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

Abstract

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.

Pemanfaatan informasi genom untuk eksplorasi struktur genetik dan asosiasinya dengan performan ternak di Indonesia

“…Pada tingkatan lebih lanjut, sebuah tinjauan terhadap proses sejarah dan pengembangan sapi lokal di Indonesia dengan menggunakan informasi total genom juga telah dipublikasikan [4]. Bangsa sapi lokal yang digunakan yaitu sapi Bali, Madura, Jabres, PO (secara umum), PO Kebumen, Aceh, dan Pesisir.…”

“…Hal ini mendukung hasil kajian sebelumnya yang menyatakan bahwa terjadi hibridisasi antara sapi Bos javanicus dan Bos indicus di Indonesia [5]. Hasil analisis juga menginformasikan bahwa berdasarkan nilai optimal fragmen dalam perhitungan estimasi ukuran populasi efektif pada waktu lampau diketahui bahwa domestikasi sapi Bali diperkirakan telah terjadi sekitar 3.400 tahun yang lalu [4]…”

“…Berbagai metode analisis untuk mengeksplorasi informasi genom saat ini telah berkembang dan dimanfaatkan oleh banyak kalangan, termasuk para peneliti di Indonesia. Studi tentang genom pada ternak lokal Indonesia pada saat ini masih fokus untuk mengetahui struktur genetiknya [2,3,4] dan baru sedikit kajian yang membahas keterkaitannya dengan sifat fenotip [5,6].…”

Effect of polymorphism of Insulin-induced gene 1 (INSIG1) (A4366G) on slaughter characteristics in unproductive Kebumen Ongole Grade cows

“…358/Kpts/PK.040/6/2015 completed with phenotypic and morphometric characteristics data [3]. Genetic diversity analysis both using morphometric and genomic data showed that Kebumen OG line was separated from the OG cattle in other population regions [4,5]. Surprisingly, Kebumen OG line were closely linked to Nellore cattle than to the OG cattle population [5].…”

“…Genetic diversity analysis both using morphometric and genomic data showed that Kebumen OG line was separated from the OG cattle in other population regions [4,5]. Surprisingly, Kebumen OG line were closely linked to Nellore cattle than to the OG cattle population [5]. In several previous studies, Kebumen OG line have significant larger measurement in body weight and body size than OG cattle in other population region or the Standard in Indonesia (SNI) for OG cattle breed [6,4].…”