A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

ABSTRACT. River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH 5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. 13096-13104 (2015) to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

Stafuzza¹,

Naressi²,

Yang³

et al. 2015

“…An extensive chromosome arm homology between both species has been established through cytogenetic studies (Di Meo et al, 2008) and genetic mapping (Amaral et al, 2008). While the bovine genome consists of 29 acrocentric autosomes (single-armed) and a pair of sex chromosomes (X/Y), the buffalo genome contains 19 acrocentric (single-armed) and 5 submetacentric (biarmed) autosomes as well as the X and Y chromosomes.…”

Section: Introductionmentioning

confidence: 99%

“…Amaral et al (2008) obtained maps for the entire buffalo genome base on cattle-derived markers, with a total of 2621 markers mapped on the buffalo genome, of which 1734 were cattle-derived SNPs and the remaining 887 markers were classified as cattle sequence tagged site, including coding genes, expressed sequence tags, and microsatellites.…”

Section: Introductionmentioning

confidence: 99%

Association between single-nucleotide polymorphisms and milk production traits in buffalo

Venturini¹,

Cardoso²,

Baldi³

et al. 2014

ABSTRACT. The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferroni's correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP GWAS for milk production traits in buffalo markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.

“…The IRF1 gene has previously been mapped on river buffalo chromosome 9 using radiation hybrid panel technology (Amaral et al, 2008). Considering that this gene could be an important candidate gene for studying disease susceptibility, we characterized its molecular structure in buffalo by sequencing a clone from the buffalo large-insert BAC library.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of interferon regulatory factor 1 in Bubalus bubalis

Stafuzza¹,

Borges²,

Amaral-Trusty³

2015

ABSTRACT. Interferon regulatory factor 1 (IRF1) is functionally diverse in the regulation of immune response and is considered to be an important candidate gene for studying disease susceptibility in mammals. In this paper, we characterized the whole sequence of the IRF1 gene in river buffalo (Bubalus bubalis) and compared genomic and the amino acid sequences between different species. The buffalo IRF1 gene was 7099 bp long and organized into 10 exons and nine introns. Its molecular structure showed exactly the same number of exons (10) and introns (nine) in bovids, mice, horses, humans, and chickens. However, rats did not have exon 5, but had the largest exon 4, which suggests that exon 5 was incorporated into exon 4. The coding and the amino acid sequences of the gene showed that identity varied from 73 to 99% at the coding sequence level and from 61 to 100% at the amino acid level when compared with other mammals and chickens. Comparative analysis of the gene sequence between two different buffalo breeds, Murrah and Mediterranean, revealed six potential SNPs that are primarily located in the 5' and 3'UTRs.