Biodiversity of Indonesian indigenous buffalo: First review of the status, challenges, and development opportunities.

In Indonesia, the buffalo is important for small and marginal farmers' livelihood and economic development as a source of food, working animal, and tourist attraction. Therefore, an in-depth study is needed to examine challenges and opportunities for buffalo development in Indonesia. In Indonesia, the buffalo is divided into two types: swamp buffalo and river buffalo. The buffalo population in Indonesia has declined significantly. A decrease of approximately 39.35% was recorded from 2022 to 2017. The decline occurred due to low reproduction rate and suboptimal rearing management systems. There are three buffalo-rearing systems: Intensive, semi-intensive, and extensive. The productivity of buffalo is diverse and closely related to the characteristics of the regional agroecosystem, consistent with existing natural resources and rearing management systems. The diversity of buffalo productivity provides a good opportunity to improve productivity. Improvement of buffalo genetics is urgently needed, by improving mating management, etc., especially to reduce potential inbreeding. In recent years, genetic and molecular research on Indonesian buffalo has made progress, including use of molecular markers, such as microsatellites and single-nucleotide polymorphisms, to evaluate genetic diversity within and among buffalo populations across Indonesia. In addition, studies are being conducted on the relationship of genotype mutations that contribute to appearance and phenotypic performance (heat stress, reproduction, behavior, coat color, and production attributes) in buffaloes. Identification of genetic diversity in local buffaloes can be improved using various genetic and genomic techniques. These findings will form a basis for the targeted conservation of local buffaloes in Indonesia. This study aimed to collect information on the genetic resources of the local buffalo, particularly its status and production system and provide recommendations for developing buffalo production in Indonesia.

Association of selected gene polymorphisms with thermotolerance traits in cattle - A review.

Thermal stress due to extreme changes in the thermal environment is a critical issue in cattle production. Many previous findings have shown a decrease in feed intake, milk yield, growth rate, and reproductive efficiency of cattle when subjected to thermal stress. Therefore, selecting thermo-tolerant animals is the primary goal of the efficiency of breeding programs to reduce those adverse impacts. The recent advances in molecular genetics have provided significant breeding advantages that allow the identification of molecular markers in both beef and dairy cattle breeding, including marker-assisted selection (MAS) as a tool in selecting superior thermo-tolerant animals. Single-nucleotide polymorphisms (SNPs), which can be detected by DNA sequencing, are desirable DNA markers for MAS due to their abundance in the genome's coding and non-coding regions. Many SNPs in some genes (e.g., HSP70, HSP90, HSF1, EIF2AK4, HSBP1, HSPB8, HSPB7, MYO1A, and ATP1A1) in various breeds of cattle have been analyzed to play key roles in many cellular activities during thermal stress and protecting cells against stress, making them potential candidate genes for molecular markers of thermotolerance. This review highlights the associations of SNPs within these genes with thermotolerance traits (e.g., blood biochemistry and physiological responses) and suggests their potential use as MAS in thermotolerant cattle breeding.

Genetic polymorphisms of the 5' untranslated regions of the HSP70 gene in Indonesian cattle populations.

Background and Aim: Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. HSP70 is a conserved, sensitive, and abundant gene associated with heat stress's physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the HSP70 gene (5' untranslated region [UTR]) in seven cattle populations in Indonesia. Materials and Methods: Polymerase chain reaction products (551 bp) of the HSP70 gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue x Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method. Results: Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy-Weinberg equilibrium (p>0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the HSP70 gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue x PO crossbred cattle were farther apart. Conclusion: The polymorphisms in the 5' UTR of the HSP70 geneidentified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.

Genetic variation in the first intron and exon of the myostatin gene in several Indonesian cattle populations.

BACKGROUND AND AIM: Myostatin (MSTN), a member of the transforming growth factor-b family, is a negative regulator of muscle mass. This study aimed to detect the genetic variation of the 1160 bp fragment of exon 1 and part of intron 1 of the MSTN gene in several cattle populations raised in Indonesia. MATERIALS AND METHODS: Polymerase chain reaction products of the MSTN gene amplified from 92 animals representing 10 cattle populations (Peranakan Ongole [PO], Belgian Blue x PO cross, Rambon, PO x Bali cross, Jabres, Galekan, Sragen, Donggala, Madura, and Bali) were sequenced, compared, and aligned with bovine MSTN of Bos taurus (GenBank Acc. No. AF320998.1) and Bos indicus (GenBank Acc. No. AY794986.1). RESULTS: Four nucleotide substitutions (nt 1045 and 1066 in intron 1; nt 262 and 418 in exon 1) and two indels (nt 807 and 869 in intron 1) were synonymous mutations. Among these substitutions, only the nt 262G>C and nt 418A>G loci were polymorphic in all populations, except Bali cattle. The frequencies of the nt 262C (0.82) and nt 418A (0.65) alleles were highest. For the nt 262G>C locus, the CC genotype had the highest frequency (0.66) followed by GC (0.30) and CC (0.03). For the nt 418A>G locus, the AG genotype had the highest frequency (0.52) followed by AA (0.39) and GG (0.09). CONCLUSION: The results, showing genetic variations in exon 1 and intron 1 of the MSTN gene, might be helpful for future association studies.

Phenotypic characterization and principal component analyses of indigenous chicken breeds in Indonesia.

BACKGROUND AND AIM: Understanding the phenotypic characteristics of indigenous livestock breeds is essential for their utilization and conservation. This study aimed to characterize indigenous chicken breeds in Indonesia based on phenotypic traits. MATERIALS AND METHODS: Data on eight qualitative and 12 quantitative traits were recorded for 250 chickens from six breeds: Black Kedu, Gaga, Merawang, Nunukan, Pelung, and Sentul. Data were analyzed using descriptive statistics and one-way analysis of variance to test the effect of breed on observed traits. Moreover, principal component analysis (PCA) was conducted separately for each chicken breed. Data on quantitative traits were subjected to Kaiser-Meyer-Olkin, which was computed to test the sampling adequacy and the pattern of correlation among the traits, and Bathlett's tests were used to assess the validity of the factor analysis of each of the datasets and determine whether the partial correlations among traits were small. RESULTS: We found considerable phenotypic variation in both qualitative and quantitative traits among indigenous chicken breeds. Multicolored plumage (96.40%), wild plumage (39.20%), gold feather flick (51.20%), yellow shank (36.80%), single comb (80.80%), red comb (94.80%), red earlobe (77.60%), and orange eyes (61.60%) were the most common features in the indigenous chickens. In addition, breed had a significant effect on all the quantitative traits that were analyzed (p<0.05). There were higher mean values for all quantitative traits for Pelung chickens than other chickens. In addition, the overall mean values for all quantitative traits in Merawang chicken were intermediate between Pelung chickens and Black Kedu, Gaga, and Nunukan chickens. The PCA showed two principal factors extracted that accounted for 77.80% and 78.38% of the total variance in the original variables for males and females, respectively. CONCLUSION: In general, body weight and body measurements, except wattle length, were loaded in PC1 as the primary factors responsible for the variation. The phenotypic variation observed in indigenous chickens in Indonesia could provide valuable basic information for the design of selection and genetic improvement programs.

Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations.

OBJECTIVE: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. METHODS: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. RESULTS: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations (FIT = 0.237), was partly due to the heterozygote deficiency within populations (FIS = 0.114) and moderate level of genetic differentiation among populations (FST = 0.137). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. CONCLUSION: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.