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

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.

Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences.

BACKGROUND: The cytochrome b (Cyt b) gene is one of the most studied mitochondrial DNA (mtDNA) genes to determine sheep's genetic profile. This study aimed to determine the genetic diversity and relationships of several Indonesian local sheep populations on Java Island, Indonesia, based on the mtDNA Cyt b gene sequences. Blood samples were collected from forty-one individual sheep in seven populations of Indonesia local sheep breeds on Java Island (Priangan = 6, Garut = 6, Batur = 7, Wonosobo = 5, Javanese Thin-Tailed/JTT = 7, Javanese Fat-Tailed/JFT = 5, and Sapudi = 5). DNA extraction was performed on blood samples, and the mtDNA Cyt b gene was amplified using specific primers (Alek-CBF: 5'-CAACCCCACCACTTACAA-3' and Alek-CBR: 5'-CCTTGAGTCTTAGGGAGGTT-3'). The polymerase chain reaction (PCR) products were then sequenced, and data were analyzed using the MEGA version 7.0, DNA SP version 6.0, and NTSYS-pc version 2.11 software. RESULTS: A total of 1140 bp complete mtDNA Cyt b gene sequences in this study obtained 1134 monomorphic sites (I), six polymorphic sites (V), one segregation site (S), and five parsimony informative sites (P) with a nucleotide diversity (Pi), the average number of nucleotide differences (K), and sequence conservation (SC) were 0.00119, 1.35610, and 0.9947, respectively. There were six haplotypes consisting of two unique haplotypes and four shared haplotypes with a haplotype diversity (Hd) of 0.5415. The genetic distance within and between populations ranged from 0.0000 to 0.0016 and 0.0000 to 0.0020, respectively. Wonosobo, JFT, and Sapudi sheep have the closest relationship, and then these three breeds were close to JTT sheep, followed by Batur, Priangan, and Garut sheep. Two haplogroups have been found based on the Ovine haplogroup clustering. All Wonosobo, JTT, JFT, Sapudi sheep, and most Batur sheep were clustered into haplogroup B. In contrast, Garut sheep were mostly clustered into haplogroup A, while Priangan sheep were clustered into both haplogroups with the same percentage. CONCLUSION: Seven Indonesian local sheep breeds on Java Island have a close relationship clustered into two haplogroups, namely haplogroups A and B. Most Indonesian local sheep breeds on Java Island in this study were clustered into haplogroup B, except for Garut and Priangan sheep.

The meta-analysis of beef cattle body weight prediction using body measurement approach with breed, sex, and age categories.

Objective: The aim of the study was to use a meta-analysis to identify the correlation between linear body measurements, including body length (BL), wither height (WH), heart girth (HG), and body volume (BV), and body weight in beef cattle by breed, sex, and age as categories. Materials and methods: These results can be used as a method for predicting beef cattle body weight. This study used systematic review and meta-analysis guidelines to create a checklist. The first stage was searching for papers relevant to the study objectives. The second stage was searching using the keywords beef cattle, body weight, body measurement, and correlation. The third stage was reviewing the title and abstract. The fourth stage was abstracting information from selected papers, and the last stage was tabulating data. Results: The results from this study were obtained, and 32 papers were eligible for the meta-analysis stage. The correlation between linear body measurement and body weight of beef cattle showed that HG (r = 0.88) and BV (r = 0.97) were significantly (p < 0.05) different compared to BL (r = 0.74) and WH (r = 0.72). The correlation between HG and body weight, and the categorization of cattle breeds showed significantly (p < 0.05) different results. The correlation between BV and body weight of cattle according to breed categories showed results that were not significantly (p > 0.05) different, while age was significantly (p < 0.05). Conclusion: In conclusion, to predict beef cattle body weight, it is necessary to use HG or BV, with breed, sex, and age of cattle as categories.

Phenotypic characterization and principal component analyses of indigenous chicken breeds in Indonesia.

BACKGROUND AND AIM: Understanding the phenotypic characteristics of indigenous livestock breeds is essential for their utilization and conservation. This study aimed to characterize indigenous chicken breeds in Indonesia based on phenotypic traits. MATERIALS AND METHODS: Data on eight qualitative and 12 quantitative traits were recorded for 250 chickens from six breeds: Black Kedu, Gaga, Merawang, Nunukan, Pelung, and Sentul. Data were analyzed using descriptive statistics and one-way analysis of variance to test the effect of breed on observed traits. Moreover, principal component analysis (PCA) was conducted separately for each chicken breed. Data on quantitative traits were subjected to Kaiser-Meyer-Olkin, which was computed to test the sampling adequacy and the pattern of correlation among the traits, and Bathlett's tests were used to assess the validity of the factor analysis of each of the datasets and determine whether the partial correlations among traits were small. RESULTS: We found considerable phenotypic variation in both qualitative and quantitative traits among indigenous chicken breeds. Multicolored plumage (96.40%), wild plumage (39.20%), gold feather flick (51.20%), yellow shank (36.80%), single comb (80.80%), red comb (94.80%), red earlobe (77.60%), and orange eyes (61.60%) were the most common features in the indigenous chickens. In addition, breed had a significant effect on all the quantitative traits that were analyzed (p<0.05). There were higher mean values for all quantitative traits for Pelung chickens than other chickens. In addition, the overall mean values for all quantitative traits in Merawang chicken were intermediate between Pelung chickens and Black Kedu, Gaga, and Nunukan chickens. The PCA showed two principal factors extracted that accounted for 77.80% and 78.38% of the total variance in the original variables for males and females, respectively. CONCLUSION: In general, body weight and body measurements, except wattle length, were loaded in PC1 as the primary factors responsible for the variation. The phenotypic variation observed in indigenous chickens in Indonesia could provide valuable basic information for the design of selection and genetic improvement programs.

Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations.

OBJECTIVE: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. METHODS: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. RESULTS: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations (FIT = 0.237), was partly due to the heterozygote deficiency within populations (FIS = 0.114) and moderate level of genetic differentiation among populations (FST = 0.137). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. CONCLUSION: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.

Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs.

Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.