RESUMO
BACKGROUND: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. RESULTS: A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). CONCLUSION: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
Assuntos
Búfalos/genética , Bovinos/genética , Genoma , Mapeamento de Híbridos Radioativos , Animais , Cromossomos de Mamíferos/genética , Etiquetas de Sequências Expressas , Marcadores Genéticos , Genômica , Repetições de Microssatélites , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
The sequence of myostatin gene (growth differentiation factor 8 [GDF 8]) in Indian riverine buffalo (Bubalus bubalis) is reported. The genomic DNA as well as mRNA were sequenced. The sequence is conserved across all the livestock species. Five nonsynonymous changes as compared to cattle were found in this study and were also confirmed by mRNA sequence. Two intronic single nucleotide polymorphisms (SNPs) were identified in buffalo.
Assuntos
Búfalos/genética , Fator de Crescimento Transformador beta/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA/química , DNA/genética , Dados de Sequência Molecular , Músculo Esquelético/fisiologia , Miostatina , Reação em Cadeia da Polimerase/veterinária , Polimorfismo de Fragmento de Restrição , Polimorfismo de Nucleotídeo Único , Alinhamento de SequênciaRESUMO
Estimation of genetic variability and relationship among different livestock breeds is important for management of genetic resources for their sustainable utilization and conservation. This is more important when the livestock species, like camel, have shown a sharp decline in head count during the last decade. In the present study we estimated genetic variability and relationship among four camel breeds of India using 23 microsatellite loci. A total of 252 alleles were observed across all the four populations with mean number of alleles per locus as 8.04, 7.30, 6.39, and 7.43 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively. The mean observed heterozygosity of the four breeds were 0.58, 0.57, 0.56, and 0.60 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively and were lower than expected heterozygosity values. The mean estimates of F statistics were 0.227+/-0.044 (F(IT)), 0.157+/-0.038 (F(IS)), and 0.082+/-0.019 (F(ST)). The values were significantly different from zero for all the three measures and point towards the existence of population structure and moderate differentiation in four camel breeds. The exact test also indicated significant population differentiation (P < 0.001). The analysis of molecular variance revealed 12% of the variation attributed to among populations and 88% within populations. Sixty-nine percent of the individuals could be correctly assigned using "leave one out" procedure. All the individuals of Mewari and 42 out of 44 Jaisalmeri were correctly assigned. The existence of strong population structure in Jaisalmeri and Mewari camel was further substantiated by Nei's standard genetic distance as well as interindividual allele sharing distance. Thus these two breeds owing to selection for specific traits are distinct from other camel breeds.
Assuntos
Camelus/genética , Alelos , Animais , Conservação dos Recursos Naturais , DNA/química , DNA/genética , Variação Genética , Genética Populacional , Índia , Repetições de Microssatélites/genética , Reação em Cadeia da Polimerase/veterinária , Análise de Sequência de DNARESUMO
The positional candidate diacylglycerol O-acyltransferase (DGAT1) gene affecting milk fat percentage is reported in Indian buffaloes (Bubalus bubalis). A comparison with Chinese buffalo (Bubalus bubalis) revealed eight exonic single nucleotide polymorphisms (SNPs), five of which were non-synonymous. A total of 19 SNPs were observed among diverse buffalo breeds in India. A Unique 22 base insertion has been reported in the intron between exon ten and eleven.
RESUMO
BACKGROUND: Indian cattle (Bos indicus) and riverine buffalo (Bubalus bubalis) give a poor yield of milk but it has a high fat and protein percentage compared to taurine cattle. The identification of QTLs (Quantitative Trait Loci) on BTA14 and BTA6 and its subsequent fine mapping has led to identification of two non conservative mutations affecting milk production and composition. Our objective was to estimate the frequency of K232A (DGAT1--diacylglycerol-acyltransferase 1) and Y581S (ABCG2--ATP binding cassette sub family G member 2) polymorphisms in diverse cattle and buffalo breeds of India having large variation in terms of milk production. RESULTS: We screened the reported missense mutations in six cattle and five buffalo breeds. The DGAT1K and ABCG2Y alleles were found to be fixed in Indian cattle and buffalo breeds studied. CONCLUSION: This study provides an indirect evidence that all the Indian cattle and buffalo breeds have fixed alleles with respect to DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent.
Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Búfalos/genética , Bovinos/genética , Diacilglicerol O-Aciltransferase/genética , Lactação/genética , Polimorfismo Genético/fisiologia , Animais , Sequência de Bases , Búfalos/fisiologia , Bovinos/fisiologia , DNA/química , Gorduras/química , Leite/química , Proteínas do Leite/química , Dados de Sequência Molecular , Mutação , Locos de Características Quantitativas/genéticaRESUMO
We report the myostatin gene sequence of Bos indicus cattle in comparison to Bos taurus. B. indicus genomic sequence was obtained by overlapping PCR amplification of genomic DNA. Exon splice sites were confirmed by mRNA sequencing. There were 5 exonic single nucleotide polymorphisms (SNP) only one of which was a non-synonymous mutation that resulted in a serine to asparagine (S214N) amino acid substitution. The B. indicus gene has two insertions of 16 and 12 bases in the first intron. In addition, SNPs in the 3' UTR and intronic regions are also reported.
