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1.  A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome one (BBU1) 
Cytogenetic and genome research  2007;119(0):100-104.
The largest chromosome in the river buffalo karyotype, BBU1, is a submetacentric chromosome with reported homology between BBU1q and bovine chromosome 1 and between BBU1p and BTA27. We present the first radiation hybrid map of this chromosome containing 69 cattle derived markers including 48 coding genes, 17 microsatellites and four ESTs distributed in two linkage groups spanning a total length of 1330.1 cR5000. The RH map was constructed based on analysis of a recently developed river buffalo-hamster whole genome radiation hybrid (BBURH5000) panel. The retention frequency of individual markers across the panel ranged from 17.8% to 52.2%. With few exceptions, the order of markers within linkage groups is identical to the order established for corresponding cattle RH maps. The BBU1 map provides a starting point for comparison of gene order rearrangements between river buffalo chromosome 1 and its bovine homologs.
doi:10.1159/000109625
PMCID: PMC3780412  PMID: 18160788
2.  Nutrition and Physical Activity in Aging, Obesity, and Cancer 
The analysis of complex genetic traits, including mapping and identification of causative genes, has long been an enigma of genetic biology, whether in the animal sciences or in medical sciences. Traits of agricultural interest and traits of medical interest are often under the influence of both environmental factors and multiple genes, each with modest contributions to the total variance in the trait. Although the number of known mutations underlying complex traits is still relatively small, advances in genomics have greatly enhanced traditional pathways to their analysis and gene mining. The candidate gene approach, linkage analysis, and association studies are all significantly more powerful with recent advances in genome mapping, sequencing, and analysis of individual variation. Avenues to gene discovery are discussed with emphasis on genome wide association studies (GWAS) and the use of single nucleotide polymorphisms (SNPs) as revealed by increasingly powerful commercially available microarrays.
doi:10.1111/j.1749-6632.2012.06733.x
PMCID: PMC3483623  PMID: 23050961
genomics; complex traits; animals, disease resistance; GWAS
6.  Water Buffalo Genome Science Comes of Age 
The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species.
PMCID: PMC2892297  PMID: 20582226
Water buffalo; Genome resources; Cytogenetics; Whole genome mapping; next generation sequencing; Genome biotechnology.
7.  A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly 
Genomics  2008;92(4):210-218.
A 10,000-rad radiation hybrid cell panel of the rhesus macaque was generated to construct a comprehensive RH map of chromosome 5. The map represents 218 markers typed in 185 RH clones. The 4,846 cR length map has an average marker spacing of 798 kb. Alignments of the RH map to macaque and human genome sequences confirm a large inversion and reveal a previously unreported telomeric inversion. The macaque genome sequence indicates small translocations from the ancestral homolog of macaque chromosome 5 to macaque chromosome 1 and 6. The RH map suggests that these are likely assembly artifacts. Unlike the genome sequence, the RH mapping data indicate the conservation of synteny between macaque chromosome 5 and human chromosome 4. This study shows that the 10,000-rad panel is appropriate for the generation of a high-resolution whole genome RH map suitable for the verification of the rhesus genome assembly.
doi:10.1016/j.ygeno.2008.05.013
PMCID: PMC2605074  PMID: 18601997
Comparative mapping; Macaque and Human genomes; Rhesus macaque; RH map; Radiation hybrid
8.  A high resolution RH map of the bovine major histocompatibility complex 
BMC Genomics  2009;10:182.
Background
The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence.
Results
Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC.
Conclusion
These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.
doi:10.1186/1471-2164-10-182
PMCID: PMC2682492  PMID: 19393056
9.  High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly 
BMC Genomics  2007;8:310.
Background
High resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high resolution RH maps of bovine chromosomes 19 (BTA19) and 29 (BTA29), and compare them with the current 7.1X bovine genome sequence assembly (bovine build 3.1). We have chosen BTA19 and 29 as candidate chromosomes for mapping, since many Quantitative Trait Loci (QTL) for the traits of carcass merit and residual feed intake have been identified on these chromosomes.
Results
We have constructed high resolution maps of BTA19 and BTA29 consisting of 555 and 253 Single Nucleotide Polymorphism (SNP) markers respectively using a 12,000 rad whole genome RH panel. With these markers, the RH map of BTA19 and BTA29 extended to 4591.4 cR and 2884.1 cR in length respectively. When aligned with the current bovine build 3.1, the order of markers on the RH map for BTA19 and 29 showed inconsistencies with respect to the genome assembly. Maps of both the chromosomes show that there is a significant internal rearrangement of the markers involving displacement, inversion and flips within the scaffolds with some scaffolds being misplaced in the genome assembly. We also constructed cattle-human comparative maps of these chromosomes which showed an overall agreement with the comparative maps published previously. However, minor discrepancies in the orientation of few homologous synteny blocks were observed.
Conclusion
The high resolution maps of BTA19 (average 1 locus/139 kb) and BTA29 (average 1 locus/208 kb) presented in this study suggest that by the incorporation of RH mapping information, the current bovine genome sequence assembly can be significantly improved. Furthermore, these maps can serve as a potential resource for fine mapping QTL and identification of causative mutations underlying QTL for economically important traits.
doi:10.1186/1471-2164-8-310
PMCID: PMC2064936  PMID: 17784962
10.  A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits 
BMC Genomics  2006;7:53.
Background
A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL.
Results
Therefore, we constructed a high-resolution radiation hybrid (RH) map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken) achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included.
Conclusion
The gene-anchored high-resolution RH map (1 locus/300 kb) for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and annotation of the currently existing bovine genome sequence draft to establish the final architecture of BTA6. Hence, a sequence-based map will provide a key resource to facilitate prospective continued efforts for the selection and validation of relevant positional and functional candidates underlying QTL for milk production and growth-related traits mapped on BTA6 and on similar chromosomal regions from evolutionary closely related species like sheep and goat. Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies.
doi:10.1186/1471-2164-7-53
PMCID: PMC1475854  PMID: 16542434
11.  Application of disease-associated differentially expressed genes – Mining for functional candidate genes for mastitis resistance in cattle 
Genetics, Selection, Evolution : GSE  2003;35(Suppl 1):S19-S34.
In this study the mRNA differential display method was applied to identify mastitis-associated expressed DNA sequences based on different expression patterns in mammary gland samples of non-infected and infected udder quarters of a cow. In total, 704 different cDNA bands were displayed in both udder samples. Five hundred-and-thirty two bands, (75.6%) were differentially displayed. Ninety prominent cDNA bands were isolated, re-amplified, cloned and sequenced resulting in 87 different sequences. Amongst the 19 expressed sequence tags showing a similarity with previously described genes, the majority of these sequences exhibited homology to protein kinase encoding genes (26.3%), to genes involved in the regulation of gene expression (26.3%), to growth and differentiation factor encoding genes (21.0%) and to immune response or inflammation marker encoding genes (21.0%). These sequences were shown to have mastitis-associated expression in the udder samples of animals with and without clinical mastitis by quantitative RT-PCR. They were mapped physically using a bovine-hamster somatic cell hybrid panel and a 5000 rad bovine whole genome radiation hybrid panel. According to their localization in QTL regions based on an established integrated marker/gene-map and their disease-associated expression, four genes (AHCY, PRKDC, HNRPU, OSTF1) were suggested as potentially involved in mastitis defense.
doi:10.1186/1297-9686-35-S1-S19
PMCID: PMC3231760  PMID: 12927078
mastitis; expressed sequence tag; gene expression; cattle; RH mapping
12.  Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection 
PLoS ONE  2011;6(11):e27744.
Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r2≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.
doi:10.1371/journal.pone.0027744
PMCID: PMC3227585  PMID: 22164200
13.  A first generation whole genome RH map of the river buffalo with comparison to domestic cattle 
BMC Genomics  2008;9:631.
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 ≥ 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 ≥ 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.
doi:10.1186/1471-2164-9-631
PMCID: PMC2625372  PMID: 19108729

Results 1-13 (13)