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

IF 2.4 2区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Animal Bioscience Pub Date : 2024-04-01 Epub Date: 2023-11-02 DOI:10.5713/ab.23.0289
Pita Sudrajad, Hartati Hartati, Bayu Dewantoro Putro Soewandi, Saiful Anwar, Angga Ardhati Rani Hapsari, Tri Satya Mastuti Widi, Sigit Bintara, Dyah Maharani
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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.

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基于基因组数据的Sumba Ongole牛的种群多样性、混合性和人口统计学趋势。
目的:Sumba Ongole(SO)牛在印尼牛的发展中发挥着重要作用,是一个有价值的品种。尽管分子技术进步迅速,但迄今为止还没有对SO牛进行基因组研究。本研究的目的是提供与SO牛的种群多样性、混合性和人口统计学趋势相关的基因组图谱。方法:使用Illumina BovineSNP50 v3 Beadchip从79头Sumba Ongole(SO)牛身上收集基因组信息,为了进行比较,纳入了来自全球209个牛群的其他基因型。检测了预期和观察到的杂合性、近交系数、群体间的成对固定指数和Nei的遗传距离。使用多维比例、混合和树混合分析来研究种群结构。基于连锁不平衡和有效的人口规模计算,观察到了人口趋势。结果:SO牛的遗传多样性与其他标记品种相似。SO牛与印度牛有亲缘关系,但与牛头牛或巴厘牛没有亲缘关系。该研究进一步证实了SO、Ongole和Nellore牛之间的密切关系。此外,Ongole混合物的一小部分目前在SO群体中占主导地位。该研究还发现,SO和Bali牛(Bos javanicus)可能是翁戈勒级牛发展的祖先,这与翁戈勒化的历史记录相对应。我们的发现表明,SO牛保持了稳定,并具有与祖先不同的独特特征。结论:总之,SO牛的遗传多样性得到了保护,这是当前人口趋势日益重要的结果。持续的努力是保持品种健康的必要条件。
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来源期刊
Animal Bioscience
Animal Bioscience AGRICULTURE, DAIRY & ANIMAL SCIENCE-
CiteScore
5.00
自引率
0.00%
发文量
223
审稿时长
3 months
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