• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.49-57
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• 2019

Objective: The first stage in both breeding and programs for the conservation of genetic resources are the identification of genetic diversity in the relevant population. The aim of the present study is to identify genetic diversity of six brown layer pure chicken lines (Rhode Island Red [RIRI, RIRII], Barred Rock [BARI, BARII], Columbian Rock [COL], and line 54 [L-54]) with microsatellite markers. Furthermore, the study aims to employ its findings to discuss the possibilities for the conservation and sustainable use of these lines that have been bred as closed populations for a long time. Methods: In the present study, a total number of 180 samples belonging to RIRI (n = 30), RIRII (n = 30), BARI (n = 30), BARII (n = 30), L-54 (n = 30), and COL (n = 30) lines were genotyped using 22 microsatellite loci. Microsatellite markers are extremely useful tools in the identification of genetic diversity since they are distributed throughout the eukaryotic genome in multitudes, demonstrate co-dominant inheritance and they feature a high rate of polymorphism and repeatability. Results: In this study, we found all loci to be polymorphic and identified the average number of alleles per locus to be in the range between 4.41 (BARI) and 5.45 (RIRI); the observed heterozygosity to be in the range between 0.31 (RIRII) and 0.50 (BARII); and $F_{IS}$ (inbreeding coefficient) values in the range between 0.16 (L-54) and 0.46 (RIRII). The $F_{IS}$ values obtained in this context points out to a deviation from Hardy-Weinberg equilibrium due to heterozygote deficiency in six different populations. The Neighbour-Joining tree, Factorial Correspondence Analysis and STRUCTURE clustering analyzes showed that six brown layer lines were separated according to their genetic origins. Conclusion: The results obtained from the study indicate a medium level of genetic diversity, high level inbreeding in chicken lines and high level genetic differentiation between chicken lines.

• Animal Bioscience
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• v.35 no.8
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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.

• Journal of Plant Biotechnology
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• v.47 no.4
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• pp.298-308
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• 2020

Genetic diversity among Thaumatococcus daniellii populations in the southwestern region of Nigeria were assessed using morphometric and molecular markers to determine the population structure and existing genetic relationship for its improvement, conservation and sustainable utilisation. Populations from five locations in each of the six states were used for the study. Morphometric data were collected on folia characters and analysed for variability. Genome DNA was isolated from the plant leaf and amplified by polymerase chain reaction with inter-simple sequence repeat markers (ISSR) to determine the allelic polymorphism, marker effectiveness and genetic relationship of the population. The results showed significant variations in petiole length and leaf dimensions of the populations within and across the states. These morphometric traits are the major parameters that delimit the populations and they correlated significantly at P≤0.05. Analysis of the electrophoregram showed that the ISSR markers are effective for the diversity study. A total of 136 loci were amplified with an average of 7.16 loci per marker, 63.2% of the loci were polymorphic. The Principal Coordinate Analysis revealed that seven factors accounted for 81.6% of the variation and the dendrogram separated the populations into two major groups at a genetic distance of 10 (about 90% similarity) with sub-groups and clusters. Most populations within the state had a high degree of similarity, nonetheless, strong genetic relationship exists among populations from different states. The close relationship between populations across the states suggests a common progenitor, which are likely separated by ecological or geographical isolation mechanisms.

• Journal of Mushroom
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• v.20 no.2
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• pp.43-49
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• 2022

Pleurotus ostreatus is a globally cultivated mushroom crop. Cap color is a quality factor in P. ostreatus. However, cap color can spontaneously mutate, degrading the quality of the mushroom on the market. Early detection and removal of mutant strains is the best way to maintain the commercial value of the crop. To detect the cap color mutant Gonji7ho, molecular markers were developed based on insertion/deletions (InDels) derived from the comparison of mitogenomes of Gonji7ho and Gonji7hoM mushrooms. Sequencing, assembly, and comparative analysis of the two mitogenomes revealed genome sizes of 73,212 bp and 72,576 bp with 61 and 57 genes or open reading frames (ORFs) in P. ostreatus Gonji7ho and Gonji7hoM, respectively. Fourteen core protein-encoding genes, two rRNA, and 24 tRNA with some OFRs were predicted. Of the 61 genes or OFRs in the wild type, dpo, rpo, and two orf139 were missing (or remnant) in the mutant strain. Molecular markers were developed based on the sequence variations (InDels) between the two mitogenomes. Six polymorphic molecular markers could detect the mutated mitochondria by PCR. These results provide basic knowledge of the mitogenomes of wild-type and mutant P. ostreatus, and can be applied to discriminate mutated mitochondria.

• Journal of Plant Biotechnology
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• v.50
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• pp.190-199
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• 2023

Date palm (Phoenix dactylifera L.: Arecaceae) is a dioecious species where only female trees bear fruits. In their natural state, date palms produce dates once a year. However, in Thailand, some trees were observed to produce dates during the off-season, despite no variations in morphology. The availability of such off-season fruits can significantly increase their market value. Interestingly, most female off-season date palms investigated in this study were obtained through micropropagation. Hence, there is an urgent need for genetic markers to distinguish female offseason flowering plantlets within tissue culture systems. In this study, we aimed to develop random amplification of polymorphic DNA-sequence characterized amplified region (RAPD-SCAR) markers for the identification of female off-season flowering date palms cultivated in Thailand. A total of 160 random decamer primers were employed to screen for specific RAPD markers in off-season flowering male and female populations. Out of these, only one primer, OPN-02, generated distinct genomic DNA patterns in female off-season flowering (FOFdp) individuals compared to female seasonal flowering genotypes. Based on the RAPD-specific sequence, specific SCAR primers denoted as FOFdpF and FOFdpR were developed. These SCAR primers amplified a single 517-bp DNA fragment, predominantly found in off-season flowering populations, with an accuracy rate of 60%. These findings underscore the potential of SCAR marker technology for tracking offseason flowering in date palms. Notably, a BLAST analysis revealed a substantial similarity between the SCAR marker sequence and the transcript variant mRNA from Phoenix dactylifera encoding the SET DOMAIN GROUP 40 protein. In Arabidopsis, this protein is involved in the epigenetic regulation of flowering time. The genetic potential of the off-season flowering traits warrants further elucidation.

• Korean Journal of Medicinal Crop Science
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• v.21 no.5
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• pp.353-360
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• 2013

Korean ginseng (P. ginseng C. A. Meyer) is one of the most important medicinal plant in the world. Understanding genetic variability among the assortment of Korean ginseng is important for breeding. The aim of this study was to molecularly characterize Korean ginseng cultivar and breeding lines through the use of eight previously reported STS markers (MFGp183, MFGp130, MFGp110, UFGp74, UFGp163, MFGp108, MFGp81 and UFGp156). All STS markers produced interpretable electropherograms from 31 accessions consisting of 11 Korean ginseng cultivars and 20 breeding lines. When eight STS markers were combined, we identified to total 19 genetic patterns; in particular, nine cultivars (Chunpoong, Yunpoong, Gopoong, Gumpoong, Sunpoong, Sunone, Cheongseon, Sunhyang, Cheonryang) and 5 breeding lines (G08012, G04079, G04075, G08036, G04110) in ginseng samples can be discriminated from the others. Together with other available markers, these STS markers will contribute to the management of ginseng genetic resources and the protection of breeders' rights.

• Clinical and Experimental Reproductive Medicine
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• v.32 no.1
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• pp.17-26
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• 2005

Objective: Preimplantation genetic diagnosis (PGD) is reserved for couples with a risk of transmitting a serious and incurable disease, and hence avoids the undesirable therapeutic abortion. In this study, we evaluated the efficacy of PGD for Duchenne muscular dystrophy (DMD) cases by the fluorescent PCR with polymorphic linked markers and the conventional duplex-nested PCR methods. Methods: Biopsy of one or two blastomeres was done from the embryos fertilized by ICSI on the third day after fertilization. We performed two cases of PGD-DMD by the duplex-nested PCR for the causative mutation loci and the SRY gene on Y chromosome. The triplex fluorescent PCR for the mutation loci, the SRY gene and the polymorphic microsatellite marker on X chromosome was applied for two cases of PGD-DMD. Results: By the duplex-nested PCR, successful diagnosis rate was 95.5% (21/22), but we could not discriminate the female embryos whether normal or carrier in this X-linked recessive disease. However, the triplex fluorescent PCR method showed 100% (27/27) of successful diagnosis rate, and all female embryos (n=17) were distinguished normal (n=10) from carrier (n=7) embryos. Unaffected and normal embryos were transferred into mother's uterus after diagnosis. A healthy normal male was achieved after PGD with the duplex-nested PCR method and a twin, a male and a female, were delivered with triplex fluorescent PCR method. The normality of dystrophin gene was confirmed by amniocentesis and postnatal genetic analysis in all offsprings. Conclusion: The fluorescent PCR with polymorphic marker might be useful in improving the specificity and reliability of PGD for single gene disorders.

• Journal of Life Science
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• v.21 no.10
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• pp.1434-1442
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• 2011

A genetic variation within 29 strains of F. velutipes was analyzed by internal transcribed spacer (ITS) sequence analysis and random amplified polymorphic DNA (RAPD). Seven hundred and twenty base pairs were sequenced during the analysis of the ITS region, but no significant variation was observed among the 29 strains of F. velutipes. Sixteen out of 40 random primers amplified polymorphic RAPD fragment patterns. The polymorphic levels of RAPD bands by some primers (OPA-2,4,3,9,10,20) were very high in all 29 strains, with 3,030 fragments ranging between 200 and 2,000 bp. Intraspecific genetic dissimilarity of the 29 strains was calculated to range from 3.3% to 45% by Nei-Li's method using these 3,030 RAPD bands. The genetic variation among Korean strains was relatively high, with dissimilarities ranging between 17% and 38.6%. In the Neighbor-Joining analysis using the genetic dissimilarities based on RAPD, all 29 strains were classified into 5 clusters. Strains in each cluster showed specific characteristics according to their origin and strains. These results suggested that OPA and OPB primers could be used for developing molecular genetic markers and screening of unidentified (F. velutipes) strains.

• Development and Reproduction
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• v.5 no.2
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• pp.151-158
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• 2001

Genomic DNA from the blood of crucian carp(Carassius carassiu) from lake and aquaculture facility in Kunsan, Korea was extracted in order to identify genetic differences by polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD). Out of 12 primers, 6 generated 266 highly reproducible RAPD markers, producing approximately 2.1 polymorphic bands per primer in crucian carp from lake. The degree of similarity varied from 0.18 to 0.76 as calculated by bandsharing analysis in crucian carp from lake. The RAPD outlines obtained with DNA of two different crucian carp populations from Kunsan were different(0.47 from lake and 0.70 from aquaculture facility, respectively). The electrophoretic analysis of polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD) products showed high levels of similarity between different individuals in crucian carp from aquaculture facility. This result implies the genetic similarity due to raising in the same environmental condition or inbreeding within the crucian carp from aquaculture facility in Kunsan. In other words, crucian carp may have high levels of genome DNA diversity due to the introduction of the wild population from the other sites of Knsan even if it may be the geographical diverse distribution of this species. Generally, the RAPD polymorphism generated by these primers may be useful as a genetic marker for strain or population identification of important aquacultural fish species, crucian carp. However, in future, additional populations and sampling sites will be necessary to complement weak points.

• Journal of Plant Biotechnology
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• v.44 no.3
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• pp.303-311
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• 2017

In this study, random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analyses were used for evaluation of genetic diversity of 61 kiwifruit (Actinidia spp.) germplasms including domestic and overseas collection cultivars. Forty RAPD primers were detected in a total of 230 polymorphic bands with an average of 5.75. Thirty-two SRAP primer combinations were detected in a total of 204 polymorphic bands with an average 6.38. By unweighted pair-group method arithmetic average cluster analysis using 434 polymorphic bands, kiwifruit germplasms were classified in three groups with similarity value of 0.680. Cluster I consisted of 46 kiwifruit germplasms belonging to A. deliciosa, A. chinensis, A. deliciosa ${\times}$ A. arguta, A. chinensis ${\times}$ A. arguta, and A. chinensis ${\times}$ A. deliciosa. Cluster II consisted of seven germplasms belonging to A. arguta and 'Skinny Green', a cultivar derived from a cross between A. arguta and A. deliciosa. Cluster III consisted of seven germplasms belonging to A. rufa, A. hemsleyana, A. macrosperma, A. polygama, and A. eriantha. Genetic similarity values among tested kiwifruit germplasms ranged from 0.479-0.991, and average similarity value was 0.717. Similarity value was highest (0.991) between NHK0038 (A. deliciosa) and NHK0040 (A. deliciosa), and lowest (0.479) between 'Hayward' (A. deliciosa) and K5-1-22 (A. arguta).