• Asian-Australasian Journal of Animal Sciences
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• v.8 no.4
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• pp.357-364
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• 1995

A biochemical genetic study on blood enzyme/protein systems in some breeds/crosses of sheep in Malaysia was carried out using horizontal starch gel electrophoresis. Blood samples were collected from 435 sheep, representing 8 breeds/crosses. These included 5 wool sheep breeds (Thai Longtail, wiltshire, Suffolk, Dorsimal and cMBLx), 1 hair sheep breed (Barbados Blackbelly) and 2 hybrids between wool sheep and hair sheep (Cameroon ${\times}$ Thai Longtail and Bali Bali ${\times}$ Malin). Twenty loci systems were examined. Of these, ten ($HB{\beta}$, ALB, TF, XP, CAT, DIA1, EsA, GPI, ME and NP) exhibited genetic variation whereas the other ten (AAT, CA, DIA2, ${\alpha}GLO$, ${\alpha}GLU$, LDH, MDH, PEP[leu-gly-gly], 6PGD and SOD) were monomorphic. The allelic frequencies which were obtained in 10 polymorphic markers are assessed and compared with the results obtained by previous workers. The estimations of inbreeding coefficient, intrabreed variation and breed relationships have been critically discussed and are used to reveal some important recommendations.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.1-11
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• 2016

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.

• Korean Journal of Plant Resources
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• v.22 no.3
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• pp.227-235
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• 2009

Single seeds of common buckwheat cultivar Suwon No. 1 when subjected to SDS-PAGE revealed very high polymorphism. High variation existed for protein or protein subunits with molecular weight 54-47kDa, 45-25kDa and 16-11kDa. The electrophoregram showed variation for globulin as well as other protein fractions. About 300 proteins were separated by two-dimensional electrophoresis in common buckwheat (Fagopyrum esculentum Moench.) seed. Seed maturation is a dynamic and temporally regulated phase of seed development that determines the composition of storage proteins reserves in mature seeds. Buckwheat seeds from 5, 10, 15, 20, and 25 days after pollination and matured stage were used for the analysis. This led to the establishment of high-resolution proteome reference maps, expression profiles of 48 spots. It was identified 48 proteins from MALDI-TOF/MS analysis of wild buckwheat seed storage proteins. The 48 proteins were found identical or similar to those of proteins reported in buckwheat and other plants; it is belonging to 9 major functional categories including seed storage proteins, stress/defense response, protein synthesis, photosynthesis, allergy proteins, amino acid, enzyme, metabolism, and miscellaneous. It appears that the major allergenic storage protein separated played the important role in buckwheat breeding and biochemical characterization.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.913-920
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• 2012

In this study, we investigated the relationship between unsaturated fatty acids influencing beef flavor and four types of SNPs (c.280A>G, c.388G>A, c.408G>C and c.456A>G) located at exon 2, 3 and 4 of the FABP4 gene, which is a fatty acid binding protein 4 in Korean cattle (n = 513). When analyzing the relationship between single genotype, fatty acids and carcass trait, individuals of GG, GG, CC and GG genotypes that are homozygotes, had a higher content of unsaturated fatty acids and marbling scores than other genotypes (p<0.05). Then, haplotype block showed strong significant relationships not only with unsaturated fatty acids (54.73%), but also with marbling scores (5.82) in $ht1{\times}ht1$ group (p<0.05). This $ht1{\times}ht1$ group showed significant differences with unsaturated fatty acids and marbling scores that affected beef flavor in Korean cattle. Therefore, it can be inferred that the $ht1{\times}ht1$ types might be valuable new markers for use in the improvement of Korean cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.309-319
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• 2017

Objective: Holsteins are known as the world's highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data. Methods: This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits. Results: We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein. Conclusion: This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.2
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• pp.157-165
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• 2002

Genetic variations of seven egg white protein loci in 1,112 samples from eight Asian countries (Yunnan province of China, Mongolia, Nepal, Vietnam, Laos, Thailand, Myanmar, Indonesia) and 360 samples from two improved breeds (Isa Brown, Boris Brown) were investigated by using starch gel and polyacrylamide gel electrophoresis. Five egg white protein loci (Ov, $G_3$, $G_2$, $G_1$ and $Tf_{EW}$) were found to be polymorphic in Asian native chicken populations. The proportion of polymorphic loci ($P_{poly}$) and average heterozygosity ($\bar{H}$) of Asian native populations varied from 0.143 to 0.714 and 0.014 to 0.225, respectively, and were higher than those of improved breeds. The subdivision index ($G_{ST}$) value among 18 native chicken populations in Asia is lower (0.0827) than among improved chicken populations (0.1693). This value means that the degree of subdivision among Asian native populations is lower than among improved breeds and gene constitutions among populations in Asia are similar.

• Parasites, Hosts and Diseases
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• v.52 no.1
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• pp.105-109
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• 2014

Plasmodium falciparum malaria is a major public health problem in Thailand due to the emergence of multidrug resistance. The understanding of genetic diversity of malaria parasites is essential for developing effective drugs and vaccines. The genetic diversity of the merozoite surface protein-1 (PfMSP-1) and merozoite surface protein-2 (PfMSP-2) genes was investigated in a total of 145 P. falciparum isolates collected from Mae Sot District, Tak Province, Thailand during 3 different periods (1997-1999, 2005-2007, and 2009-2010). Analysis of genetic polymorphisms was performed to track the evolution of genetic change of P. falciparum using PCR. Both individual genes and their combination patterns showed marked genetic diversity during the 3 study periods. The results strongly support that P. falciparum isolates in Thailand are markedly diverse and patterns changed with time. These 2 polymorphic genes could be used as molecular markers to detect multiple clone infections and differentiate recrudescence from reinfection in P. falciparum isolates in Thailand.

• Parasites, Hosts and Diseases
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• v.60 no.6
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• pp.393-400
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• 2022

Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n=34) were combined with those from the previous study (n=26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π=0.0172) than exon I (π=0.0128). The diversity of the total coding region (π=0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π=0.0041) and PvRAP1 (π=0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6299-6303
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• 2012

Insulin-like growth factor-binding protein-3 (IGFBP3) has been identified as a putative tumor suppressor with multifunctional roles in the IGF axis. Recently, there have been a growing body of studies investigating the relation between the IGFBP3 A-202C polymorphism, circulating IGFBP3 and prostate cancer risk, but their outcomes varied leading to controversy. Hence, it is necessary to perform a meta-analysis covering all eligible studies to shed a light on the association of IGFBP3 A-202C and cancer risk. Finally, we included a total of 11 relevant articles between 2003 and 2010 covering 14 case-control studies including 9,238 cases and 8,741 controls for our analysis. Our results showed that A-202C was a marginal risk factor of prostate cancer (allele contrast: OR=1.08, 95% CI :1.01-1.16; dominant model: OR=1.11, 95% CI :1.01-1.22; heterozygote codominant model: OR=1.11, 95% CI :1.03-1.18; homozygote contrast: OR=1.19, 95% CI :1.03-1.37). Stratification analysis revealed that sample size and control source were two major heterogeneous meta-factors especially in the recessive model (source: Population-based control group :p=0.30,I2=16.7%, Hospital-based control group: p=0.20, I2=30.3%; sample size: Small: p=0.22,I2= 32.8%, Medium: p=0.09,I2=48%, Large p=0.60,I2=0.0%); However, contrary to previous findings, no significance was found in racial subgroups. No significant publication bias was found in our analysis. Considering the robustness of the results and the discrepancy among some studies, there might be some unsolved confounding factors, and further more critical large studies are needed for confirmation.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.938-943
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• 2017

Objective: Qingyu pig, a Chinese indigenous pig breed, exhibits two types of coat colour phenotypes, including pure black and white with black spotting respectively. Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two widely reported pivotal genes that significantly affect the regulation of coat colour. The objectives of this study were to investigate whether the polymorphisms of these two genes are associated with coat colour and analyze the molecular mechanism of the coat colour separation in Qingyu pig. Methods: We studied the phenotype segregation and used polymerase chain reaction amplification and Sanger sequencing to investigate the polymorphism of MC1R and ASIP in 121 Qingyu pigs, consisting of 115 black and 6 white with black spotted pigs. Results: Coat colour of Qingyu pig is associated with the polymorphisms of MC1R but not ASIP. We only found 2 haplotypes, $E^{QY}$ and $E^{qy}$, based on the 13 observed mutations from MC1R gene. Among which, $E^{qy}$ presented a recessive inheritance mode in black spotted Qingyu pigs. Further analysis revealed a g.462-463CC insertion that caused a frameshift mutation and a premature stop codon, thus changed the first transmembrane domain completely and lost the remaining six transmembrane domains. Altogether, our results strongly support that the variety of Qingyu pig's coat colour is related to MC1R. Conclusion: Our findings indicated that black coat colour in Qingyu pig was dominant to white with black spotted phenotype and MC1R gene polymorphism was associated with coat colour separation in Qingyu pig.