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Population diversity, admixture, and demographic trend of the Sumba Ongole cattle based on genomic data

  • Pita Sudrajad;Hartati Hartati;Bayu Dewantoro Putro Soewandi;Saiful Anwar;Angga Ardhati Rani Hapsari;Tri Satya Mastuti Widi;Sigit Bintara;Dyah Maharani
    • Animal Bioscience
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    • v.37 no.4
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    • pp.591-599
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    • 2024
  • Objective: Sumba Ongole (SO) cattle are valuable breed due to their important role in the development of Indonesian cattle. Despite rapid advances in molecular technology, no genomic studies on SO cattle have been conducted to date. The aim of this study is to provide genomic profile related to the population diversity, admixture, and demographic trends of SO cattle. Methods: Genomic information was gathered from 79 SO cattle using the Illumina Bovine SNP50 v3 Beadchip, and for comparative purposes, additional genotypes from 209 cattle populations worldwide were included. The expected and observed heterozygosity, inbreeding coefficient, pairwise fixation indices between-population, and Nei's genetic distance were examined. Multidimensional scaling, admixture, and treemix analyses were used to investigate the population structure. Based on linkage disequilibrium and effective population size calculations, the demographic trend was observed. Results: The findings indicated that the genetic diversity of SO cattle was similar to that of other indicine breeds. SO cattle were genetically related to indicines but not to taurines or Bali cattle. The study further confirmed the close relationship between SO, Ongole, and Nellore cattle. Additionally, a small portion of the Ongole mixture were identified dominant in the SO population at the moment. The study also discovered that SO and Bali cattle (Bos javanicus) could have been ancestors in the development of Ongole Grade cattle, which corresponds to the documented history of Ongolization. Our finding indicate that SO cattle have maintained stability and possess unique traits separate from their ancestors. Conclusion: In conclusion, the genetic diversity of the SO cattle has been conserved as a result of the growing significance of the present demographic trend. Consistent endeavors are necessary to uphold the fitness of the breed.

The spatio-temporal expression analysis of parathyroid hormone like hormone gene provides a new insight for bone growth of the antler tip tissue in sika deer

  • Haihua Xing;Ruobing Han;Qianghui Wang;Zihui Sun;Heping Li
    • Animal Bioscience
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    • v.37 no.8
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    • pp.1367-1376
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    • 2024
  • Objective: Parathyroid hormone like hormone (PTHLH), as an essential factor for bone growth, is involved in a variety of physiological processes. The aim of this study was to explore the role of PTHLH gene in the growth of antlers. Methods: The coding sequence (CDS) of PTHLH gene cDNA was obtained by cloning in sika deer (Cervus nippon), and the bioinformatics was analyzed. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the differences expression of PTHLH mRNA in different tissues of the antler tip at different growth periods (early period, EP; middle period, MP; late period, LP). Results: The CDS of PTHLH gene was 534 bp in length and encoded 177 amino acids. Predictive analysis results revealed that the PTHLH protein was a hydrophilic protein without transmembrane structure, with its secondary structure consisting mainly of random coil. The PTHLH protein of sika deer had the identity of 98.31%, 96.82%, 96.05%, and 94.92% with Cervus canadensis, Bos mutus, Oryx dammah and Budorcas taxicolor, which were highly conserved among the artiodactyls. The qRT-PCR results showed that PTHLH mRNA had a unique spatio-temporal expression pattern in antlers. In the dermis, precartilage, and cartilage tissues, the expression of PTHLH mRNA was extremely significantly higher in MP than in EP, LP (p<0.01). In the mesenchyme tissue, the expression of PTHLH mRNA in MP was significantly higher than that of EP (p<0.05), but extremely significantly lower than that of LP (p<0.01). The expression of PTHLH mRNA in antler tip tissues at all growth periods had approximately the same trend, that is, from distal to basal, it was first downregulated from the dermis to the mesenchyme and then continuously up-regulated to the cartilage tissue. Conclusion: PTHLH gene may promote the rapid growth of antler mainly through its extensive regulatory effect on the antler tip tissue.

Infection status of bovine viral diarrhea virus in Korean native cattle in Jeonbuk State, Korea (전북지역 한우의 소 바이러스성 설사 바이러스 감염 현황 조사)

  • Woo Ri Jung;Mi Seon Kang;Keum-Suk Chu
    • Korean Journal of Veterinary Service
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    • v.47 no.2
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    • pp.73-79
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    • 2024
  • Bovine viral diarrhea virus (BVDV) is distributed in cattle worldwide and causes significant economic losses to the livestock industry. Identification and remove of BVDV persistently infected (PI) cattle is very important to control BVDV infection in cattle herd. The objective of this study is to investigate the infection status of BVDV infection in Korean native cattle (Bos taurus coreanae) farms located in Jeonbuk State. From 2021 to 2022, a total of 1,497 samples were collected from 17 cattle farms and tested for BVDV antigen using a commercial ELISA kit. By the first ELISA testing, 24 cattle from six farms were positive for BVDV antigen, showing the farm-level or cattle-level prevalence of 35.3% or 1.6%, respectively. By the second ELISA testing which carried out with the first ELISA-positive samples after three-weeks, 12 cattle (0.8%) from five farms (29.4%) were positive for BVDV antigen, indicating these cattle were PI cattle. Genotypes of BVDV were determined with 12 BVDV-positive samples using a previously described RT-PCR assay and the results showed that 3 (25.0%) and 9 (75.0%) were confirmed to be type 1 and type 2, respectively. These results will be helpful to establish the effective control strategy for BVDV in cattle farms in Jeonbuk State.

Studies on Development of Breeding Technique to Increase Hanwoo (Bos taurus coreanae) III. Hormonal Treatment of Reproductive Disorders and Effect of Intraovarian $\textrm{PGF}_{2a}$ Administration in Hanwoo (한우의 신속한 증식을 위한 번식기술 개발에 관한 연구 - III. 한우에서 번식장애 처치 및 $\textrm{PGF}_{2a}$의 난소실질내 투여효과에 관한 연구)

  • 손창호;오병철;임원호;백종환;오명환;이강남;정근기;강성근;김대영
    • Journal of Embryo Transfer
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    • v.17 no.2
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    • pp.153-162
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    • 2002
  • In order to develop the breeding techniques to increase Hanwoo (Bos taurus coreanae) population, the present study was performed 1) to establish the treatment protocol on reproductive disorders with GnRH or PGF/sub 2$\alpha$/, 2) to improve intraovarian PG $F_{2}$$\alpha$/ administration for reducing open period. Among total of 43 diagnosed, high percentage of cows (41.9%, 18 cows) were diagnosed as silent heat, followed by inactive ovaries (32.6%, 14 cows), ovarian cysts (9.3%, 4 cows), persistent corpus luteum (7.0%, 3 cows), endometriosis (4.7%, 2 cows), pyometra (2.3%, 1 cow) and luteal cysts (2.3%, 1 cow). To treat silent heat, 18 cows were administrated with 25 mg PGF/sub 2$\alpha$/, heat-detected, artificially inseminated and monitored pregnancy. All treated cows were heat-detected and 16 cows (88%) were successfully pregnant. With 200 $\mu\textrm{g}$ GnRH treatment, 7 cows (70%) with inactive ovaries and 3 cows (75%) with ovarian cysts were successfully pregnant. Administration with 25mg PGF/sub 2$\alpha$/, successfully treated 3 cows (100%) with persistent corpus luteum and 1 cow (100%) with luteal cysts, followed by 100% pregnancy rate. With the combined treatment of 25 mg PG $F_{2}$$\alpha$/and antibiotics, 2 cows (100%) with endometriosis were effectively treated and got pregnant after. artificial insemination (AI). In order to reduce open period, 5 mg PGF/sub 2$\alpha$/ was administrated intraovarian to 20 days cows after delivery, heat-detected, artificially inseminated and monitored pregnancy. In the first experiment, in order to recover uterus, 5mg PGF/sub 2$\alpha$/were administrated, followed by administration of 5mg PGF/sub 2$\alpha$/ at the interval of 14 days. As results, 74% (17/23 cows) of pregnancy rate after AI. In order to further reduce the open period, 5 mg PGF/sub 2$\alpha$/was administrated at the interval of 11 days without the period of uterus recovery, resulted in 94% (16/17 cows) pregnancy rate. In conclusion, these results showed that PGF/sub 2$\alpha$/ and GnRH treatment were effective hormonal treatment resume in Hanwoo with various reproductive disorders. In addition, modified protocol of intraovarian PGF/sub 2$\alpha$/ administration could be the effective method for reducing the open period.

Nutrient Utilization, Body Composition and Lactation Performance of First Lactation Bali Cows (Bos sondaicus) on Grass-Legume Based Diets

  • Sukarini, I.A.M.;Sastradipradja, D.;Sutardi, T.;Mahardika, IG.;Budiarta, IG.A.
    • Asian-Australasian Journal of Animal Sciences
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    • v.13 no.12
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    • pp.1681-1690
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    • 2000
  • A study on energy and protein utilization, and milk production of Bali cows on grass-legume diets was carried out using 12 first lactation cows (initial BW $263.79{\pm}21.66kg$) during a period of 16 weeks starting immediately post calving. The animals were randomly allotted into 4 dietary treatment groups R1, R2, R3 and R4, receiving from the last 2 months of pregnancy onwards, graded improved rations based on a mixture of locally available grass and legume feed ad libitum. R1 contained on a DM basis 70% elephant grass (PP, Penisetum purpureum) plus 30% Gliricidia sepia leaves (GS), R2 was 30% PP plus 55% GS supplemented with 15% Hibiscus tilliactus leaves (HT, defaunating effect), R3 and R4 were 22.5% PP+41.25% GS+11.25% HT+25% concentrate, where R3 was not and R4 supplemented with zinc di-acetate. TDN, CP and zinc contents of the diets were 58.2%, 12.05% and 18.3 mg/kg respectively for R1, 65.05%, 16.9% and 25.6 mg/kg respectively for R2, 66.03%, 16.71% and 29.02 mg/kg respectively for R3 and 66.03%, 16.71% and 60.47 mg/kg respectively for R4. Milk production and body weight were monitored throughout the experimental period. In vivo body composition by the urea space technique validated by the body density method and supported by carcass data was estimated at the start and termination of the experiment. Nutrient balance and rumen performance characteristics were measured during a balance trial of 7 days during the 3rd and 4th week of the lactation period. Results indicated that quality of ration caused improvement of ruminal total VFA concentration, increments being 52 to 65% for R2, R3 and R4 above R1, with increments of acetate being less (31 to 48%) and propionate being proportionally more in comparison to total VFA increments. Similarly, ammonia concentrations increased to 5.24 to 7.07 mM, equivalent to 7.34 to 9.90 mg $NH_3-N/100ml$ rumen fluid. Results also indicated that feed quality did not affect DE and ME intakes, and heat production (HP), but increased GE, UE, energy in milk and total retained energy (RE total) in body tissues and milk. Intake-, digestible- and catabolized-protein, and retained-protein in body tissues and milk (Rprot) were all elevated increasing the quality of ration. Similar results were obtained for milk yield and components with mean values reaching 2.085 kg/d (R4) versus 0.92 kg/d (R1) for milk yield, and 170.22 g/d (R4) vs 71.69 g/d (R1), 105.74 g/d (R4) vs 45.35 g/d (R1), 101.34 g/d (R4) vs 46.36 g/d (R1) for milk-fat, -protein, and -lactose, respectively. Relatively high yields of milk production was maintained longer for R4 as compared to the other treatment groups. There were no significant effects on body mass and components due to lactation. From the relationship $RE_{total}$ (MJ/d)=12.79-0.373 ME (MJ/d); (r=0.73), it was found that $ME_{m}=0.53MJ/kgW^{0.75}.d$. Requirement of energy to support the production of milk, ranging from 0.5 to 3.0 kg/d, follows the equation: Milk Prod. ($Q_{mp}$, kg/d)=[-2.48+4.31 ME($MJ/kg^{0.75}.d$)]; (r=0.6) or $Q_{mp}$=-3.4+[0.08($ME-RE_{body\;tissue}$)]MJ/d]; (r=0.94). The requirement for protein intake for maintenance ($IP_m$) equals $6.19 g/kg^{0.75}.d$ derived from the relationship RP=-47.4+0.12 IP; (r=0.74, n=9). Equation for protein requirement for lactation is $Q_{nl}$=[($Q_{mp}$)(% protein in milk)($I_{mp}$)]/100, where $Q_{nl}$ is g protein required for lactation, $Q_{mp}$ is daily milk yield, Bali cow's milk-protein content av. 5.04%, and $I_{mp}$ is metabolic increment for milk production ($ME_{lakt}/ME_{m}=1.46$).

Effects of Physically Effective Neutral Detergent Fiber Content of TMR Feed on the Productivity and Carcass Characteristics in Hanwoo (Bos taurus coreanae) Steers (TMR 사료의 물리적 유효 NDF 함량이 한우 거세비육우의 생산성과 도체특성에 미치는 영향)

  • Jeon, Byong Tae;Park, Jae Hyun;Cho, Won Mo;Kim, Sang Woo;Jang, Se Young;Moon, Sang Ho
    • Journal of The Korean Society of Grassland and Forage Science
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    • v.35 no.1
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    • pp.12-16
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    • 2015
  • This study was carried out to evaluate accurately physical characteristics of total mixed rations (TMR) by investigating the effects of physically effective neutral detergent fiber content on the growth performance and carcass characteristics in fattening steers. Twelve Hanwoo (Bos Taurus coreanae) steers aged 26 months were used in this trial. Steers were offered one of two total mixed ration (TMR) diets - High or Low physically effective neutral detergent fiber (peNDF) content groups-that were differentiated by mixing time. The carcass traits of the experimental animals were evaluated by Korea Institute for Animal Products Quality Evaluation (KAPE) after slaughter. Body weight gain during the experimental period was significantly higher (P<0.05) in the High group ($30.00{\pm}10.27kg$) compared with the Low group ($17.20{\pm}6.34kg$), and daily weight gain was also high in the former. Although there was no significant difference, the carcass weight was higher in the High group ($414.60{\pm}34.28kg$) compared with the Low group ($377.80{\pm}11.97kg$). However, the beef quality grade of the Low group ($1^{++}$) was higher than that of the High group ($1^+$). Increases in body weight gain, daily gain, and carcass weight for the High group were mainly influenced by a high level of dry matter (DM) intake and digestibility; consequently, back-fat thickness increased and the beef quality grade was lowered. Because growth performance and carcass characteristics were affected by the physical traits of the diet, we suggested that proper peNDF content is also needed for fattening steers.

Effect of Different Stocking Density on Eating Behavior of Hanwoo Steers (Bos taurus coreanae) During Growing Period (거세 한우 육성우 사육밀도가 채식행동에 미치는 영향)

  • Lee, Sang-Moo;Jang, Jae-Won
    • Journal of Animal Science and Technology
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    • v.53 no.5
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    • pp.489-496
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    • 2011
  • This study was carried out to investigate the effects of stocking density on the eating and ruminating behavior of growing Hanwoo steer (Bos taurus coreanae). A total of thirty growing Hanwoo steers were divided into four stocking density groups (G1: 1 head/32 $m^2$, G2: 2 heads/32 $m^2$, G3: 3 heads /32 $m^2$, G4: 4 heads/32 $m^2$) with 3 replicates (12 pens). The results of eating behaviors for 48 hours are summarized as follows: Total intake was higher in 2G, 3G and 4G than in 1G, but not significantly different among thetreatments. Intake of roughage was the highest in 2G (3.32 kg), while 1G (2.85 kg) was the lowest (P<0.05). Eating time of concentrate was highly in the order of 1G > 2G > 3G > 4G (P<0.05). But eating time (concentrate + roughage) and ruminating time were not significantly difference among the treatments. Resting time (standing + lying) was the highest in 4G (P<0.01), and lying time was the highest in 2G. Chewing time (Eating + ruminating) was higher in 3G than in 1G, 2G, and 4G (P<0.05). Number of bolus, number of total chews, ruminating time per bolus and number of bolus per minute were not significantly difference among the treatments. But number of chews per bolus was significantly lower in 1G than those of the other treatments (p<(0.05). Number of urinating was in the order of 1G > 4G > 2G > 3G (P<0.05). However, stocking density had no effect on drinking and defecating. Eating rate and chewing efficiency were the highest in 4G (P<0.01, 0.05), but ruminating efficiency was not significantly difference among the treatments.

Effects of Pregnancy Stage on Eating Behaviors of Hanwoo Heifers (Bos taurus coreanae) (한우 미경산우 임신 단계가 채식행동에 미치는 영향)

  • Byoun, Byung Hyun;Lee, Jae Hun;Lee, Sang Moo
    • Journal of The Korean Society of Grassland and Forage Science
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    • v.36 no.1
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    • pp.41-49
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    • 2016
  • The objective of this study was to determine the effect of different pregnancy stages on the eating and ruminating behavior of Hanwoo heifers (Bos taurus coreanae). A total of twelve Hanwoo heifers were divided into four groups depending on pregnancy stage: C: before pregnancy, 9 months old, T1: 3 months pregnant, 16 months old, T2: 6 months pregnant, 19 months old, T3: 9 months pregnant, 22 months old (3 replicates per group). Concentrate of 1% of the body weight was fed to them. Roughage was provided at ad libitum to all treatments. Our results revealed that the intake of roughage was the highest in the T3 group (at 3.68 kg) and the lowest in the C group (at 1.02 kg, p<0.05). Total intake in the order from high to low was: T3 > T2 > T1 > C (p<0.05). The rate of dry matter intake compared to body weight (DMI/BW, %) from high to low order was: T3 > T2 > T1 > C (p<0.05). Eating time, ruminating time, and chewing time were the highest in T3 group (p<0.05). Resting time was the highest in C group (p<0.05). The number of bolus and the number of total chews were significantly higher in T3 compared to those in other groups. However, ruminating time per bolus was not significantly difference among groups. The number of chews per bolus from high to low order was: C > T1 > T3 > T2 (p<0.05). The number of bolus per minute was not significantly different among groups. The number of drinking and the number of defecating were significantly higher in C and T1, respectively (p<0.05). However, the number of urinating had no effect according to pregnancy stage. Eating rate and chewing efficiency were significantly higher (p<0.05) in accordance with pregnancy stage (T3 > T2 > T1 > C). Ruminating efficiency was significantly (p<0.05) higher T1 than that in other groups.

Effect of Red Ginseng Marc, Mineral and Black Sugar® Supplementation on the Production of Holstein Steers (Bos taurus) (홍삼박, 무기물® 및 흑설탕® 첨가 급여가 Holstein 거세 비육우 생산성에 미치는 영향)

  • Lee, Sang Moo
    • Journal of The Korean Society of Grassland and Forage Science
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    • v.41 no.4
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    • pp.273-279
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    • 2021
  • This study was carried out to investigate the effects of a dietary addition of red ginseng marc, mineral® and black sugar® on the dry matter intake, daily gain, yield grade and quality grade of Holstein steers(Bos taurus). A total of 32 fattening Holstein steers(avg. BW 590kg) were assigned to four treatments which included a control diet(mixed concentrate and forage; namely, C) and three treatments diet(T1; control diet+red ginseng marc 200g, T2; control diet+red ginseng marc 100g+mineral 50g, T3; control diet+mineral 50g+ black sugar 20g). The results are summarized as follows; the total feed intake and daily feed intake were significantly(p<0.05) higher in T2 and T3 than in the other two treatments(C and T1). The daily gain was higher in T2 than in the other treatments, but there was no significant difference. The back fat thickness, longissimus muscle area and meat yield grade were no significant difference. The marbling score showed significantly(p<0.05) higher in order of T3(4.5) > T1(4.0) > T2(2.7) > C(2.5). The meat color, fat color, texture and maturity were no significant difference. The quality grade was higher in T3 than in the other treatments(C, T1 and T2), but there was no significant difference. T3, which numerically had a higher daily gain and carcass quality grade, showed higher economic efficiency, whereas C showed low economic efficiency. Based on the above results, T3 treatment compared to the other treatments improved the daily gain, carcass quality grade and economic efficiency.

Development of Local Animal BLAST Search System Using Bioinformatics Tools (생물정보시스템을 이용한 Local Animal BLAST Search System 구축)

  • Kim, Byeong-Woo;Lee, Geun-Woo;Kim, Hyo-Seon;No, Seung-Hui;Lee, Yun-Ho;Kim, Si-Dong;Jeon, Jin-Tae;Lee, Ji-Ung;Jo, Yong-Min;Jeong, Il-Jeong;Lee, Jeong-Gyu
    • Bioinformatics and Biosystems
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    • v.1 no.2
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    • pp.99-102
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    • 2006
  • The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

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