breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean native Commercial Chicken: C, Ogal chicken: S, Hy-Line Brown: H, White Leghorn: W). Genetic diversity indices including mean allele number among loci, unbiased heterozygosity ($h_i$) within locus, effective number of alleles ($N_e$) and polymorphism information content (PIC) as well as the unbiased average heterozygosity (H) among loci in the populations were calculated using the generated allele frequencies by each marker. Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The nearest distance (0.119) was observed between the C and Y strains. The generated unbiased average heterozygosity among loci in each population was integrated to the global formula of CPD and the result demonstrated that the CPD within the six chicken populations was 99.461%.

• Journal of Animal Science and Technology
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• v.47 no.1
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• pp.1-10
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• 2005

Intramuscular fat content(lMF) is considered as one of major economic traits in the pig breeding and industry. In general, high IMF results in better meat quality. Several approaches to detect quantitative trait 10ci( QTL) for IMF indicated a strong possibility of the existence of a QTL related to IMF between the microsatellite marker SW71 and SW1881 on SSC6q. Porcine FABP3 has been considered as a candidate gene affecting IMF due to its physiological roles and position on the pig genome. Two novel mutations, g.-114T> C and g.-158T>G were detected by duplicate sequencing of the porcine FABP3 promoter region. These two mutations were identified as absolute linkage disequilibrium. The g.-158T> G mutation was used for investigating relationships with growth and fat deposition traits. The GG genotype of the g.-158T> G polymorphism showed highly negative effects(P< 0.01) on body weights at 3 and 12 weeks of age, and a positive effect(P< 0.05) on IMF. However, backfat thickness(BF) and carcass fat(CF) content were not significantly associated with the genotype. The result indicates that the novel mutations, identified in this study, could be utilized as possible genetic markers to improve IMF, independent with BF.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.142-153
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• 2016

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.10
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• pp.1501-1510
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• 2019

Objective: An experiment was conducted to evaluate genetic diversity of 26 Chinese indigenous goats by 30 microsatellite markers, and then to define conservation priorities to set up the protection programs according to the weight given to within- and between-breed genetic diversity. Methods: Twenty-six representative populations of Chinese indigenous goats, 1,351 total, were sampled from different geographic regions of China. Within-breed genetic diversity and marker polymorphism were estimated calculating the mean number of alleles, observed heterozygosities, expected heterozygosities, fixation index, effective number of alleles and allelic richness. Conservation priorities were analyzed by statistical methods. Results: A relatively high level of genetic diversity was found in twenty-four population; the exceptions were in the Daiyun and Fuqing goat populations. Within-breed kinship coefficient matrices identified seven highly inbred breeds which should be of concern. Of these, six breeds receive a negative contribution to heterozygosity when the method was based on proportional contribution to heterozygosity. Based on Weitzman or Piyasatian and Kinghorn methods, the breeds distant from others i.e. Inner Mongolia Cashmere goat, Chengdu Brown goat and Leizhou goat obtain a high ranking. Evidence from Caballero and Toro and Fabuel et al method prioritized Jining Gray goat, Liaoning Cashmere goat, and Inner Mongolia Cashmere goat, which agree with results from Kinship-based methods. Conclusion: Conservation priorities were determined according to multiple methods. Our results suggest Inner Mongolia Cashmere goat (most methods), Jining Gray goat and Liaoning Cashmere goat (high contribution to heterozygosity and total diversity) should be prioritized based on most methods. Furthermore, Daiyun goat and Shannan White goat also should be prioritized based on consideration of effective population size. However, if one breed can continually survive under changing conditions, the straightforward approach would be to increase its utilization and attraction for production via mining breed germplasm characteristics.