Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences.

BACKGROUND: The cytochrome b (Cyt b) gene is one of the most studied mitochondrial DNA (mtDNA) genes to determine sheep's genetic profile. This study aimed to determine the genetic diversity and relationships of several Indonesian local sheep populations on Java Island, Indonesia, based on the mtDNA Cyt b gene sequences. Blood samples were collected from forty-one individual sheep in seven populations of Indonesia local sheep breeds on Java Island (Priangan = 6, Garut = 6, Batur = 7, Wonosobo = 5, Javanese Thin-Tailed/JTT = 7, Javanese Fat-Tailed/JFT = 5, and Sapudi = 5). DNA extraction was performed on blood samples, and the mtDNA Cyt b gene was amplified using specific primers (Alek-CBF: 5'-CAACCCCACCACTTACAA-3' and Alek-CBR: 5'-CCTTGAGTCTTAGGGAGGTT-3'). The polymerase chain reaction (PCR) products were then sequenced, and data were analyzed using the MEGA version 7.0, DNA SP version 6.0, and NTSYS-pc version 2.11 software. RESULTS: A total of 1140 bp complete mtDNA Cyt b gene sequences in this study obtained 1134 monomorphic sites (I), six polymorphic sites (V), one segregation site (S), and five parsimony informative sites (P) with a nucleotide diversity (Pi), the average number of nucleotide differences (K), and sequence conservation (SC) were 0.00119, 1.35610, and 0.9947, respectively. There were six haplotypes consisting of two unique haplotypes and four shared haplotypes with a haplotype diversity (Hd) of 0.5415. The genetic distance within and between populations ranged from 0.0000 to 0.0016 and 0.0000 to 0.0020, respectively. Wonosobo, JFT, and Sapudi sheep have the closest relationship, and then these three breeds were close to JTT sheep, followed by Batur, Priangan, and Garut sheep. Two haplogroups have been found based on the Ovine haplogroup clustering. All Wonosobo, JTT, JFT, Sapudi sheep, and most Batur sheep were clustered into haplogroup B. In contrast, Garut sheep were mostly clustered into haplogroup A, while Priangan sheep were clustered into both haplogroups with the same percentage. CONCLUSION: Seven Indonesian local sheep breeds on Java Island have a close relationship clustered into two haplogroups, namely haplogroups A and B. Most Indonesian local sheep breeds on Java Island in this study were clustered into haplogroup B, except for Garut and Priangan sheep.

Genetic variability of the prion protein gene in Indonesian goat breeds.

Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goats. Resistance or susceptibility of small ruminants to classical scrapie is influenced by polymorphisms in the prion protein gene (PRNP). PRNP variability in Indonesian indigenous goat breeds has not been investigated so far and therefore was the goal of this study. Sanger sequencing of the PRNP gene coding region in 72 goats of the seven Indonesian breeds Kacang, Gembrong, Samosir, Kejobong, Benggala, Jawarandu, and Peranakan Etawah revealed three amino acid substitutions, namely W102G, H143R, and S240P. Some silent mutations were also found at codons 42 (a/g), 138 (c/t), and 179 (g/t). The PRNP alleles K222 and D/S146 known to have significant protective effects on resistance to classical scrapie in goats were not detected. The allele R143, which may have a moderate protective effect, had a frequency of 12% among the analyzed Indonesian goat breeds. While R143 was missing in Kacang and Benggala, its frequency was highest in the breed Gembrong (32%). No scrapie cases have been reported in Indonesia until now. However, in the case that selection for protective PRNP variants would become a breeding goal, the analyzed breeds will not be very useful resources. Other goat breeds which are present in the country should be investigated regarding resistance to scrapie, too.

The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences.

BACKGROUND AND AIM: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. MATERIALS AND METHODS: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. RESULTS: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. CONCLUSION: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

The impact of religious festival on roadside livestock traders in urban and peri-urban areas of Yogyakarta, Indonesia.

BACKGROUND AND AIM: Eid al-Adha is one of the most important festivals celebrated by Muslims in Indonesia. Roadside livestock traders open their stalls during the Eid al-Adha period. This study aimed to investigate the characteristics and behaviors of roadside livestock traders in urban and peri-urban areas in Yogyakarta, Indonesia. MATERIALS AND METHODS: In-depth interviews with 36 roadside livestock traders were conducted on August 7-23, 2018 in urban (n=20) and peri-urban (n=16) areas of Yogyakarta. The collected data were analyzed by descriptive and statistical analysis using one-way analysis of variance. RESULTS: The results indicate that the trading activities of roadside livestock traders in urban areas last longer (p<0.05) than in peri-urban areas. No difference was found in the opening day of stalls, the number of buyers, and trends in animal prices set by roadside livestock traders in urban and peri-urban areas. Most traders sell sheep and goats, buy livestock at the animal market, and only open their stalls during Eid al-Adha. Prices are high in this period, and buyers directly visit the stalls. A significant difference exists in the selling price of livestock between Eid al-Adha and ordinary days (non-festival), and most roadside traders benefit from the Eid al-Adha momentum. CONCLUSION: Significant similarities exist among roadside livestock traders during the Eid al-Adha period in urban and peri-urban areas of Yogyakarta, Indonesia. Sheep are more desirable than goats and cattle in this period, and Eid al-Adha generates a high profit for roadside livestock traders.

Effects of rations containing formaldehyde-protected soybean meal on meat production in Kacang goats.

AIM: This study aimed to investigate effects of rations containing formaldehyde-protected soybean meal on meat production in Kacang goats. MATERIALS AND METHODS: Fourteen yearling Kacang bucks, weighing 15.8-19.8 kg, were arranged in a completely randomized design. The treatments included a control (PSBM0): 100% untreated SBM; PSBM50: 50% untreated SBM + 50% formaldehyde-protected SBM; and PSBM100: 100% formaldehyde-protected SBM. RESULTS: The goats disliked the protected SBM. Therefore, differences in their intakes were reflected in their average daily gain (ADG). The ADG and slaughtered weight of the control group were the highest, while those of the PSBM100 and PSBM50 groups were similar. The carcass weights and meat production of the control group were higher than those of the PSBM50 group, but the retained protein to the meat conversion ratio of the PSBM50 group was lower than that of the control. The carcass percentages were similar between the treatments. CONCLUSION: The retained protein to meat conversion ratio of Kacang goats fed with 50% formaldehyde-protected SBM showed the lowest value, indicating that these rations efficiently produced meat in the carcass.

Fat-tailed sheep in Indonesia; an essential resource for smallholders.

This paper discusses the historical development of fat-tailed sheep in Indonesia, the dynamics of production systems, production and reproduction performances under farmers' conditions, and roles of sheep in livelihoods. In the eighteenth and nineteenth century, fat-tailed sheep from southwest Asia and Africander sheep from South Africa were introduced. Crossing of fat-tailed sheep with the local thin-tailed sheep produced the Javanese fat-tailed sheep. Main motives for the gradual change-over to fat-tailed sheep have been their potential larger body size and the preference of consumers for their meat. Management systems are changing in response to the intensification of land use. The reproductive performances of fat-tailed sheep are good. Households keep four to six animals, housed close to the family quarters. This results in very high levels of faecal bacteria contamination of drinking water sources. Sheep provide a small income, manure, security and help to accumulate capital. Sheep also play a key role in religious festivities. Farmers hardly profit from the increased demand for the feast of sacrifice; animals are sold mainly when the owners have urgent cash needs. Systematic sheep fattening can contribute to higher economic results, if sufficient family labour and crop residues are available.