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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.

Background and Aim: Parasitic diseases, including trematode invasions, result in losses to livestock in Indonesia, hindering the government's efforts to achieve meat self-sufficiency. This study aimed to estimate the prevalence of Amphistomes and Fasciola in large ruminants reared by smallholder farmers., Materials and Methods: Fecal samples from 199 buffalo and cattle were collected from the districts of East Lampung (Lampung Province) and Lebak (Banten Province). Fecal samples were examined for the presence of trematode eggs using a sedimentation technique., Results: Parasite invasion rate was 48.2% (95% confidence interval [CI]: 41.3%-55.2%). Rate of invasion was 63.3% (95% CI: 52.7%-73.9%) in Lampung and 38.3% (95% CI: 29.6%-47.0%) in Lebak-Banten. The prevalence of multiple invasions of both Amphistomes and Fasciola was 20% in buffalo and local cattle, whereas invasion rate was 12.8% in crossbred cattle. Invasion rate of Amphistomes alone was 27.1%, and that of Fasciola was 4.5%. A higher invasion rate of Amphistomes (29.8%) occurred in crossbred animals. There were no significant differences between age groups for trematode invasion. The Chi-square test showed that the prevalence of trematode invasion in females was significantly higher than in males (51.5% and 30.0%, respectively). Amphistomes more commonly infected females than males (29.0% and 16.7%, respectively)., Conclusion: All breeds were vulnerable to invasion by both trematode species and single invasions with different invasion rates. These findings contribute to determining the magnitude of the disease and provide a basis for studies on prevention and treatment of trematode invasion., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Martindah, et al.)

Background and Aim: In several countries, two Entamoeba porcine species, Entamoeba suis and Entamoeba polecki (subtype 1 and 3), have been detected using molecular methods and identified pathogenicity associated with enteritis. However, globally, Entamoeba infection prevalence in pigs is extremely limited. This study aimed to coprologically and genetically examine pig parasites to estimate prevalence of Entamoeba in three pig farms in East Java, Indonesia., Materials and Methods: Hundred porcine fecal samples (Landrace) were collected from three East Javan farms in well-known swine industry regions. Fecal samples were examined under a microscope after sugar-flotation centrifugation, and molecular species and subtype identification were performed using polymerase chain reaction (PCR) and primer pairs targeting small-subunit ribosomal RNA., Results: Microscopy examinations identified parasites in 89/100 fecal samples; Entamoeba spp. cysts were the most frequent in these samples. Polymerase chain reaction showed that 58 samples were comprised of mixed Entamoeba suis and Entamoeba polecki , 22 E. suis alone, and nine E. polecki alone infections. Epolec F6-Epolec R6 primers successfully amplified E. polecki ST1-4 subtypes, while Epolecki 1-Epolecki 2 amplified only the E. polecki ST1 subtype. Entamoeba polecki ST1-specific primers successfully detected the ST1 subtype in 19/67 E. polecki positive samples., Conclusion: Entamoeba spp. prevalence in Indonesian pigs was previously shown to be high. On coprological examination of East Javan pigs, we detected high Entamoeba spp. levels, in which we genetically identified as E. suis (80.0%), E. polecki (67.0%), and E. polecki ST1 (19%)., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Chrismanto, et al.)

Background and Aim: In Indonesia, Madura cattle are native breeds that are expected to contribute to the improvement of regional meat self-sufficiency. Eimeria spp. are protozoans that are commonly found in ruminants. This study aimed to identify the occurrence and diversity of Eimeria spp. in Madura cattle., Materials and Methods: In this study, fresh fecal samples were collected from 100 cattle in Kamal Subdistrict, Bangkalan District, Madura Island, Indonesia. Morphological detection was performed using a light microscope, and molecular identification was performed using a polymerase chain reaction. DNA amplification was conducted using various species-specific primers for Eimeria bovis , Eimeria zuernii , Eimeria auburnensis , Eimeria alabamensis , Eimeria ellipsoidalis , and Eimeria cylindrica ., Results: The results obtained 21% (21/100) of Eimeria spp. based on morphological detection. A total of 15 positive samples with 500-25,000/mL oocysts were selected for DNA extraction and amplification, resulting in 12 positive samples. Four Eimeria spp. were obtained based on molecular identification: E. bovis , E. zuernii , E. auburnensis , and E. cylindrica ., Conclusion: Four species of Eimeria namely E. bovis , E. zuernii , E. auburnensis , and E. cylindrica were identified from fecal sample of Madura cattle using PCR method in this study. Further comprehensive studies are required to investigate the pathogenicity of Eimeria spp. in Madura cattle. Therefore, improved and integrated management practices should be strengthened by local governments to prevent pathogenic diseases and increase national livestock productivity in Indonesia., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Hastutiek, et al.)

Some experts believe that organic agriculture is more adaptable compared to conventional agriculture. Accordingly, the purpose of this study is to assess organic and conventional farmers' perception and adaptation to climate change and analyse the factors that influence such decisions. The survey was conducted in Java, involving 112 organic farmers and 112 conventional farmers. The chi-square test was used to differentiate climate change perceptions and adaptation strategies applied by farmers. The factors that influenced the selection of the adaptation strategies were analysed using logistic regression. The results of analysis found that organic farmers have more precise perceptions of climate change than that of conventional farmers. Organic farmers more commonly implement mixed cropping, crop rotation, increasing organic manure, using shade, and changing irrigation techniques as their adaptation strategies, while conventional farmers more commonly prefer to adjust planting and harvesting dates and use traditional climate prediction called Pranata Mangsa. The selection of farmers' adaptation strategies is influenced by age, education, experience, distance to extension services, access to credit, information about climate and farmer groups, as well as farmers' perceptions of climate change. The results of the study recommend that policy makers increase farmers' adaptive capacity through investment in education and institutions to support climate change adaptation., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2022 Irham Irham et al.)

Background and Aim: Pleomorphic adenoma gene 1 ( PLAG1 ) encodes a multifunctional transcription factor that controls many genes and pathways and is associated with cattle body weight and measurements. This study aimed to evaluate the association between PLAG1 polymorphisms with body weight and measurements in Bali cattle., Materials and Methods: A total of 87 Bali cattle, consisting of 48 bulls and 39 heifers at the Breeding Center for Bali Cattle, were used as the population in this study. Cattle were 2 years old and kept semi-intensively in the pasture. Phenotype data consisting of body weight, withers height, body length, chest girth, waist height, and chest depth were measured. Birth weight data were obtained from birth records, and weight gain, adjusted weaning weight, and yearling weight were calculated using formulas. Blood samples were taken from the jugular vein as much as 5 mL, and genomic DNA was isolated using the salting-out method. Polymerase chain reaction (PCR) was performed to amplify three target polymorphisms, namely, g.48308 C>T, g.32212 (19 bp indel), and g.45233 T>C. The presence of a 19 bp indel was determined by direct observation of the PCR product on a 2% agarose gel. Two other polymorphisms were detected by PCR-restriction fragment length polymorphism using the restriction endonuclease enzymes Sac II and Bcl I. PLAG1 genotype and phenotype associations were analyzed using a general linear model., Results: The results showed that two of the target polymorphisms in PLAG1 did not vary. The DD genotype indicated by 123 bp of PCR product was the only genotype identified for g.32212 19 bp indel, and TT genotype was the only genotype found for g.45233 T>C single-nucleotide polymorphism (SNP). Conversely, g.48308 C>T SNP was found to be polymorphic. In addition, the g.48308 C>T polymorphism of PLAG1 was significantly associated with body length of Bali cattle. Cattle with the CC genotype had a greater body length than the other two genotypes., Conclusion: The g.48308 C>T SNP in PLAG1 was associated with Bali cattle body length characteristics. This finding could be used as a basis for selecting Bali cattle based on body length characteristics., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Cahyadi, et al.)

Background and Aim: Bali Cattle ( Bos j. javanicus ) is a local breed originating in Indonesia, accounting for 32.3% of the total cattle population. To date, no studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. Therefore, a study that used molecular breeding technologies to characterize the demography of Bali cattle would be timely. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size ( N e ) values in the cattle population., Materials and Methods: In this study, we explored the population structure and genetic diversity of Bali cattle using genomic-level analyses. Our study primarily studied cattle that had been bred in livestock breeding centers since these breeds had subsequently spread throughout Indonesia. We focused on characterizing the genetic structure, determining the level of LD present, and estimating the N of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data.e of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data., Results: We found that the LD values of Bali cattle from the breeding center and those raised elsewhere were 0.48±0.43 and 0.39±0.40, respectively. Subsequently, the N e value of Bali cattle from the breeding center and farmers was 151 and 96, respectively., Conclusion: Our results suggest that the selection program of the breeding center is beneficial for maintaining the genetic diversity of Bali cattle., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Sudrajad, et al.)

Fasciolopsiasis is a parasitic infection caused by the flatworm Fasciolopsis buski . Since 1982, fasciolopsiasis has been reported in Indonesia's Hulu Sungai Utara (HSU) Regency, South Kalimantan Province. Fasciolopsiasis occurs when contaminated raw or undercooked aquatic plants are consumed. Cercariae of the parasite encyst in a variety of aquatic plants and grow into metacercariae that infect and reproduce in the human intestine. Until now, treatment for F. buski infection in the HSU Regency has been comparatively short, with patients receiving only a single dose of praziquantel, 30 mg/kg body weight, without further observation. A long-term effort through health promotion activities and intensive health education, particularly for elementary school children enrolled in the School Health Program, is ongoing to help prevent fasciolopsiasis from spreading and to improve environmental sanitation. Through 2018, intervention efforts successfully reduced the incidence of F. buski infection. Sustaining surveillance and investigation of fasciolopsiasis, including identification of new cases and community education, is critical for the elimination of the parasite from Indonesia. This review describes the spread of F. buski and its possible impact on public health to understand the critical nature of continuing F. buski surveillance and control efforts., (Copyright: © Ridha, et al.)

Indigenous fungi can suppress infection by pathogens and produce secondary metabolites that directly or indirectly affect plant growth. This study aimed to test indigenous fungi collected from corn plants as biological control agents and their effects on the viability and vigor of corn seeds. Purposive sampling method was used for sampling where soil samples taken from the rhizosphere zone, corn stem and leaf tissue from three locations namely Maros-South Sulawesi, Bone-South Sulawesi, Sigi-Central Sulawesi, Indonesia. Rhizospheric fungi were isolated from soil collected at the rhizosphere and rhizoplane using a serial dilution technique, while the endophytic fungi isolated from the leaves and stem tissues using surface sterilization method. The isolated fungi were cultured on a potato dextrose agar (PDA) medium. An antagonism test was performed using the dual culture method on PDA media with F. verticillioides as target pathogen. Pathogenicity test and the effect of fungi on corn seed germination was carried out using the blotter test method. Parameters observed were; necrotic symptoms on seedlings, growth potential, germination, growth rate, growth simultaneity, vigor index, germination rate, and time needed for 50% of the total germination. The effect of the isolated indigenous fungi on corn growth was carried out in-planta using seedling trays. The results of the blotter test and in-planta test were further confirmed by a physiological characteristic test. And assessing the fungi's ability to dissolve potassium, phosphate, and produce protease enzymes. A total of 89 fungal isolates were isolated and collected from various parts of the corn plant. Nineteen of the 89 fungal isolates showed inhibitory activity against F. verticillioides by ≥ 50% inhibition. The fungal isolates JRP 5 MRS, JRP 9 MRS, JRP 10 MRS, JRP 7 MRS, and JEDF 1B BN were selected based on the tests and showed a consistently positive effect on seed viability and vigor with a value of ≥90%. The isolates did not cause necrosis in corn, and had the ability to suppress the growth of pathogenic F. verticillioides by ≥ 50%., Competing Interests: The authors declare no conflict of interest., (© 2021 The Author(s).)

Background and Aim: Eimeria spp. are gastrointestinal protozoans that affect animal productivity, thereby causing symptoms that range from bloody diarrhea to death. These symptoms cause economic losses to farmers. The distribution of Eimeria spp. in cattle has, therefore, been reported to have spread widely, especially in the tropics and subtropics. Indonesia is a tropical country at high risk of Eimeria infections. This study aimed to identify the prevalence and risk factors related to the levels of eimeriosis in beef cattle originating from different geographic areas in Indonesia., Materials and Methods: Here, 817 fecal samples were collected from beef cattle in Indonesia, including 282 calves, 535 adults, 530 males, and 287 females. In addition, 156 semi-intensively and 661 intensively managed cattle were randomly collected. Then, fecal samples were analyzed by parasitology examinations., Results: Screening examination using the sugar flotation modification method showed that Eimeria spp. were prevalent in Indonesia, as 65.4% of the bacterial strain was detected. The prevalence of identified Eimeria spp. in Indonesia was highest in North Maluku (Maluku Island) (94.1%), whereas the lowest levels were observed in West Java (24.0%) (Java Island). The prevalence was also found to be higher in males (79.3%) than females (51.9%). Similarly, levels in semi-intensively managed cattle (66.7%) were higher than those subjected to intensive management (65.9%). However, its prevalence in calf and adult cattle was similar., Conclusion: Bovine eimeriosis spp. were detected at high prevalence in Indonesia, and high-level risks were observed in infected males, including those under the semi-intensive management. In addition, although the results from oocyst examinations were based on qualitative analysis, the endemicity levels of Eimeria spp. among farms in Indonesia should be considered because Eimeria spp. were distributed in most parts of Indonesia. Based on the results of this study, we provide the first information about the prevalence of bovine eimeriosis from different geographical locations in Indonesia, which have differing climates associated with the level of the existing risk factors. Hence, farmers are advised to pay more attention to strict biosecurity techniques on their farms, thereby favoring the early control of bovine eimeriosis., (Copyright: © Ekawasti, et al.)

Rice bran (RB), a by-product of the rice milling process, is a rich source of bioactive compounds. Current studies have suggested that fermentation can enhance the bioactivities of RB. This study is aimed to analyse the volatile compounds and sensory profile of fermented RB from two cultivars (Inpari 30 and Cempo Ireng) that are well-known in Indonesia, as well as to measure total phenolic content (TPC) and antioxidant activity. Volatile compounds of fermented RB were analyzed using gas chromatography-mass spectrometry combined with headspace-solid phase microextraction. The optimum TPC and antioxidant activity were observed after 72 h fermentation of RB. The 55 volatile compounds were identified in fermented and non-fermented RB. They were classified into alcohols, aldehydes, acids, ketones, phenols, esters, benzene, terpenes, furans, lactone, pyridines, pyrazines, and thiazoles. Volatile compounds were significantly different among the varieties. The sensory analysis showed that the panelists could differentiate sensory profiles (color, taste, flavor, and texture) between the samples. Fermentation can enhance the acceptance of RB. These studies may provide opportunities to promote the production of fermented RB as a functional ingredient with enhanced bioactivity for health promotion.

Background and Aim: Ultrasonography (USG) is useful for non-invasively identifying changes that occur in soft tissue architecture. The objective of this research was to demonstrate postpartum (PP) uterine involution through the changes of perineal muscle intensity and thickness in Madura beef cow by ultrasonography., Materials and Methods: Madura's breed cows used in the research consist of eight non-pregnant (NP) cows and three PP cow. The transrectal and transperineal USG imaging of NP cows was performed on days 1, 33, and 65. USG imaging of PP cows was performed every day starting from day 1 (24 h after parturition) until day 21 PP. Transrectal USG of the reproductive tract was performed for the cervix, corpus uteri, and cornua uteri. USG was performed transcutaneously over the perineal area for coccygeus and levator ani muscles at the longitudinal and transverse angles. Reproductive tract diameter and perineal muscle intensity and thickness were measured with ultrasound imaging., Results: The analysis of the sonogram of PP cows showed that the diameter of the cervix, corpus uteri, and cornua uteri decreased within 21 days PP. The transverse view of the coccygeus muscle of PP cows showed decreased muscle intensity and thickness. On the other hand, the longitudinal view showed increased coccygeus muscle intensity and thickness. The transverse view of the coccygeus muscle of NP cows showed increased muscle intensity, while muscle thickness was reduced. Sonogram analysis of the levator ani muscle of PP cows showed decreased muscle intensity with increasing muscle thickness. However, imaging of the levator ani muscle of NP cows showed a decrease in both intensity and muscle thickness. There was a significant difference in the mean value intensity of the scanning view analysis results of the levator ani muscle of the PP cow (523.6 AU increased to 672.1 AU) and the NP cow (515.9 AU decreased to 465.4 AU). Furthermore, there was a significant difference (p<0.05) in the mean value thickness of both scanning view analyses of the coccygeus and levator ani muscles of PP cows (5.8 mm increased to 6.5 mm and 3.8 mm increased to 4.8 mm, respectively) and NP cows (8.8 mm increased to 9.1 mm and 5.9 mm decreased to 4.9 mm, respectively)., Conclusion: We found that the perineal muscles, namely, the levator ani muscle and coccygeus muscle, change in size, and intensity during uterine involution as demonstrated on Madura beef cow., (Copyright: © Hayanti, et al.)

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity., Competing Interests: The authors have declared that no competing interests exist.

Soil-environmental correlation has been extensively studied as a cost-effective method for regional-scale soil attribute modeling. However, the limitations of commonly used statistical methods in soil-factorial modeling entail multicollinearity in bigdata soil-factorial prediction data and mixed type of soil-environmental variables (categorical and continuous). Both of these shortcomings were addressed resulting in a new soil-factorial modeling approach. The objective of this study was to develop a novel statistical technique for factorial modeling of topsoil soil total (TC), organic (SOC), recalcitrant (RC), moderately-available (MC), and hot-water extractable carbon (HC) in Florida. This article introduced a two-step regression technique (2Step-R) combining linear regressions (i.e., Ridge Regression-RR and Bayesian Linear Regression) and latent variable models (i.e., Partial Least Squares Regression-PLSR and Sparse Bayesian Infinite Factor-SBIF) for the integration of mixed type soil-environmental datasets. Results of this research showed the new technique capabilities to derive acceptable models for TC, SOC, RC, and MC predictions (R 2  > 0.65; residual prediction deviation, RPD > 1.6), but fair for HC prediction (R 2  ≤ 0.60; RPD ≤ 1.6). This novel method improved TC, SOC, and MC prediction accuracies compared with standard PLSR and RR methods. In conclusion, the new modeling approach that incorporates categorical along with continuous soil-environmental predictor variables in latent variable models has profound potential to improve soil attribute predictions in other regions., (Copyright © 2019 Elsevier B.V. All rights reserved.)

This study investigated the effect of dietary nutmeg oil (NO) on growth performance, blood parameters, lipid peroxidation and heat shock protein (HSP) 70 expression in Korean native chicken (KNC) reared under hot temperature. We allocated 273 meat-type KNCs (Hanhyup-3, 4-week-old, body weight [BW] = 539.93 ± 1.75 g) to the following three treatments with seven replicate pens (13 birds/pen) per treatment. Three treatment diets were as follows: (a) Control, basal diet without NO supplementation; (b) NO 250; and (c) NO 500, basal diet supplemented with 250 and 500 ppm NO respectively. Diets and water were provided ad libitum throughout the 6-week feeding trial. During overall period (0-6 weeks), no differences (p > 0.05) were observed in BW gain (BWG), feed intake (FI) and feed conversion rate (FCR) among treatments. However, the FI at 0-3 weeks decreased (p < 0.05) quadratically with increasing NO levels. Most blood parameters did not differ (p > 0.05) among treatments, although the monocyte level of the NO 500 group was considerably lower (p > 0.05) than that of the other groups. Furthermore, dietary NO did not affect serum triglyceride, cholesterol, total protein, albumin, calcium, phosphorus and alanine aminotransferase (ALT) levels (p > 0.05); however, it linearly decreased serum aspartate aminotransferase (AST) level (p < 0.05). Additionally, serum malondialdehyde (MDA) concentration decreased (p < 0.05) and heart MDA concentration was lower (p = 0.08) with increasing dietary NO supplementation. After a 3-hr heat (35°C) challenge, the rectal temperature (RT) reduced (p < 0.05) linearly with increasing NO levels. Dietary NO did not affect liver HSP70 (p > 0.05) gene expression. In conclusion, NO potentially enhanced the ability of chickens to alleviate heat stress. Furthermore, our findings suggest that lipid oxidation inhibition by dietary NO likely mediated the enhanced heat-stress tolerance of the chickens., (© 2019 Blackwell Verlag GmbH.)

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS&#95;RIR&#95;C) and ND (NIAS&#95;RIR&#95;D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract., (© 2016 Stichting International Foundation for Animal Genetics.)

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

Background: Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight., Results: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle., Conclusions: This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.