• Asian-Australasian Journal of Animal Sciences
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• v.19 no.5
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• pp.622-626
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• 2006

Molecular characterization of Hallikar, the native cattle breed of Karnataka, was undertaken using 19 cattle specific, highly polymorphic microsatellite markers recommended by FAO. The genomic DNA was subjected to PCR amplification and alleles were resolved through six per cent denaturing PAGE with a 10 bp DNA ladder followed by silver staining. Genotyping of animals was done based on allele size. The number of alleles ranged from three to nine with allele sizes ranging from 102 bp to 294 bp. These alleles were distributed in the frequency range between 0.0306 and 0.8673 in the population. The mean observed number of alleles was $6.368{\pm}1.4225$. The mean observed and expected heterozygosities were $0.7515{\pm}0.1734$ and $0.7850{\pm}0.1381$, respectively. The high heterozygosity observed implies presence of higher genetic variability within Hallikar breed. The PIC (Polymorphism Information Content) values ranged from 0.2322 (ETH152) to 0.8654 (ETH225). The percentage of polymorphic loci obtained was 100 as all the 19 microsatellite markers were found to be polymorphic. Except for ETH152, all the other loci had high PIC values, indicating that these markers are highly informative for characterization of Hallikar breed. The population was tested for Hardy-Weinberg equilibrium at 19 microsatellite loci, and at 74 per cent of the loci the population was found to be in disequilibrium.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1221-1225
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• 2005

The peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear hormone receptors. Lots of studies in rodents and humans have shown that PPARs were involved in lipid metabolism and adipocyte differentiation. The main objective of this work was to detect the single nucleotide polymorphisms (SNPs) in whole coding regions of peroxisome proliferator-activated receptor alpha (PPAR-$\alpha$) and gamma (PPAR-$\gamma$) genes with approach of single strand conformation polymorphism (SSCP) in the chicken population of Arber Acres broiler, Hyline layer and three Chinese native breeds (Shiqiza, Beijing You, Bai'r). Two SNPs of C1029T and C297T were found in chicken PPAR-$\alpha$ and PPAR-$\gamma$ genes respectively and each SNP found three genotypes in the experimental populations. The results showed that the distribution frequency of 3 genotypes in Arber Acres broiler, Hyline layer and Chinese native breeds had significant differences on the PPAR-$\alpha$ and PPAR-$\gamma$ gene respectively (p<0.01). Furthermore, in the PPAR-$\alpha$ gene, the results of least square estimation for genotypes and body composition traits showed the BB genotype birds had higher abdominal fat weight (AFW) and percentage of abdominal fat (AFP) than AA genotype birds (p<0.05). From these we conjecture the PPAR-$\alpha$ and PPAR-$\gamma$ genes were suffered intensive selection during the long term commercial breeding and the PPAR-$\alpha$ gene may be a major gene or linked to the major genes that impact chicken fat metabolism and the SNPs could be used in molecular assistant selection (MAS) as a genetic marker for the chicken fatness traits.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1399-1403
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• 2006

A total of 80 cows, including 40 top mastitis resistant and 40 top mastitis susceptible animals as Group I and Group II, were selected from a population of 520 cows based on clinical mastitis occurrence. PCR-SSCP analysis on four fragments within the 5'region and two fragments of Exons 4,15 of bovine lactoferrin (bLF) revealed that four fragments-P1,P4,E4,E15-had polymorphisms which totally included six base mutations, and only two of them had significant differences in allele frequencies between resistant and susceptible groups, P1 (53.7% vs. 70.0%, p<0.05) and P4 (55.0% vs. 68.8%, p<0.05). Further study on these two promising markers combined with the milk performance traits of cows demonstrated that their selection would result in higher fat percentage (p<0.05), lower Somatic Cell Score (SCS) (p<0.05) and Clinical Mastitis Residuals (CMR) (p<0.01) indicating higher mastitis resistance and lower milk yield (p<0.05). The putative transcription factor binding sites in the 5'region were also studied by using MatInspector 7.2.2 software, and two signal pathways regulating the expression of bLF including the NF-${\kappa}B$ pathway and nuclear hormone receptor pathway were predicted.

• Plant Breeding and Biotechnology
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• v.5 no.3
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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.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1542-1547
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• 2005

The Melanocortin-4 Receptor (MC4R) and Insulin-like Growth Factor 2 (IGF2) are two important candidate genes related to fat deposition and carcass traits. MC4R was found on study on human obesity and then was studied as candidate gene affecting food intake and fat deposition traits in mice and pigs. Insulin-like Growth Factor 2 (IGF2) gene plays an important role on tumor cell proliferation and muscle growth. It also affects fat traits and live weight in pigs. In this paper, MC4R and IGF2 were studied as two candidate genes associated with important economic traits such as fat deposition and carcass traits in five different pig populations. Taq I-PCR-RFLP and Bcn I-PCR-RFLP were respectively used to detect the polymorphism of genotypes of MC4R and IGF2 genes. Different MC4R genotype frequencies were observed in four populations. IGF2 genotype frequencies were also different in two populations. The results of association analysis show both MC4R and IGF2 genes were significantly associated with fat deposition and carcass traits in about 300 pigs. This work will add new evidence of MC4R and IGF2 affecting fat deposition and carcass traits in pigs and show that two genes can be used as important candidate genes for marker assistant selection (MAS) of growth and lean meat percentage in pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.10
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• pp.1404-1410
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• 2008

This study was performed to clarify whether the variation of stress related heat shock protein 70 (HSP70) (GenBank X68213) gene was associated with the nuclear morphological change of in vitro maturation and in vitro capacitation in oocytes of pig ovaries obtained at the slaughterhouse. The nucleic acid substitution of C to G at the 483rd position was found out in HSP70 K1 (290-512) from X68213. The ovaries were categorized into CC, CG, and GG genotypes using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) (BsiHKA I). After the second in vitro maturation of immature fresh oocytes, the relation of nuclear morphological change in oocytes with the genotype of HSP70 K1 gene was such that the MII ratios of the genotype GG and CG (46.93% and 42.20%, respectively) were significantly higher than that of the CC genotype (10.71%) (p<0.05). With respect to in vitro maturation of frozen-thawed oocytes by an open pulled straw (OPS) method, the percentage of oocytes matured to MII stage of the CG genotype showed a higher trend than CC and GG genotypes. After the in vitro maturation of immature fresh oocytes and frozen-thawed oocytes by the OPS method, the relation of the pronuclei change in oocytes matured in vitro with HSP70 genotype was assessed, and the result showed that the enlarged sperm heads (ESH) of matured fresh oocytes and frozen-thawed oocytes were 80.0% and 60.0% in the CC genotype, respectively. The CC genotype group had a significantly higher rate of ESH than the CG and the GG genotype group (p<0.05). The ratios of polyspermic invasion were not different among HSP70 of the three genotypes. It was considered that the rate of in vitro maturation of fertilized oocytes was expected to differ according to genotype of the stress related gene.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.2
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• pp.103-109
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• 2000

Complete senuences of the mitochondrial rRNA Benes were determined among six salmonines in Korean Waters (Brachpmystax lenok, Onoorhpchus keta, O. masou mason, O. mason ishikawae, O. mykiss, and albino mutant of O. mykiss). The purposes of this study were to provide the basic information on levels of mtDNA polymorphism among these species for genetic characterization; discuss phylogentic relationships among three Oncorhynchus sepecies; demonstrate the utility of rRNA gene sequence data as a genetic marker for disringuishinf among Korean salmonines. PCR/direct sequencing data indicated the following consistent results; 1) 12S rRNA genes was 945 bases long in Oncorhynchus species, and 946 bases in B. lenot including one insertion. 2) Of sequence variation in mitochondrial rRNA regions, transitional substitutions were superior to transversion. 3) The significant differences were not shown in the intraspecific variation values in these gene regions. The percentage sequence divergence values were ranged from $0.066 to 0.212{\%}$. 4) The interspecific divergences were greater than the intraspecific variation. Nevertheless, ribosomal RMh genes were more conserved among species than the other mitochondrial genes, and they showed potentiality as an intergenic marker for systematics. In addition, phylogenetic trees, constructed from this data, supported that cherry salmon was closer to chum salmon than to rainbow trout, and that lenok was most distantly related species in six salmonid species.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7781-7784
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• 2015

Background: The commonly held view of the tumor suppressor p53 is as a regulator of cell proliferation, apoptosis and many other biological processes as well as external and internal stress responses. Mdm2 SNIP309 is a negative regulator of p 53. Therefore, this study aimed to determine the correlation between the patterns of Mdm2 SNIP 309 and the inflammation grading of Helicobacter pylori associated gastritis in a Thai population. Materials and Methods: A cross-sectional study was carried out from November 2014 through June 2015. Biopsy specimens were obtained from infected patients and infection was proved by positive histology. The gastric mucosa specimens were sent to the Molecular Genetic Unit, Institute of Medicine, Suranaree University of Technology where they were tested by molecular methods to detect the patterns of Mdm2 SNIP 309 using the real-time PCR hybridization probe method. The results were analyzed and compared with the Updated Sydney classification. Results: A total of 100 infected patients were interviewed and gastric mucosa specimens were collected. In this study the percentage of Mdm2 SNIP 309 T/T homozygous and Mdm2 SNIP309 G/T heterozygous was 78% and 19 % respectively whereas Mdm2 SNIP309 G/G homozygous was 3%. Mdm2 SNIP 309 T/T homozygous and Mdm2 SNIP309 G/T heterozygous correlated with mild to moderate inflammation (P<0.01) whereas Mdm2 SNIP309 G/G homozygous correlated with severe inflammation (P<0.01). Conclusions: Our study found the frequency of Mdm2 SNP309 G/G in our Thai population to be very low, and suggests that this can explain to some extent the low incidence of severe inflammation and gastric cancer changes in the Thai population. Mild to moderate inflammation are the most common pathologic gradings due to the unique genetic polymorphism of Mdm2 SNIP 309 in the Thai population.

• Genomics & Informatics
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• v.15 no.1
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• pp.2-10
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• 2017

Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine. We compared the detection abilities of the QX200, RainDrop, and QuantStudio 3D dPCR systems. The QX200 was the most accurate and sensitive. Plasma and/or urine samples were isolated from 34 kidney recipients at multiple time points after transplantation, and analyzed by dPCR using the QX200. We found that donor DNA was almost undetectable in plasma DNA samples, whereas a high percentage of donor DNA was measured in urine DNA samples, indicating that urine is a good source of cfDNA for patient monitoring. We found that at least 24% of the highly polymorphic SNPs used to identify individuals could also identify donor cfDNA in transplant patient samples. Our results further showed that autosomal, sex-specific, and mitochondrial SNPs were suitable markers for identifying donor cfDNA. Finally, we found that donor-derived cfDNA measurement by dPCR was not sufficient to predict a patient's clinical condition. Our results indicate that donor-derived cfDNA is not an accurate predictor of kidney status in kidney transplant patients.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.7
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• pp.943-954
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• 2009

Diacylglycerol acyltransferase (DGAT) is a key enzyme that catalyzes the final and rate-limiting step of triglyceride synthesis. Both DGAT1 and DGAT2 genes code proteins with DGAT activity. Studies have shown DGAT1 polymorphisms associate with intramuscular fat deposition in beef cattle, but fewer associations between DGAT2 and beef cattle economic traits have been reported. The objective of this study was to investigate single nucleotide polymorphism (SNP) in intron3 of bovine DGAT2 and evaluate the associations of that with carcass, meat quality, and fat yield traits. Test animals were 157 commercial feedlot steers belonging to 3 Chinese native breeds (22 for Luxi, 24 for Jinnan, and 23 for Qinchuan), 3 cross populations (20 for Charolais${\times}$Fuzhou, 18 for Limousin ${\times}$Luxi, and 17 for Simmental${\times}$Jinan) and 1 Taurus pure breed population (16 Angus steers). In the current study, 15 SNP were discovered in intron3 and exon4 of DGAT2 at positions 65, 128, 178, 210, 241, 255, 270, 312, 328, 334, 365, 366, 371, 415, and 437 (named as their positions in PCR amplified fragments). Only 7 of them (128, 178, 241, 270, 312, 328, and 371) were analyzed, because SNP in three groups (65-128-255, 178-210-365 and 241-334-366) were in complete linkage disequilibrium within the group, and SNP 415 was a deletion and 437 was a null mutation. Frequencies for rare alleles in the 3 native breed populations were higher than in the 3 cross populations for 178 (p = 0.04), 270 (p = 0.001), 312 (p = 0.03) and 371 (p = 0.002). A general linear model was used to evaluate the associations between either SNP genotypes or allele substitutions and the measured traits. Results showed that SNP 270 had a significant association with the fat yield associated with kidney, pelvic cavity, heart, intestine, and stomach (KPHISY). Animals with genotype CC and CT for 270 had less (CC: -7.71${\pm}$3.3 kg and CT: -5.34${\pm}$2.5 kg) KPHISY than animals with genotype TT (p = 0.02). Allele C for 270 was associated with an increase of -4.26${\pm}$1.52 kg KPHISY (p = 0.006) and $-0.92{\pm}0.45%$ of retail cuts weight percentage (NMP, Retail cuts weight/slaughter body weight) (p = 0.045); allele G for 312 was associated with an increase of -5.45${\pm}$2.41 kg KPHISY (p = 0.026). An initial conclusion was that associations do exist between DGAT2 gene and carcass fat traits. Because of the small sample size of this study, it is proposed that further effort is required to validate these findings in larger populations.