All identified alleles in this study were able to classify the cattle population into three clusters i.e. Bos taurus cluster (Simmental Purebred, Simmental Crossbreed, and Friesian Holstein cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).

ABSTRAKTelah dilakukan suatu penelitian untuk mengevaluasi keragaman genetik sapi Sumba Ongole (SO) berdasarkan DNA mikrosatelit dan mengkaji potensi sapi SO sebagai sapi potong lokal Indonesia berdasarkan kemampuan produksi karkasnya. Sebanyak 28 sampel darah sapi SO digunakan untuk melakukan karakterisasi genetik menggunakan 12 pasang primer DNA mikrosatelit yang direkomendasikan oleh FAO. Data produksi karkas dan bobot kulit berasal dari 506 ekor sapi SO yang dipotong di rumah potong hewan Karawaci, Banten, Indonesia. Nilai heterozigositas 12 lokus mikrosatelit berkisar antara 0,143 sampai dengan 1,000 (rata-rata 0,536). Nilai PIC tertinggi (0,814) ditemukan pada lokus TGLA122 sedangkan nilai terendah (0,280) ditemukan pada lokus BM1818. Sapi dengan bobot potong 351-475 kg merupakan sapi yang paling banyak dipotong pada tahun 2013 dan 2014 dengan persentase karkas antara 52,89% sampai dengan 53,43%. Persentase karkas tertinggi (56,34%) diperoleh dari sapi dengan bobot potong 626-650 kg. Sementara itu persentase karkas terendah (51,42%) diperoleh dari sapi dengan bobot potong 250-275 kg. Hasil karakterisasi genetik menunjukkan bahwa seluruh lokus mikrosatelit berada dalam kondisi beragam dan dapat digunakan untuk mendeteksi level keragaman genetik populasi sapi SO. Hasil studi produksi karkas menunjukkan bahwa sapi SO memiliki potensi yang sangat baik sebagai sapi potong bila dibandingkan dengan bangsa sapi potong lokal lain di Indonesia. ABSTRACTA study was conducted to assess the genetic characterization of the Sumba Ongole (SO) cattle based on DNA microsatellites and also to study the potency of SO cattle based on carcass productivity. Blood samples were collected from 28 individual cattle and 12 microsatellite primers as recommended by FAO were used to identify the genetic characterization of the SO cattle population. Data of carcass productivity were collected from 506 individual cattle that slaughtered in Karawaci abattoir, Banten, Indonesia. The heterozygosity values of microsatellite loci ranged from 0.143 to 1.000 (mean 0.536). The highest PIC values was 0.814 (locus TGLA122), while the lowest was 0.280 (locus BM1818). Cattle in range of 351-475 kg slaughter weight was most slaughtered in year 2013 and 2014 with carcass percentage ranged from 52.89% to 53.43%. The highest carcass percentage (56.34%) was obtained from cattle in range of 626-650 kg slaughter weight while the lowest (51.42%) was obtained from cattle in range of 250-275 kg slaughter weight. The results of genetic characterization showed that all microsatellite locus were highly polymorphic and highly informative for detecting the level of genetic diversity in the SO cattle population. The results of carcass productivity showed that the SO cattle has excellent potential as beef cattle compare with other local breeds cattle in Indonesia.

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.

Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.

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