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Population diversity, admixture, and demographic trend of the Sumba Ongole cattle based on genomic data |
Pita Sudrajad1,2 
, Hartati Hartati2
, Bayu Dewantoro Putro Soewandi2
, Saiful Anwar3
, Angga Ardhati Rani Hapsari4
, Tri Satya Mastuti Widi1
, Sigit Bintara1
, Dyah Maharani1,*
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1Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
2Research Center for Animal Husbandry, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
3Research Center for Applied Zoology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
4Indonesian Research Institute for Animal Production, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Bogor, 16002, Indonesia |
Correspondence:
Dyah Maharani, Tel: +62-274-513363, Email: d.maharani@ugm.ac.id
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Received: 7 August 2023 • Revised: 18 September 2023 • Accepted: 20 October 2023 |
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| Abstract |
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. |
| Keywords:
Admixture; Demography; Diversity; Genom; Sumba Ongole Cattle |
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