• Asian-Australasian Journal of Animal Sciences
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• v.32 no.3
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• pp.320-333
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• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1342-1348
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• 2007

POU1F1 is a positive regulator for GH, PRL and TSH${\beta}$ and its mutations associate with production traits in ruminant animals. We described a DdeI PCR-RFLP method for detecting a silent allele in the goat POU1F1 gene: TCT (241Ser)>TCG (241Ser). Frequencies of $D_1$ allele varied from 0.600 to 1.000 in Chinese 801 goats. Significant associations of DdeI polymorphism with production traits were found in milk yield (*p<0.05), litter size (*p<0.05) and one-year-old weight (*p<0.05) between different genotypes. Individuals with genotype $D_1D_1$ had a superior performances when compared to those with genotype $D_1D_2$ (*p<0.05). Hence, the POU1F1 gene was suggested to the potential candidate gene for superior milk performance, reproduction trait and weight trait. Genotype $D_1D_1$, characterized by a DdeI PCR-RFLP detection, was recommended to geneticists and breeders as a molecular marker for better performance in the goat industry.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.163-169
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• 2012

Interferon regulatory factor 6 (IRF6) gene is a member of the IRF-family, and plays functionally diverse roles in the regulation of the immune system. In this report, the 13,720 bp porcine IRF6 genomic DNA structure was firstly identified with a putative IRF6 protein of 467 amino acids. Alignment and phylogenetic analysis of the porcine IRF6 amino acid sequences with their homologies to other species showed high identity (over 96%). Tissues expression of IRF6 mRNA was observed by RT-PCR, the results revealed IRF6 expressed widely in eight tissues. One SNP (HQ026023:1383 G>C) in exon7 and two SNPs (HQ026023:130 G>A; 232 C>T) in the 5′ promoter region of porcine IRF6 gene were demonstrated by DNA sequencing analysis. A further analysis of SNP genotypes associated with immune traits including IFN-${\gamma}$ and IL10 concentrations in serum was carried out in three pig populations including Large White, Landraces and Songliao Black pig (a Chinese indigenous breed). The results showed that the SNP (HQ026023:1383 G>C) was significantly associated with the level of IFN-${\gamma}$ (d 20) in serum (p = 0.038) and the ratio of IFN-${\gamma}$ to IL10 (d 20) in serum (p = 0.041); The other two SNPs (HQ026023:130 G>A; 232 C>T) were highly significantly associated with IL10 level in serum both at the day 20 (p = 0.005; p = 0.001) and the day 35 (p = 0.004; p = 0.006). Identification of the porcine IRF6 gene will help our further understanding of the molecular basis of the IFN regulation pathway in the porcine immune response. All these results should indicate that the IRF6 gene can be regarded as a molecular marker associated with the IL10 level in serum and used for genetic selection in the pig breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.11
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• pp.1721-1728
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• 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.

• Animal Bioscience
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• v.35 no.9
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• pp.1340-1350
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• 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
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• v.30 no.5
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• pp.666-671
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• 2017

Objective: Aim of the current comparative study was to evaluate production outputs, reproduction efficiency and functional traits in dual-purpose Fleckvieh and Braunvieh cows, reared under temperate European conditions. Methods: A data-set from 414 Fleckvieh and 42 Braunvieh cows and 799 lactations was analysed. ID tag number, milk yield per milking session, number of steps/interval and milk conductivity were recorded and collected daily using AfiMilk 3.076 A-DU software (Afimilk Ltd., Kibbutz, Israel). Production and milk quality data were taken from the results of the official performance recordings and the reproductive outputs of cows were recorded by the research stations veterinarians. Comparisons between the two genotypes were carried out using the one way analysis of variance protocol, with categorical factor being considered the breed of cows. All the statistical inferences were carried out using Statistica software (StatSoft Inc., Tulsa, OK, USA). Results: Fleckvieh cows significantly outperformed ($p{\leq}0.05$) the Braunvieh herd, with average milk yields of $5,252.1{\pm}35.79kg$ and $4,897.6{\pm}128.94kg$, respectively. Age at first calving was significantly ($p{\leq}0.01$) influenced by the breed, with Fleckvieh heifers being more precocious ($32.8{\pm}0.29mo$) compared to those of Braunvieh breed ($35.7{\pm}0.84mo$). Reproduction efficiency as defined by the number of inseminations per gestation, calving interval, dystocia, days dry and days open, was not influenced by genotype (p>0.05). Incidences of sub-clinical mastitis, clinical mastitis, lameness and abortions were not influenced by the breed factor (p>0.05). Stay-ability of cows was significantly ($p{\leq}0.001$) influenced by genotype, with Braunvieh cows having an average age at culling of $117.88{\pm}11.78$ months compared to $90.88{\pm}2.89$ months in Fleckvieh. Conclusion: Overall, results have shown that genotype significantly influenced milk yield, age at first calving and longevity.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.2
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• pp.237-244
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• 2018

Objective: Piglet pre-weaning mortality is an important variable indicating the efficacy of farrowing management and animal well-being during lactation. The present study determined the association of newborn traits measured soon after birth with piglet pre-weaning mortality and growth. Methods: In total, 805 piglets born from 57 multiparous sows were investigated. Their blood oxygen saturation, blood glucose and rectal temperature at 24 h after birth (RT24h) were monitored. Birth order, sex, skin color, integrity of the umbilical cord, attempts to stand and birth intervention were monitored. Piglets were weighed at day 0, 7, and 21 to evaluate average daily gain (ADG). Results: Piglet pre-weaning mortality for lactation period was 12.6% and cumulative mortality during the first 7 days of age was 8.6%. A higher proportion of piglets with pale skin color died compared to piglets with normal skin color (26.7% vs 7.7%, p<0.001). A higher (p<0.001) proportion of piglets that attempted to stand after 5 min (38.5%) died compared to piglets that attempted to stand within 1 min (6.3%) after birth. Piglet body weight at birth ($BW_B$), blood glucose and the number of piglets born alive (BA) were correlated with ADG (p<0.05). Piglets with $BW_B$ <1.30 kg had higher (p<0.001) mortality rate than piglets with $BW_B{\geq}1.80 kg$ (19.0% vs 3.3%) and piglets with $BW_B$ 1.30 to 1.79 kg (4.0%). Piglet with RT24h <$37.0^{\circ}C$ had higher (p<0.001) mortality rate (86.2%) than piglets with RT24h >$38.5^{\circ}C$ (3.9%). Conclusion: Low $BW_B$ and low RT24h compromise piglet survival during the lactation period in the tropical conditions. Piglets in the litters with a high BA, low $BW_B$ and low blood glucose have reduced ADG.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.777-789
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• 2020

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1353-1362
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• 2016

Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.3
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• pp.321-325
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• 2002

Karyotype analysis was carried out on blood samples of 30 water buffaloes belonging to different breed groups (i.e. Philippine Carabao (PC), Indian Murrah (IM), Bulgarian Murrah (BM), "$F_1$ 50% IM-50% PC", "$F_1$ 50% BM-50% PC" and "75% IM-25% PC"), using the modified Leucocyte Culture Technique. The modal chromosome numbers of the PC, "$F_1$ 50% IM-50% PC", "$F_1$ 50% BM-50% PC", IM, BM and "75% IM-25% PC" were 2n=48, 49, 49, 50, 50 and 50, respectively. The water buffalo chromosomes are mostly acrocentric (79.67%) and the remainder submetacentric (20.33%). Results of the ordinary least square analysis showed significant breed effects (p<0.01) on other karyotypic characteristics (i.e. relative length, arm ratio and centromeric index). Significant correlation between karyotypic characteristics and some animal performance traits were also found. The significant correlation values imply that karyotypic characteristics can be used as important criteria to select potentially productive young water buffaloes. In the future, more production and reproduction traits from non-institutional herds should be included in the analysis to reveal meaningful correlations with various karyotypic characteristics.