• Journal of Plant Biotechnology
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• 제44권3호
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• pp.312-319
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• 2017

The need to preserve and use plant genetic resources is widely recognized, and the prospect of dwindling plant genetic diversity, coupled with increased demands on these resources, has made them a topic of global discussion. In the present study, the genetic diversity and population structure of 73 ginseng accessions collected from six regions in China were analyzed using eight simple sequence repeat (SSR) markers. Major allele frequencies ranged between 0.38 ~ 0.78, with a mean allele frequency value of 0.571. The number of alleles discovered ranged from 3 to 10 per accession, with a mean number of 7; 56 alleles were discovered in total. Gene diversity (GD) and polymorphic information content (PIC) values were similar to each other, and they ranged from 0.36 ~ 0.77 (mean 0.588) and 0.33 ~ 0.74 (mean 0.548), respectively. Accessions were divided into three clusters based on their phylogenetic relationships and genetic similarities, and although the populations were similar, they were not classified according to the region. Regional genetic diversity was also similar, with slight differences observed based on the number of accessions per region. It is expected that the findings of the present study can provide basic data for future studies on ginseng genetic diversity and for breeding ginseng cultivars.

• Molecules and Cells
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• 제19권3호
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• pp.428-435
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• 2005

This study was carried out to assess the potential of SSR markers for variety identification by comparing SSR markers and morphological traits in tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Twenty-seven SSR markers were polymorphic in 66 pepper varieties, revealing a total of 89 alleles. Average polymorphism information content (PIC) value was 0.529, ranging from 0.03 to 0.877. Cluster analysis of the band patterns separated the varieties into three groups corresponding to varietal types. Morphological trait-based clustering showed some degree of similarity to dendrogram topologies based on the SSR index. However, no significance correlation was found between the SSR and morphological data. SSR markers could be used to complement a DUS test of a candidate variety and to select complimentary varieties by pre-screening existing varieties in the context of protecting new varieties of pepper.

• 한국자원식물학회지
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• 제30권3호
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• pp.323-330
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• 2017

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in northeast Asia. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus. By sequencing 711 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.

• Plant Breeding and Biotechnology
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• 제5권3호
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• pp.183-191
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• 2017

Finger millet (Eleusine coracana L. Gaertn.) is an important cereal crop in eastern Africa and southern India with excellent grain storage capacity and the unique ability to thrive in extreme environmental conditions. In this study, we analyzed the genetic diversity and population structure of finger millet using 12 developed microsatellites. By sequencing 815 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in finger millet accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 76 finger millet accessions in Asia, Africa, and unknown origins. The number of alleles ranged from 2 to 9, with an average of 3.3 alleles. The mean values of observed heterozygosity and expected heterozygosity were 0.27 and 0.35, respectively. The average polymorphism information content was 0.301 in all 76 finger millet accessions. AMOVA analysis showed that the percentage of molecular variance among the populations was 1%, that among individuals was 5%, and that within individuals was 94%. In STRUCTURE analysis, the 76 finger millet accessions were divided into two subpopulations which had an admixture of alleles. There was a correspondence among PCoA, AMOVA, and population structure. This study may form the basis for a finger millet breeding and improvement program.

• Horticulture, Environment, and Biotechnology : HEB
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• 제59권6호
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• pp.875-888
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• 2018

Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRU CTU RE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.321-336
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• 2018

Sesame (Sesamum indicum L.) is an important oilseed crop grown in tropical and subtropical areas. The objective of this study was to investigate the genetic relationships among 129 sesame landraces and cultivars using simple sequence repeat (SSR) markers. Out of 70 SSRs, 23 were found to be informative and produced 157 alleles. The number of alleles per locus ranged from 3 - 14, whereas polymorphic information content ranged from 0.33 - 0.86. A distance-based phylogenetic analysis revealed two major and six minor clusters. The population structure analysis using a Bayesian model-based program in STRUCTURE 2.3.4 divided 129 sesame accessions into three major populations (K = 3). Based on pairwise comparison estimates, Pop1 was observed to be genetically close to Pop2 with $F_{ST}$ value of 0.15, while Pop2 and Pop3 were genetically closest with $F_{ST}$ value of 0.08. Analysis of molecular variance revealed a high percentage of variability among individuals within populations (85.84%) than among the populations (14.16%). Similarly, a high variance was observed among the individuals within the country of origins (90.45%) than between the countries of origins. The grouping of genotypes in clusters was not related to their geographic origin indicating considerable gene flow among sesame genotypes across the selected geographic regions. The SSR markers used in the present study were able to distinguish closely linked sesame genotypes, thereby showing their usefulness in assessing the potentially important source of genetic variation. These markers can be used for future sesame varietal classification, conservation, and other breeding purposes.

• 한국조류학회지
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• 제25권2호
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• pp.77-81
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• 2018

세계적으로 멸종위기종인 따오기 (Nipponia Nippon)는 한국에서도 멸종위기종으로 구분되어 있으며, 이를 복원하기 위해 2008년 10월에 중국에서 따오기 1쌍을 도입하여 한국 최초로 인공번식에 성공하였다. 이 후 우포늪 따오기 종 복원을 통해 2017년까지 개체수가 200마리 이상으로 늘어났다. 본 연구에서는 우포늪 따오기 228 개체를 대상으로 성별을 결정하고, microsatellite 마커를 이용하여 유전적 유연관계를 분석하였다. 그 결과, 115마리의 암컷과 113마리의 수컷으로 판별되었으며, 2016년보다 2017년에 서식하고 있는 개체의 이형접합도와 다형성 정보지수가 모두 감소한 것으로 나타났다. 이는 작은 집단으로부터 개체 수를 늘려나가다 보니 2017년에 근친율이 증가한 것으로 사료된다. 향 후 본 연구는 한국 따오기의 번식사업 및 복원사업을 위한 기초자료로 유용하게 활용될 것으로 기대된다.

• Mycobiology
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• 제49권4호
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• pp.376-384
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• 2021

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy-Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.

• Animal Bioscience
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• 제35권8호
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• pp.1121-1128
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• 2022

Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei's DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure. Results: On average, the number of alleles, expected heterozygosity (H_Exp), observed heterozygosity (H_Obs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei's DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation. Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.

• Animal Bioscience
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• 제35권12호
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• pp.1839-1849
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• 2022

Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (F_PED) was significantly different from those estimated from runs of homozygosity (F_ROH) and single nucleotide polymorphism (F_SNP) based on genome. The Pearson correlation coefficient between F_ROH and F_SNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40