Swamp Buffalo Populations Research Articles

Genetic Divergence of Two Vietnamese Swamp Buffalo Populations using Microsatellite Markers

Genetic Divergence of Two Vietnamese Swamp Buffalo Populations using Microsatellite Markers

Genetic Diversity of Philippine Carabao (Bubalus bubalis) Using Mitochondrial DNA D-loop Variation: Implications to Conservation and Management

Developing rational conservation programs for Philippine carabao (PC) (Bubalus bubalis) requires knowledge on the pattern of genetic variability within and between populations of swamp buffalo. Studying the genetic diversity and phylogeographic structure is essential to understand the distribution of the Philippine swamp buffalo maternal haplotypes towards the PC conservation. This study aimed to determine the genetic diversity and the phylogeographic structure of PC using molecular approaches. D-loop of the mitochondrial DNA (mtDNA) on the PC B. bubalis (n = 107) were randomly selected from 23 populations across the islands of Luzon, Visayas, and Mindanao as major islands sub-groups. DNA was isolated from the whole blood, and the D-loop region of the swamp buffalo was amplified using the polymerase chain reaction (PCR). Purified PCR products were sequenced with the Applied Biosystems Automated 3730. Results showed that the phylogenetic analyses detected 16 mtDNA haplotypes observed with 12 variable sites and haplotype and nucleotide diversities of 0.695 ± 0.042 and 0.004 ± 0.001, respectively. This study also identified the delineation of swamp buffalo populations into major and minor groups. Among the major groups, 14 haplotypes were included, and sequences were incorporated in the maternal lineage A. Minor groups which fell in the maternal lineage B identified two new haplotypes. Thus, the current findings revealed the moderate mtDNA haplotype diversity and weak phylogeographic structure of the PC. In addition, the results of this study will serve as a vital starting point in planning effective strategies and prioritizing the genetic resources for PC conservation and management programs.

Mitochondrial sequence-based evolutionary analysis of riverine-swamp hybrid buffaloes of India indicates novel maternal differentiation and domestication patterns.

In this study, mitochondrial D-loop sequence data on riverine, swamp and hybrid buffaloes from India have been generated and compared with other reported Indian riverine, Chinese and Bangladeshi swamp buffalo populations. Sequence analysis revealed the presence of 132 haplotypes, with a haplotype diversity of 0.9611±0.0045 and a nucleotide diversity of 0.04801±0.00126. For the first time, the existence of riverine-swamp hybrids among the Indian Chilika buffalo population has been recorded, having 49 chromosomes, which was also confirmed by mitochondrial haplotype sharing between Chilika and Indian swamp as well as Chinese swamp buffalo populations in the network analysis. Phylogenetic analysis documents the sharing of reported pre-domestication haplogroups 'SA1', 'SA2', 'SA3' and 'SB1' between the Chilika and swamp buffalo populations of India, China and Bangladesh, an indication of the migration of swamp buffaloes towards Bangladesh and adjoining lower parts of India and north towards Chinese domestication sites. The results have also been supplemented by multidimension scaling, grouping Indian and Chinese swamp buffaloes more closely together with Bangladeshi buffaloes, but into a separate quadrant, whereas Chilika grouped away from other riverine as well as swamp buffaloes. These findings thus confirm the previous reports that the northeast region of India, close to the Indo-China border, is the point of evolution of swamp buffaloes with multiple sites of domestication.

Genetic Variation of Eight Indonesian Swamp-Buffalo Populations Based on Cytochrome b Gene Marker

Genetic variation is a major concern in animal genetic resources conservation program. This study aimed to analyze genetic variation and phylogeography of eight Indonesian swamp-buffalo populations based on cytochrome b gene marker. A total of 78 DNA fragment samples originating from eight Indonesian swamp-buffalo populations were used in this study, namely Bombana Island, Bombana mainland, Kolaka, Konawe, North Toraja, West Nusa Tenggara, Banten, and Aceh with 11, 10, 13, 14, 10, 10, 5, and 5 samples, respectively. The cytochrome b gene sequence and genetic variation parameters were analyzed in MEGA software (ver 6), and DnaSP software (ver 5.10.01). The results of this study showed that all DNA-fragment samples were successfully amplified by PCR technique with the size target (906 bp). Based on the distribution of all samples, it was found 9 polymorphic sites, and 10 haplotypes with the haplotype diversities were 0.6590. The average of genetic distances between populations ranged from 0.0000-0.002. They were grouped into two main clusters. The first cluster consisted of Aceh, North Toraja, West Nusa Tenggara, Banten, Kolaka, and Konawe populations, meanwhile, the second cluster consisted of Bombana Island, Bombana mainland, Kolaka, and Konawe populations. The results of the study were concluded that eight Indonesian local swamp-buffalo populations were grouped into two main clusters where Bombana Island and Bombana mainland populations were specific breeds because they were only found in the second cluster and also had specific nucleotides sites on the 57 nucleotides which C base changed to T. The results of this study were useful in formulating the program of conservation and utilization of Indonesian buffalo genetic resources, especially in the buffalo population with specific breeds.

Asian water buffalo: domestication, history and genetics.

The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000-7000years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.

Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it's uniqueness with riverine buffaloes

The present investigation was focused to study genomic diversity of Indian swamp buffalo populations through reduced representation approach (ddRAD). The heterozygosity (FST) among the swamp buffaloes was 0.11 between Assam and Manipuri; 0.20 between swamp (Manipuri) and riverine buffaloes; 0.30 between swamp (Manipuri) and cattle. The average observed and expected heterozygosity in swamp buffalo populations was 0.254 and 0.221 respectively. The Inbreeding coefficient (FIS) value was 0.02 among the swamp buffaloes. PCA and structure analysis revealed Manipuri swamp buffalo was genetically distinct and closely related to Nagaland swamp buffalo and least to Assam swamp buffalo. Identification of selective sweeps revealed 1087 regions to have undergone selection related to immune response, adaptation and nervous system. A total of 3451 SSRs were identified in the genome of swamp buffaloes. The study evidenced the genomic diversity in the swamp buffalo populations and its uniqueness in comparison with riverine buffalo and cattle.

Sequence-based structural analysis and evaluation of polymorphism in buffalo Nod-like receptor-1 gene.

In this study, we have sequence characterized and analyzed the polymorphism in buffalo NOD1 (nucleotide-binding oligomerization domain 1) gene as well as its expression analysis. Full-length sequence analysis of NOD1 revealed this gene in buffalo being conserved with respect to the domain structures, similar to other species. Alternate splice variants having exon3 skipping also identified for the first time in the gene expressed in buffalo-purified peripheral blood mononuclear cells (PBMCs). Phylogenetically ruminant species were found to be clustering together and buffalo displaying maximum similarity with cattle. Sequencing of NOD1 across 12 Indian buffalo breeds identified 23 polymorphic sites within coding region, among which 16 were synonymous and 7 changes found to be non-synonymous. Four SNPs (single nucleotide polymorphisms) of them were genotyped in 393 animals belonging to 12 riverine, swamp and hybrid (riverine × swamp) buffalo populations of diverse phenotypes and utilities, showing variable allelic frequencies. Principal component analysis revealed, riverine and swamp buffaloes being distinctly placed with the distribution of breeds within the group based on the geographical isolation. Further, quantitative real-time PCR detected NOD1 expression in multiple tissues with PBMCs and lungs showing highest expression among the tissues examined. Structural analysis based on the translated amino acid sequence of buffalo NOD1 identified four protein interaction motifs LxxLL important for ligand binding. Molecular interaction analysis of iE-DAP and NOD1-LRR and their complex stability and binding-free energy studies indicated variable binding energies in buffalo and cattle NOD1. Overall, the study reveals unique structural features in buffalo NOD1, important for species-specific ligand interaction.

Y-chromosome haplotype analysis revealing multiple paternal origins in swamp buffaloes of China and Southeast Asia.

To further probe into the paternal origins and domestication area of swamp buffaloes, we examined Y-chromosome diversity of 482 bulls representing 22 populations from China and Southeast Asia. A total of 40 bovine Y-chromosome-specific microsatellite (Y-STR) markers were screened in this study. The results showed that seven Y-STR markers (UMN2405, UMN0504, UMN0103, UMN1307, BC1.2, UMN0304 and INRA008) were specific and polymorphic in male swamp buffaloes, which can define 9 Y-haplotypes corresponding to four Y-haplogroups (Y1, Y2, Y3 and Y4). Haplogroup Y1 was predominant (83.4%) in all swamp buffalo populations, indicating haplogroup Y1 was the major domestication event of swamp buffalo. In addition, the abundant genetic background and backbone of haplogroup Y1 suggested Yangtze Valley as the major domestication area of swamp buffalo. Interestingly, haplogroup Y4 was only confined in Hainan Island which was more ancient than other haplogroups. We hypothesized that haplogroup Y4 was the descendants of the wild Asian buffalo trapped on Hainan Island in prehistoric glacier period and preserved by later introgression into domesticated cows after the domestication. In conclusion, our findings revealed four divergent paternal origins in swamp buffaloes based on Y-STR markers.

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data.

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.

Genetic diversity at MHC-DRB3 locus suggests distinctness of the riverine-swamp buffalo populations in North-East region of India

Northeast region of India is a transition zone for two genetically distinct types of water buffalo (Bubalus bubalis) - riverine (Bubalus bubalis bubalis, N=50) and swamp (Bubalus bubalis carabanesis, N=48), wherein, both types of buffalo populations and their hybrids (riverineswamp, N=49) coexist. In present study, we studied genetic variability of highly polymorphic major histocompatibility complex (MHC) class II- DRB3 gene in 94 riverine-swamp buffaloes of three different locations - central Assam (ASW; riverine and hybrid types), Silchar region (ASW-SL, swamp and hybrid types), Dibrugarh region (ASW-DB, swamp) of Assam through PCR-RFLP. A total of nine HaeIII restriction patterns HaeIII- A to I, were observed in overall populations, although only six patterns were present in ASW-DB buffaloes. The HaeIII-A, -C, -F and -H patterns were found to be homozygous, accounting about 48 percent of the total buffalo population. Based on DRB3-HaeIII restriction diversity, the genetic divergence was the highest (0.460) between ASW-SL and ASW-DB buffaloes whereas, the lowest (0.063) between ASW and ASW-DB buffaloes among three populations. In Principle Coordinate Analysis (PCA), these populations were found to be distantly located in different coordinates, indicating their genetic distinctness. Our results support that North-east region of India constitute a transition zone for both riverine and swamp buffalo populations, however, with quite distinctness of these mixed populations derived through different genetic pools. Polymorphic DRB3 locus in these riverine-swamp buffalo populations of North-East region also indicates their genetic richness.

Exploring polymorphism of prolactin gene and its possible association with repeat breeding in buffaloes

Prolactin (PRL), a polypeptide hormone is important for a number of biological functions. In livestock, genetic polymorphism of PRL has been found to be associated with various production and reproduction traits. Here, we explored genetic variability in regulatory and signal peptide encoding regions of PRL gene and its possible association with fertility trait in water buffalo (Bubalus bubalis) – a major livestock species of South Asia. Showing low genetic variability overall across the buffalo populations, a total of three SNPs – two in promoter (-C754T and -A516G) and one in exon 2 (C3666T) were identified in 2.2kb long region characterized from a pool of 12 buffalo populations. Importantly, the SNP at C3666T locus in exon 2 region caused a substitution of hydrophilic arginine (Arg, CGC) residue with hydrophobic cysteine (Cys, TGC) of signal peptide, leading to expansion of hydrophobic domain; and predictably found afflicting the cleavage site. Genotyping of two SNPs (-C754T and C3666T) was carried out by PCR-RFLP (BsrI) and tetra primer-ARMS PCR, respectively in 288 animals belonging to eight different riverine and swamp buffalo populations. The frequency of T allele, encoding hydrophobic cysteine in signal peptide at C3666T locus was found to be very high (0.882) in buffaloes, overall. Principle Coordinates Analysis revealed clustering of riverine buffalo populations (except Toda and Chilika), diverging from swamp type. A univariate logistic regression analysis conducted to explore association of buffalo PRL SNPs with fertility trait revealed that the genotypic frequencies for both loci (-C754T and C3666T) were found to have no significant difference between normal (n=25) and repeat (n=36) breeder Murrah buffaloes. Interestingly, a very high frequencies of T allele – responsible for Arg>Cys substitution – at C3666T locus were observed in both repeat (0.972) and normal (0.920) breeder groups. Since, maturation and secretion of the PRL hormone is strongly determined by signal peptide, our study provides an insight on the genetic variability in PRL promoter and signal peptide regions and its possible role in repeat breeding in buffaloes.

HSFY and ZNF280BY show copy number variations within 17 water buffalo populations.

Recent transcriptomic analysis of the bovine Y chromosome revealed abundant presence of multi-copy protein coding gene families on the male-specific region of the Y chromosome (MSY). Copy number variations (CNVs) of several MSY genes are closely related to semen quality and male reproduction in cattle. However, the CNVs of MSY genes in water buffalo are largely unknown. Therefore, this study aimed to investigate the CNVs of HSFY and ZNF280BY of 298 buffaloes from 17 populations distributed in China, Vietnam and Laos using quantitative PCR. Our results revealed that the median copy numbers of the HSFY and ZNF280BY genes were 47 (ranging from 20 to 145) and 269 (ranging from 73 to 974) respectively. In conclusion, this study indicated that HSFY and ZNF280BY showed abundant CNVs within swamp buffalo populations.

Identification of polymorphism in fatty acid binding protein 3 (FABP3) gene and its association with milk fat traits in riverine buffalo (Bubalus bubalis)

The fatty acid binding protein 3 (FABP3) gene, known to be associated with fat percentage of milk and meat in bovines, was screened among swamp and riverine buffaloes for polymorphism detection and further association with milk fat contents. An SNP g.307C > T was identified in the intron 2 (+53 exon 2) region of FABP3 gene of Indian buffaloes. The SNP identified was genotyped in 692 animals belonging to 15 riverine, swamp and hybrid (riverine × swamp) buffalo populations of diverse phenotypes and utilities, by PCR-RFLP. A marked contrast was observed between the C and T allele frequencies in three types of buffaloes. The frequency of C allele ranged from 0.67 to 0.96 in pure swamp buffalo populations, with the highest in Mizoram (0.96). Whereas the frequency of T allele was high across all the Indian riverine buffalo breeds, ranging from 0.57 to 0.96. None of the genotypes at FABP3 g.307C > T locus was found to have significant association with milk fat and other production traits in Mehsana dairy buffalo breed. Our study revealed marked differences in the allele frequencies between riverine and swamp buffaloes at FABP3 g.307C > T locus, without any significant association with different milk traits in riverine buffaloes.

De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.

The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.

Genetic diversity analysis of buffalo fatty acid synthase (FASN) gene and its differential expression among bovines

Fatty Acid Synthase (FASN) gene seems to be structurally and functionally different in bovines in view of their distinctive fatty acid synthesis process. Structural variation and differential expression of FASN gene is reported in buffalo (Bubalus bubalis), a bovine species close to cattle, in this study. Amino acid sequence and phylogenetic analysis of functionally important thioesterase (TE) domain of FASN revealed its conserved nature across mammals. Amino acid residues at TE domain, responsible for substrate binding and processing, were found to be invariant in all the mammalian species. A total of seven polymorphic nucleotide sites, including two in coding region of TE domain were identified across the 10 buffalo populations of riverine and swamp types. G and C alleles were found almost fixed at g18996 and g19056 loci, respectively in riverine buffaloes. Principal component analysis of three SNPs (g18433, g18996 and g19056) revealed distinct classification of riverine and swamp buffalo populations. Reverse Transcription-PCR amplification of mRNA corresponding to exon 8–10 region of buffalo FASN helped in identification of two transcript variants; one transcript of 565 nucleotides and another alternate transcript of 207 nucleotides, seems to have arisen through alternative splicing. Both the transcripts were found to be expressed in most of the vital tissues of buffalo with the highest expression in mammary gland. Semi-quantitative and real-time expression analysis across 13 different buffalo tissues revealed its highest expression in lactating mammary gland. When compared, expression of FASN was also found to be higher in liver, adipose and skeletal muscle of buffalo tissues, than cattle. However, the FASN expression was highest in adipose among the three tissues in both the species. Results indicate structural and functional distinctiveness of bovine FASN. Presence of alternate splicing in buffalo FASN also seems to be a unique phenomenon to the bovines, probably associated with mRNA based regulation of the biological functions of FASN in these species.

Phylogeography and Domestication of Chinese Swamp Buffalo

To further probe into whether swamp buffaloes were domesticated once or multiple times in China, this survey examined the mitochondrial DNA (mtDNA) Control Region (D-loop) diversity of 471 individuals representing 22 populations of 455 Chinese swamp buffaloes and 16 river buffaloes. Phylogenetic analysis revealed that Chinese swamp buffaloes could be divided into two distinct lineages, A and B, which were defined previously. Of the two lineages, lineage A was predominant across all populations. For predominant lineage A, Southwestern buffalo populations possess the highest genetic diversity among the three hypothesized domestication centers (Southeastern, Central, and Southwestern China), suggesting Southwestern China as the most likely location for the domestication of lineage A. However, a complex pattern of diversity is detected for the lineage B, preventing the unambiguous pinpointing of the exact place of domestication center and suggesting the presence of a long-term, strong gene flow among swamp buffalo populations caused by extensive migrations of buffaloes and frequent human movements along the Yangtze River throughout history. Our current study suggests that Southwestern China is the most likely domestication center for lineage A, and may have been a primary center of swamp buffalo domestication. More archaeological and genetic evidence is needed to show the process of domestication.

Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo

The origins of the domestic water buffalo remain contentious. To better understand the origins of Chinese water buffalo, we sequenced the complete mitochondrial cytochrome b (MT-CYB) gene from 270 individuals representing 13 Chinese domestic swamp buffalo populations. We found genetic evidence of introgression of river buffalo into Chinese swamp buffalo herds. Swamp buffalo haplotypes can be divided into two highly divergent lineages (A and B), suggesting that Chinese native swamp buffalo have two maternal origins. We found that the A→G transition in the buffalo MT-CYB gene stop codon resulted in buffalo haplotypes being terminated by one of two stop codons: AGA or AGG. AGA is common to river buffalo and lineage A of swamp buffalo, while AGG is specific to lineage B of swamp buffalo. Lineage A appears to have been domesticated in China. Further genetic evidence is required to clarify the origins of lineage B.

Genetic distance estimation of local swamp buffaloes through morphology analysis approach.

Information about genetic distances among populations (geographics) of local swamp buffalo is less published. Genetic distance analysis was done among seven local swamp buffalo populations trhough a morphological analysis. Female and male buffaloes were observed for a total number of 905 hds, originating from the Provices of NAD (100 hds), North Sumatera (51 hds), Banten (180 hds), Central Java (203 hds), South Kalimantan (121 hds), NTB (200 hds), dan South Sulawesi (50 hds). Genetic variation among buffalo populations was calculated by discriminant function of Mahalonobis distance. Genetic distance was estimated by MEGA program. Morphometric measurements of female buffalo in North Sumatera were larger (P < 0,01) than those of buffaloes in Banten, South Kalimantan, NAD and South Sulawesi. Morphometric measurements of male buffalo in South Sulawesi were larger than those of buffaloes in Central Java, Banten, and NAD. Chest width was the highest different morphometric factor (0.969). Buffalo from NTB had the highest similarity (95.0%), followed by buffaloes from North Sumatera (74.51%) and South Sulawesi (74.19%); while the lowest one was from South Sulawesi (38.02%) and Banten (49.44%). Morphological distribution map indicated existence of three local swamp buffalo groups. Grup 1 was presented by buffalo from NTB, distributed in the II and III quadrants. Group 2 was presented by buffaloes from five locations (North Sumatera, Central Java, South Kalimantan, South Sulawesi, and Banten), distrributed in I and II quadrants, and a smaller part distributed in III and IV quadrants. Group 3 was presented by buffaloes from NAD and a smaller part from South Kalimantan and Banten, distributed in IV quadrant. The lowest genetic distance was identified between buffaloes in NAD and South Kalimantan (0.348), while the highest one was between buffloes in Banten and South Kalimantan (1.883). Based on phenogram tree structure, the observed local swamp buffaloes could be classified into 3 cluster, namely: Cluster 1 from South Kalimantan, NAD and Banten; Cluster 2 from South Sulawesi, Central Java and North Sumatera, and Cluster 3 from NTB. Key Words: Swamp Buffalo, Morphology, Discriminant Analysis, Genetic Distance

Genetic characteristics on exon 4 of prolactin gene in 12 water buffalo populations

The prolactin exerts obvious adjustment and control function for mammary gland development, lactation and milk protein gene expression in water buffalo. In this study the sequence features and polymorphisms of the exon 4 in prolactin gene were examined in 385 individuals which came from 12 river and swamp type buffalo populations using DNA direct sequencing and PCR-SSCP methods. The results showed that the sequence of exon 4 in prolactin gene was consists of 180 nucleotides, the fragment had high conservative character in different species. The e4. 109 C>T substitution was detected in nine swamp buffalo populations, and it was a silent mutation and was not associated with the traits of milk yield in buffalo. The PBA gene was the predominant gene in seven swamp type buffalo populations, while PBB gene was the dominant gene in Dehong and Fuzhong populations. The frequencies of PBA in swamp type buffalo was 0.400 -0.917 and the average value was 0.629+/-0.049. The polymorphism wasn't found in river buffalo, all the samples from river buffalo were holding nucleotides e4.109 C. The results indicate that there is distinct genetic differentiation between swamp and river type buffalo.

Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers

To determine genetic diversity and evolutionary relationships among Chinese buffalo populations, 18 indigenous swamp buffalo populations and two introduced river buffalo breeds were genotyped for 30 microsatellite loci. The mean number of alleles across the 30 loci was 8.13, and the expected heterozygosity ranged from 0.517 (Yanjin) to 0.609 (Dehong). Although there was abundant genetic variation, genetic differentiation between Chinese buffalo populations was low, with only 2.8% of the total genetic variance among populations. The genetic differentiation pattern and genetic relationships among Chinese buffalo populations were consistent with their geographic distribution. The Dehong population was discerned as a distinct indigenous population, but suffered genetic admixture with river buffalo. The remaining populations were divided into four major clusters, i.e. the Upper and Middle Reaches of Yangtze Valley cluster (Guizhou, Guizhoubai, Yanjin, Fuling, Enshi and Jianghan), the Lower Reaches of Yangtze Valley cluster (Haizi, Shanqu and Dongliu), the South China cluster (Fuan and Xinfeng) and the Southwest China cluster (Xinglong, Xilin, Diandongnan and Dechang).