• Genomics & Informatics
• /
• 제13권4호
• /
• pp.137-145
• /
• 2015

Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc. These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

• 한국동물생명공학회지
• /
• 제38권3호
• /
• pp.177-187
• /
• 2023

Background: The grading of Hanwoo (Korean native cattle) is based on four economic traits, and efforts have been continuously made to improve the genetic traits associated with these traits. There is a technology to predict the expected grade based on the 4 economic genetic SNP characteristics of Korean cattle calves using single nucleotide polymorphism (SNP) technology. Selection of highly proliferative, self-renewing, and differentiating satellite cells from cattle is a key technology in the cultured meat industry. Methods: We selected the Hanwoo with high and low-scored of genomic estimated breeding value (GEBV) by using the Hanwoo 50K SNP bead chip. We then isolated the bovine satellite cells from the chuck mass. We then conducted comparative analyses of cell proliferation, immunocytochemistry, qRT-PCR at short- and long-term culture. We also analyzed the differentiation capability at short term culture. Results: Our result showed that the proliferation was significantly high at High scored GEBV (Hs-GEBV) compared to Low scored GEBV (Ls-GEBV) at short- and long-term culture. The expression levels of Pax3 were significantly higher in Hs-GEBV bovine satellite cells at long-term culture. However, there were no significant differences in the expression levels of Pax7 between Hs- and Ls-GEBV bovine satellite cells at short- and long- term culture. The expression levels of MyoG and MyHC were significantly high at Ls-GEBV bovine satellite cells. Conclusions: Our results indicated that selection of bovine satellite cells by Hanwoo 50K SNP bead chip could be effective selection methods for massive producing of satellite cells.

• Asian-Australasian Journal of Animal Sciences
• /
• 제33권5호
• /
• pp.753-762
• /
• 2020

Objective: The aim of the present study was to determine the effect of supplementing pasture-finished steers with corn silage on the expression level of the calpain system proteins and beef tenderization. Methods: Thirty Braford steers grazing on summer pasture were used for the study. For 120 days fifteen animals were supplemented with corn silage at 1% of body weight per head per day (Suppl) whereas the remaining 15 steers only received pasture (Contr). Carcass and meat traits were evaluated and compared between groups. Gene expression and activities of proteases (calpain 1 and calpain 2) and inhibitor (calpastatin) were measured using real-time polymerase chain reaction and casein zymography. Results: Carcass and meat traits were significantly different between feeding systems. Supplemented steers showed higher hot carcass weight (p<0.01), fat content (p = 0.02), and Warner-Bratzler shear force (p = 0.03). Furthermore, the control group showed higher protease:inhibitor ratios, at mRNA (p = 0.01) and protein levels (p<0.10). Warner-Bratzler shear force and mRNA calpains:calpastatin ratio were associated in both feeding systems (p<0.01). Conclusion: Based on the results obtained in the study, beef tenderness differences among finishing strategies could be modulated through differential expression of the calpain system proteins.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권11호
• /
• pp.1721-1728
• /
• 2018

Objective: The use of genetic markers can help to enhance reproduction in cattle, which is a very important trait for profitability in dairy production systems. This study evaluated the association between genotypes of leptin (LEP), toll-like receptor 4 (TLR4), and chemokine receptor of interleukin 8 C-X-C motif (CXCR1) genes and fertility traits in Czech Fleckvieh cattle. Methods: Phenotypic data from 786 Czech Fleckvieh cows raised on 5 farms in the Czech Republic were used, along with information from the 1st three parities. To determine genotype, the polymerase chain reaction-restriction fragment length polymorphism method was used. Results: Except for LEP g.-963C>T, all studied genotype frequencies of single nucleotide polymorphisms (SNPs) were distributed according to the Hardy-Weinberg equilibrium. Two LEP SNPs (g.-963C>T and c.357C>T) were associated with the age at the 1st calving, days open (DO), pregnancy rate after 1st service (PR), and calving interval (CLI). In LEP g.-963C>T the TT genotype heifers firstly calved 24 days earlier than CC genotype and the CT genotype cow showed a tendency for shorter DO and higher PR. In LEP c.357C>T we observed longer CLI and DO period in TT cows. In general, we can propose the TT genotype of g.-963C>T as favorable and the TT genotype of c.357C>T as unfavorable for a cow's fertility. Heterozygotes in TLR4 c.-226C>G were significantly associated with shorter CLI, and presented a nonsignificant tendency to be associated with higher PR. In CXCR1 c.777 C>G, we did not observe any relationship of this SNP with reproduction. Conclusion: Overall, the results showed that LEP could be an effective marker for improving reproduction in Czech Fleckvieh cattle. This study also provides novel insights into the relationship between TLR4 and CXCR1 SNPs and reproduction in dual-purpose cattle.

• Asian-Australasian Journal of Animal Sciences
• /
• 제20권3호
• /
• pp.453-460
• /
• 2007

An overview of developments important in the future of animal breeding is discussed. Examples from the application of quantitative genetic principles to selection in chickens and mice are given. Lessons to be learned from these species are that selection for production traits in livestock must also consider selection for reproduction and other fitness-related traits and inbreeding should be minimized. Short-term selection benefits of best linear unbiased predictor methodology must be weighed against long-term risks of increased rate of inbreeding. Different options have been developed to minimize inbreeding rates while maximizing selection response. Development of molecular genetic methods to search for quantitative trait loci provides the opportunity for incorporating marker-assisted selection and introgression as new tools for increasing efficiency of genetic improvement. Theoretical and computer simulation studies indicate that these methods hold great promise once genotyping costs are reduced to make the technology economically feasible. Cloning and transgenesis are not likely to contribute significantly to genetic improvement of livestock production in the near future.

• 한국가축번식학회지
• /
• 제22권4호
• /
• pp.359-366
• /
• 1998

본 조사연구는 산차에 따른 한우 번식우의 초종부, 초임 및 초산일령과 분만후 발정재귀일수, 수태당 종부회수, 분만후 수태일수, 분만간격 등을 검토하기 위하여 1996년 1월부터 1997년 12월까지 20농가에서 사육중인 한우 성빈우 670두를 대상으로 조사를 수행하였다. 1. 한우 미경산우의 초종부일령은 평균 443.0일이었고 초임일령은 평균 457.0 일이었으며 초산일령은 평균 746.6 일이었다. 2. 산차에 따른 분만후 발정재귀일수는 평균 70.1일이었고 산차별로는 2산차, 3산차, 4산차, 5산차 이상이 각각 70.5일, 66.4일, 79.7일, 60.4일로 5산차 이상이 가장 빨랐고 (p＜0.05), 4산차가 가장 늦은 경향을 나타내었다 (p＜0.05). 3. 산차에 따른 수태당 종부회수는 평균 1.53 회였고 미경산우, 2.산차, 3산차, 4산차 및 5산차가 각각 1.56 회, 1.43회, 1.48회, 1.67회 및 1.73회로 2산차가 가장 적었고 (p＜0.005) 5산차 이상이 가장 많았으며 (p＜0.05) 미경산우를 제외하고는 산차가 증가함에 따라 수태당 종부회수가 증가하는 경향을 나타내었다. 4. 산차에 따른 분만후 수태일수는 평균 91.2 일이었고 산차별로는 2산차, 3산차, 4산차, 5산차 이상이 각각 86.9일, 89.6일, 104.5일 및 107.0일로 산차간에 유의적인 차이는 인정되지 않았으나 (p＞0.05) 대체로 산차가 증가함에 따라 길어지는 경향을 나타내었다. 5. 산차에 따른 분만간격은 평균 375.3 일이었고 산차별로는 2산차, 3산차, 4산차 및 5산차 이상이 각각 370.8 일, 371.0일, 395.2일 및 383.9일로 2산차가 가장 짧았고 (p＜0.05) 4 산차가 가장 긴(p＜0.005) 경향을 나타내었다.

• Animal Bioscience
• /
• 제35권9호
• /
• pp.1340-1350
• /
• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Asian-Australasian Journal of Animal Sciences
• /
• 제18권2호
• /
• pp.179-184
• /
• 2005

First lactation records (174) of Jersey${\times}$Sahiwal and Holstein Friesian${\times}$Sahiwal half breds under 9 sires maintained at Chandra Shekher Azad University of Agriculture and Technology, Kanpur, Uttar Pradesh, India from 1975-1983, were used to estimate the genetic parameters and to predict herd life milk yield and average milk yield per day of herd life from first lactation traits. The traits included were: age at first calving, first service period, first lactation period, first calving interval, first lactation milk yield, milk yield per day of first calving interval, herd life milk yield, herd life and average milk yield per day of herd life. Most of the production and reproduction traits were found to have positive and significant correlations between them on genetic as well as phenotypic scales. Total twelve regression equations were fitted. The prediction equation of herd life milk yield in both the genetic groups showed linear relationship with AFC, FSP, FLP, FLMY and MY/DCI and was apparent and significant. Similarly, polynomials for milk yield per day of herd life for J${\times}$S and HF${\times}$S half breds also showed linear trend, which was found highly significant. The highest and lowest $R^2$ values were found for FCI and AFC, respectively.

• Asian-Australasian Journal of Animal Sciences
• /
• 제15권5호
• /
• pp.695-698
• /
• 2002

Performance data (from 1985 to 2000) of Jersey cattle imported from USA and maintained at Islamabad, Pakistan were evaluated. The purpose of this study was to assess the genetic merit of Jersey breed under Pakistani environment for further propagation. Cows with at least two calvings were considered for this study; records on 50 daughter-dam pairs were available on production and reproduction performance traits for genetic evaluation. The average age at first calving in parents was $25.2{\pm}2.4$ m as compared to $23.9{\pm}6.6$ m in progeny. Calving interval in parents and progeny was $416{\pm}74$ and $446{\pm}105$ d; lactation length $301{\pm}51$ and $325{\pm}73$ d; lactation milk yield $2,908{\pm}669$ and $2,707{\pm}903$ lit respectively. All these differences were found to be statistically significant except lactation length. The correlations between age at first calving and total lactation milk was -0.25, between calving interval and total lactation milk yield was 0.14, and between lactation length and total lactation milk yield was 0.79. The $h^2$ of these traits were low indicating important role of environment in expressing the genetic potential of animals. The S.E of $h^2$ of all the traits was high due to large variation in data.

• Animal cells and systems
• /
• 제16권2호
• /
• pp.135-144
• /
• 2012

$Dendronephthya$ $castanea$ Utinomi, 1952 is a member of the family Nephtheidae, and dominates shallow waters adjacent to the southern part of Jejudo Island, Korea. This species is a gonochoric internal brooder with a sex ratio of 1:1, and releases planulae around the time of the full and new moon from July to September, when the seawater temperature peaks. The gametogenic cycle is annual, and oogenesis (12 months) is longer than spermatogenesis (4-5 months). No difference in reproductive features including sexuality, sex ratio, gametogenesis and gametogenic cycles was found between the sympatric species $D.$ $castanea$ and $D.$ $gigantea$, and there was no temporal reproductive isolation. Investigation of the morphological taxonomy and molecular biology of these species indicates that they have very similar or identical traits, suggesting an absence of speciation and a need for taxonomic reclassification.