The bovine and ovine TRG genes have previously been shown to be located in two loci, TRG1 and TRG2, in contrast to human and mouse TRG genes that are located in a single locus. The bovine TRG1 and TRG2 loci are located on chromosome 4 at 4q3.1 and 4q1.5-2.2, respectively. The complete genomic organization of the two bovine loci is described: each locus comprises three cassettes, each one includes one or several variable genes (TRGV) and one or several joining genes (TRGJ) preceding a constant (TRGC) gene. The location of the TRGC5 cassette is conclusively described in 5' of the TRG1 locus. Analysis of 17 TRGV belonging to 10 different subgroups, 8 TRGJ and 6 TRGC genes is conducted which comprises the most comprehensive list to date.

Pleistocene fragmentation of the Great BahamaBank resulted in one large and several smallpopulations of rock iguanas (Cycluracychlura). We explore patterns of geneticvariation within and among these islandpopulations using mitochondrial sequence data(partial ND4 to tRNALeu) in combinationwith eight polymorphic microsatellite loci (2to 10 alleles). Genetic data support twophylogeographically distinct groups, AndrosIsland and the Exuma cays. This resultconflicts with current subspecific taxonomy inwhich three subspecies are described. Analysesof allelic data indicate that most islandpopulations are currently demographicallyindependent. Pairwise Fst values between eightisland populations range from 0.18 to 0.63, and6 of 135 individuals are misassigned in anassignment test. Population-genetic diversityis characterized using standard measures suchas number of alleles and heterozygosity (H) inaddition to a normalized Shannon-Weaver indexof diversity (D). We find genetic diversity inthe Andros Island population comparable to thatin other non-piscine animals (avg. # ofalleles = 5, avg. H = 0.56, avg. D = 0.66) while inthe Exuma cays populations these measures aremuch lower (avg. # of alleles = 2.75–1.625, avg.H = 0.43–0.17, avg. D = 0.45–0.18). These dataare used to discuss conservation managementstrategies, including prioritization andtranslocation.

Pleistocene fragmentation of the Great Bahama Bank resulted in one large and several small populations of rock iguanas (Cyclura cychlura). We explore patterns of genetic variation within and among these island populations using mitochondrial sequence data (partial ND4 to tRNALeu) in combination with eight polymorphic microsatellite loci (2 to 10 alleles). Genetic data support two phylogeographically distinct groups, Andros Island and the Exuma cays. This result conflicts with current subspecific taxonomy in which three subspecies are described. Analyses of allelic data indicate that most island populations are currently demographically independent. Pairwise Fst values between eight island populations range from 0.18 to 0.63, and 6 of 135 individuals are misassigned in an assignment test. Population-genetic diversity is characterized using standard measures such as number of alleles and heterozygosity (H) in addition to a normalized Shannon-Weaver index of diversity (D). We find genetic diversity in the Andros Island population comparable to that in other non-piscine animals (avg. # of alleles = 5, avg. H = 0.56, avg. D = 0.66) while in the Exuma cays populations these measures are much lower (avg. # of alleles = 2.75–1.625, avg. H = 0.43–0.17, avg. D = 0.45–0.18). These data are used to discuss conservation management strategies, including prioritization and translocation.

Carcass data and Warner-Bratzler shear force (WBSF) data on strip loin steaks were collected from nearly 8,500 cattle in contemporary groups of progeny from the more popular sires in 14 different beef cattle breeds in the Carcass Merit Traits project funded by Beef Checkoff dollars, the breed associations, and MMI Genomics. In addition, trained sensory panel evaluations were conducted on over 2,500 strip loin steaks from contemporary groups of progeny from five sires included in the DNA marker validation component of the project. The correlation between WBSF and tenderness scored by the trained sensory panel was -0.82, indicating that as WBSF increased, tenderness scored by the sensory panel decreased. Our results showed that a WBSF value of ≥11.0 lb generally results in a sensory score of slightly tough or tougher. In this study, 22.8% of the cattle had WBSF values ≥11.0 lb and 26.3% had sensory scores of slightly tough or tougher. The phenotypic range of WBSF means for sires within breeds ranged from 1.9 to 6.6 lb. The phenotypic range of WBSF means across breeds was 8.9 lb, whereas the range among sires across breeds was a dramatic 14.4 lb. The phenotypic range for flavor intensity scores among sires within and across breeds was much smaller than for tenderness, with juiciness scores being intermediate. The 40 widely used sires that produced progeny with steaks that were unacceptable in tenderness in this study might be expected to be sires of several thousand bulls used in commercial herds. This demonstrates that seedstock producers should aggressively utilize sires that have genetics for tender meat.

La caracterización genética del ganado criollo colombiano (gcc) ha demostrado el valor de estas razas en los sistemas productivos tropicales, lo que ha despertado el interés para desarrollar programas de conservación y multiplicación. Se adelantó un estudio de análisis genético con las siete razas de ganado criollo colombiano, (rgcc): Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) y Casanareño (Ca), utilizando el Cebú (C) como control, con el objeto de evaluar su diversidad genética y relaciones filogenéticas. Se usaron 7 microsatélites (STR) para establecer las distancias genéticas amplificadas mediante PCR. El tamaño de los loci se definió mediante marcaje con ɣ32 P seguido de un pase en geles de poliacrilamida (PAGE) o marcados con fluorescencia y electroforesis capilar. Los datos se analizaron usando los programas Genepop, GDA y Phylip. El número promedio de alelos por locus fue de 8,9 y Ia heterocigosidad promedia observada fue de o,52. El árbol filogenético construido con el programa Phylip, empleando la distancia de Nei y el algoritmo de Neighbour-joining, agrupó en dos las gcc. En el grupo uno las razas: BON, SM, R, CCC y H; y en el grupo dos las razas: Ch, Ca y C. Los resultados de evaluación filogenética de las gcc indicaron que existe diversidad genética adecuada en estas razas para programas de mejoramiento genético; sin embargo, se recomienda continuar el estudio con un mayor número de marcadores genéticos.

IgD has been suggested to be a recently developed Ig class, only present in rodents and primates. However, in this paper the cow, sheep, and pig Ig δ genes have been identified and shown to be transcriptionally active. The deduced amino acid sequences from their cDNAs show that artiodactyl IgD H chains are structurally similar to human IgD, where the cow, sheep, and pig IgD H chain constant regions all contain three domains and a hinge region, sharing homologies of 43.6, 44, and 46.8% with their human counterpart, respectively. According to a phylogenetic analysis, the Cδ gene appears to have been duplicated from the Cμ gene >300 million yr ago. The ruminant μCH1 exon and its upstream region was again duplicated before the speciation of the cow and sheep, ∼20 million yr ago, inserted upstream of the δ gene hinge regions, and later modified by gene conversion. A short Sδ (switch δ) sequence resulting from the second duplication, is located immediately upstream of the bovine Cδ gene and directs regular μ-δ class switch recombination in the cow. The presence of Cδ genes in artiodactyls, possibly in most mammals, suggests that IgD may have some as yet unknown biological properties, distinct from those of IgM, conferring a survival advantage.

Carcass and Warner-Bratzler shear force data on strip loin steaks have been obtained on over 4,200 cattle from contemporary progeny groups from the most widely used sires in 15 beef cattle breed associations (16 breeds).Trained sensory panel evaluations have been conducted on over 1,500 strip loin steaks from a sample of contemporary progeny groups from sires included in the QTL (quantitative trait loci) validation component of the project.One breed association has published Warner-Bratzler shear force Expected Progeny Differences (EPDs) for 57 sires of two breeds.DNA analyses and screening have been completed for 1 1 QTL on eight sires from several breeds.EPDs for carcass traits, Warner-Bratzler shear force, and sensory panel traits may be completed for several breeds within the year 2001.Information from this project should allow seedstock producers to improve carcass traits, tenderness, and other palatability traits through classical genetic selection or through DNA marker-assisted selection.

The improvement of overall tenderness and the reduction in variability of tenderness was identified by the National Cattlemen’s Beef Carcass Quality Task Force as a high priority and a major issue facing the beef industry. The National Beef Tenderness Survey (Morgan et al., 1991) evaluated the overall tenderness of beef cuts in the retail meat case. Sources of variation in beef tenderness were identified as: 1) regional effects that could be contributed to either management differences among regions (prefeedlot management, days in the feedlot, feedlot management, level of nutrition, etc.) or breed type differences; 2) post-mortem conditions and handling practices; aging time varied from 3 to over 90 days post-fabrication with an overall mean postfabrication time of 17 days, this likely added to, not reduced, the variation in tenderness; 3) the shift from roasts to steaks and more single-muscle cuts as steaks from the same cut are tougher than roasts, most likely due to differences in cooking methods. From these results, a research program was initiated with the long term goal to identify critical control points from conception to consumer for beef tenderness and to subsequently identify methods of either controlling or monitoring critical control points. Ultimately, our goal is to test a system from conception to consumer to determine the efficacy of this approach. While much of this research is either on-going or in the planning stages, only the components that have been completed and that provide new information to the scientific literature will be presented. Critical Control Points For Meat Tenderness

We previously elucidated five distinct protein domains (I–V) for bovine submaxillary mucin, which is encoded by two genes, BSM1 and BSM2. Using Southern blot analysis, genomic cloning and sequencing of the BSM1 gene, we now show that the central domain (V) consists of ≈ 55 tandem repeats of 329 amino acids and that domains III–V are encoded by a 58.4‐kb exon, the largest exon known for all genes to date. The BSM1 gene was mapped by fluorescence in situ hybridization to the proximal half of chromosome 5 at bands q2.2–q2.3. The amino‐acid sequence of six tandem repeats (two full and four partial) were found to have only 92–94% identities. We propose that the variability in the amino‐acid sequences of the mucin tandem repeat is important for generating the combinatorial library of saccharides that are necessary for the protective function of mucins. The deduced peptide sequences of the central domain match those determined from the purified bovine submaxillary mucin and also show 68–94% identity to published peptide sequences of ovine submaxillary mucin. This indicates that the core protein of ovine submaxillary mucin is closely related to that of bovine submaxillary mucin and contains similar tandem repeats in the central domain. In contrast, the central domain of porcine submaxillary mucin is reported to consist of 81‐amino‐acid tandem repeats. However, both bovine submaxillary mucin and porcine submaxillary mucin contain similar N‐terminal and C‐terminal domains and the corresponding genes are in the conserved linkage regions of the respective genomes.

Polymorphic microsatellites have been developed in the vicinity of nine genes on bovine chromosome (BTA) 24, all orthologous to genes on human chromosome (HSA) 18. The microsatellites have been isolated from bacterial and yeast artificial chromosome clones containing the genes. A linkage map was developed including these polymorphic markers and four anonymous, published microsatellites. Yeast artificial chromosomes containing six of these genes have also been mapped using fluorescent in situ hybridization (FISH), thereby tying the linkage map together with the physical map of BTA24. Comparing gene location on HSA18 and BTA24 identifies four regions of conserved gene order, each containing at least two genes. These genes identify six regions of conserved order between human and mouse, two more than in the human-bovine comparison. The breakpoints between regions of conserved order for human-bovine are also breakpoints in the human-mouse comparison. The centromere identifies a fifth conserved region if the BTA24 centromere is orthologous with the HSA18 centromere.

. A size-selected Balaena mysticetus genomic library was screened for clones containing simple sequence repeat, or microsatellite, loci. A total of 11 novel loci was identified. These loci were combined with a set of 9 published loci, for a total of 20 markers, and were scored across a sample of 108 bowhead whales from the Bering–Chukchi–Beaufort Seas population of bowhead whales. Genetic variability was measured in terms of polymorphism information content values and unbiased heterozygosity. From the latter, estimates of long-term effective population size were obtained. In addition, gametic phase disequilibrium among loci was investigated. Moderate to high levels of polymorphism were found overall, and the long-term effective size estimates were large relative to total population size. Tests of heterozygosity excess (Cornuet and Luikart 1996) and allele frequency distribution (Luikart et al. 1998) indicated that the possibility of a recent genetic bottleneck in the Bering–Chukchi–Beaufort Seas population of bowhead whales is highly unlikely. However, the fact that five loci displayed a statistically significant heterozygote deficiency remains to be explained.

Many species are currently undergoing reductions in population size due to widespread habitat loss and expanding human activities. Because interspecific hybridization is often a consequence of population decline and fragmentation, identification of individuals or populations with hybrid ancestry is an increasingly important issue in conservation biology. In many wild cattle and bison species, the problem of natural hybridization has been compounded by indiscriminate crossbreeding with domestic cattle for the purpose of improving domesticated stocks. Therefore, a genetic test using the polymerase chain reaction was developed so that wild cattle and bison with domestic cattle mitochondrial DNA (mtDNA) haplotypes could be rapidly identified. Using this genetic test, domestic cattle mtDNA haplotypes were detected in Bos grunniens (yak), Bison bonasus (European bison), and 6 out of the 15 (40%) Bison bison (North American bison) populations tested. In total, 30 out of the 572 (5.2%) North American bison tested, were found to have domestic cattle mtDNA. The hybrid origin of these mtDNA haplotypes was verified in a phylogenetic analysis using the parametric bootstrap. These results are discussed in terms of their implications for the conservation status and future management of wild cattle and bison species.

River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.