An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

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.

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.

Morphometric and physical characteristics of Indonesian beef cattle

To assess their potential for beef production, this study describes the morphometrics, physical traits, and body weight of 1034 Indonesian beef cattle from eight breeds, namely Bali, Rambon, Madura, Ongole Grade, Kebumen Ongole Grade, Sasra, Jabres, and Pasundan. An analysis of variance in addition to cluster, Euclidean distance, dendrogram, discriminant function, stepwise linear regression, and morphological index analyses were performed to describe the differences in traits among breeds. The morphometric proximity analysis revealed two distinct clusters with a common ancestor, where the first cluster included Jabres, Pasundan, Rambon, Bali, and Madura cattle and the second included Ongole Grade, Kebumen Ongole Grade, and Sasra cattle, with an average suitability value of 93.20 %. This showed that the classification and validation methods can be used to distinguish breeds. The most important factor in estimating body weight was the heart girth circumference. Ongole Grade cattle had the highest cumulative index, followed by Sasra, Kebumen Ongole Grade, Rambon, and Bali cattle. A cumulative index value > 3 can be used as a threshold for determining the type and function of beef cattle.

Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.

Comparison of growth curve models for Ongole Grade cattle

Growth curves are important for understanding the growth phase and specific characteristics of farm animals. This study evaluated growth curve models to predict the age at puberty and growth rate of Ongole Grade cattle. The study used the weights of cattle from birth to 5 years old in 2011 to 2019 obtained from the Beef Cattle Research Station. The data were analyzed using four non-linear growth curve models: Brody, von Bertalanffy, logistic, and Gompertz. The coefficients of determination (R²) of the growth equation for the respective models were in the high range. The lowest Akaike's information criterion (AIC) value for males and females was obtained by the Brody and logistic models, respectively. Males with the von Bertalanffy, logistic, and Gompertz models had an estimated age and body weight at puberty of 12.56 months and 198.93 kg, 21.46 months and 298.43 kg, and 15.71 months and 235.49 kg, respectively, while females had an estimated age and body weight of 11.79 months and 166.44 kg, 13.94 months and 164.08 kg, and 11.76 months and 169.57 kg, respectively. The Brody function best fit the growth rate and exhibited the smallest mean deviation.

Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

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_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.