Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Mitochondrial genotype segregation and effects during mammalian development: Applications to biotechnology

Mitochondria are endosymbiotic organelles responsible for energy production in practically every eukaryotic cell. Their uniparental fashion of inheritance, maternally inherited in mammals, and the homogeneity of mitochondrial DNA (mtDNA) within individuals and matrilineages, are biological phenomena that remain unexplained. This paper reviews some of the recent findings on mitochondrial influences on the manner in which embryos develop and how their genotypes are inherited in mammals, with particular emphasis on the genetic bottleneck effect. Animal models carrying a mix of mtDNAs (heteroplasmic) have been produced by karyoplast and cytoplast transplantation to analyze the segregation patterns at different stages during embryogenesis, in fetuses and offspring. Comparisons performed between murine and bovine reveal interesting changes in segregation and replication of transplanted mtDNAs. We have recently obtained Bos indicus and Bos taurus fetuses and calves from embryos reconstructed using enucleated polymorphic oocytes of Bos taurus origin. These and other findings on mitochondrial biology will have important implications in determining the cytoplasmic genotype of clones and in the preservation of endangered breeds and species. (C) 1999 by Elsevier B.V.

Germ Cell Transplantation in Felids: A Potential Approach to Preserving Endangered Species

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Occurrence of Atta laevigata (Hymenoptera: Formicidae) in the South of Espirito Santo State, Brazil. Recently Introduced or Endangered Species?

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Polymorphism analysis of the hsp70 stress gene in Broiler chickens (Gallus gallus) of different breeds

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Muscular Dystrophy in Dogs: Does the Crossing of Breeds Influence Disease Phenotype?

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

African-Derived mitochondria in South American native cattle breeds (Bos taurus): Evidence of a new taurine mitochondrial lineage

This article reports the nucleotide diversity within the control region of 42 mitochondrial chromosomes belonging to five South American native cattle breeds (Bos taurus). Analysis of these data in conjunction with B. taurus and B. indicus sequences from Africa, Europe, the Near East, India, and Japan allowed the recognition of eight new mitochondrial haplotypes and their relative positions in a phylogenetic network. The structure of genetic variation among different hypothetical groupings was tested through the molecular variance decomposition, which was best explained by haplotype group components. Haplotypes surveyed were classified as European-related and African-related. Unexpectedly, two haplotypes within the African cluster were more divergent from the African consensus than the latter from the European consensus. A neighbor-joining tree shows the position of two haplotypes compared to European/African mitochondrial lineage splitting. This different and putatively ancestral mitochondrial lineage (AA) is supported by the calibration of sequence divergence based on the Bos-Bison separation. The European/African mitochondria divergence might be subsequent (67,100 years before present) to that between AA and Africans (84,700 years before present), also preceding domestication times. These genetic data could reflect the haplotype distribution of Iberian cattle five centuries ago.

Auxin-producing bacteria isolated from the roots of Cattleya walkeriana, an endangered Brazilian orchid, and their role in acclimatization

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phylogeography and Pleistocene demographic history of the endangered marsh deer (Blastocerus dichotomus) from the Rio de la Plata Basin

The marsh deer is the largest neotropical cervid with morphological and ecological adaptations to wetlands and riparian habitats. Historically, this now endangered species occupied habitats along the major river basins in South America, ranging from southern Amazonia into northern Argentina to the Parana river delta. This particularly close association with wetlands makes marsh deer an excellent species for studying the effects of Pleistocene climatic changes on their demographic and phylogeographic patterns. We examined mitochondrial DNA variation in 127 marsh deer from 4 areas distributed throughout the Rio de]a Plata basin. We found 17 haplotypes in marsh deer from Brazil, Bolivia and Argentina that differed by 1-8 substitutions in a 601 bp fragment of mitochondrial control region sequence, and 486 bp of cytochrome b revealed only 3 variable sites that defined 4 haplotypes. Phylogeny and distribution of control region haplotypes suggest that populations close to the Pantanal area in central Brazil underwent a rapid population expansion and that this occurred approximately 28,000-25,000 years BP. Paleoclimatic data from this period suggests that there was a dramatic increase for precipitation in the medium latitudes in South America and these conditions may have fostered marsh deer's population growth.

Identification of the endangered small red brocket deer (Mazama bororo) using noninvasive genetic techniques (Mammalia; Cervidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Synaptonemal complex analysis of the Holstein-Friesian, Piemontese and Simmental breeds of Bos taurus taurus

The synaptonemal complex (SC) of specimens of Sos taurus taurus from the Holstein-Friesian, Piemontese, and Simmental breeds, was analysed. The analysis included quantification of the frequency of various types of abnormalities in the SC, and the frequency of calls with SC abnormalities. All animals had 29 autosomal bivalents and one sexual bivalent and the most frequently recorded abnormality was pairing failure. The number of cells with abnormalities in the Holstein-Friesian breed was 29.41%, in the Piemontese breed was 30.00% and in the Simmental breed it was 29.54%. The subspecies Bos taurus taurus had 29.63% of cells showing abnormalities with 57.33% of these abnormalities occurring in zygotene and 42.67% occurring in pachytene. Statistical analyses showed that there were no significant differences in the number of cells with SC abnormalities among the breeds studied. The frequency of cells with abnormalities, and the efect on the fertility of the Holstein-Friesian, Piemontese and Simmental breeds are discussed.

Relationship of abomasal histology and parasite-specific immunoglobulin A with the resistance to Haemonchus contortus infection in three breeds of sheep

This study was carried out to evaluate the relationship of abomasal inflammatory cells and parasite-specific immunoglobulin A (IgA) in mucus, with the resistance to Haemonchus contortus infection in three breeds of sheep naturally infected with gastrointestinal nematodes. The breeds were the native Santa Ines sheep, and the European Suffolk and Ile de France breeds. Mast cells, eosinophils and globule leucocytes were enumerated in abomasal mucosa. Eosinophils within the sub-mucosa also were counted separately. Histamine concentration was estimated in abomasal tissue samples. Enzyme-linked immunosorbent assay was carried out in mucus samples to determine the level of IgA anti-H. contortus third and fifth instar. There were no significant differences among group means of these variables (P > 0.05). The correlation coefficients between fecal egg counts (FEC) x mast cells (r = -0.490; P < 0.05) and FEC x eosinophils in sub-mucosa (r = -0.714; P < 0.01) was significant in the Santa Ines sheep. In the Ile de France group, the correlation coefficients between globule leucocytes x FEC (r = -0.879; P < 0.001) and histamine x worm burden (r = -0.833; P < 0.01) were also significant. In the Santa Ines and Ile de France sheep, correlation coefficients between IgA anti-L3 x worm burden and IgA anti-L3 x FEC were negative. In general, inflammatory cells and IgA-parasite-specific in abomasum were inversely associated with H. contortus worm burden and FEC indicating that they may impair parasite development or fecundity in the three breeds of sheep. However, similar mean values of inflammatory cells and IgA were found in the resistant (Santa Ines) and in the susceptible (Suffolk and Ile de France) breeds of sheep. The enumeration of cells by histological assessment does not provide information on their functional activity, which may be different among breeds. Thus, the effect of breed on the functional activity of these and other inflammatory cells is an important area for further study. (c) 2004 Elsevier B.V. All rights reserved.

Survey for Foot-and-mouth Disease in the Endangered Marsh Deer (Blastocerus dichotomus) from Marshlands of the Parana River Basin, Brazil

Habitat fragmentation and diseases have resulted in a decline of the marsh deer (Blastocerus (dichotomus) throughout its South American range. Our objectives were to determine whether marsh deer intended for translocation from a region of the Rio Parana Basin had been infected previously by foot-and-mouth disease virus (FMDV) and whether they were carrying virus We captured marsh deer from June to October 1998 and collected blood from 108 animals and esophageal-pharyngeal fluid from 53 Serum was tested for antibodies against three FMDV serotypes (O, A, and C) by liquid-phase-blocking sandwich enzyme-linked immunosorbent assay (ELISA) Esophageal-pharyngeal fluid was tested for FMDV RNA by reverse transcription polymerase chain reaction (RT-PCR) and inoculation into three successive baby hamster kidney (BHK-21) cell subcultures, followed by RT-PCR of cultures We detected low log(10) titers (range 1 0-1 5) to FM DV subtype A(24) Cruzeiro in 19 of 108 sampled marsh deer, but failed to isolate FMDV or detect FMDV RNA in any samples we conclude that marsh deer from our study site were unlikely to carry FMDV, however, as a preventive measure, the 19 animals with titers for FMDV were not sent to FMDV-free Brazilian states