A Quasi-Exclusive European Ancestry in the Senepol Tropical Cattle Breed Highlights the Importance of the slick Locus in Tropical Adaptation

Background: The Senepol cattle breed (SEN) was created in the early XXth century from a presumed cross between a European (EUT) breed (Red Poll) and a West African taurine (AFT) breed (N'Dama). Well adapted to tropical conditions, it is also believed trypanotolerant according to its putative AFT ancestry. However, such origins needed to be verified to define relevant husbandry practices and the genetic background underlying such adaptation needed to be characterized. Methodology/Principal Findings: We genotyped 153 SEN individuals on 47,365 SNPs and combined the resulting data with those available on 18 other populations representative of EUT, AFT and Zebu (ZEB) cattle. We found on average 89% EUT, 10.4% ZEB and 0.6% AFT ancestries in the SEN genome. We further looked for footprints of recent selection using standard tests based on the extent of haplotype homozygosity. We underlined i) three footprints on chromosome (BTA) 01, two of which are within or close to the polled locus underlying the absence of horns and ii) one footprint on BTA20 within the slick hair coat locus, involved in thermotolerance. Annotation of these regions allowed us to propose three candidate genes to explain the observed signals (TIAM1, GRIK1 and RAI14). Conclusions/Significance: Our results do not support the accepted concept about the AFT origin of SEN breed. Initial AFT ancestry (if any) might have been counter-selected in early generations due to breeding objectives oriented in particular toward meat production and hornless phenotype. Therefore, SEN animals are likely susceptible to African trypanosomes which questions the importation of SEN within the West African tsetse belt, as promoted by some breeding societies. Besides, our results revealed that SEN breed is predominantly a EUT breed well adapted to tropical conditions and confirmed the importance in thermotolerance of the slick locus. (Résumé d'auteur

Relationship between asymptomatic infections with anaplasma marginale, babesia spp. And trypanosoma vivax in bulls and testosterone levels.

Algunas infecciones causadas por hemotrópicos están asociadas con una disminución del potencial reproductivo en toros; sin embargo, los mecanismos involucrados han sido poco estudiados. El principal objetivo de este estudio transversal fue determinar la infección con Anaplasma marginale, Babesia spp. y/o Trypanosoma vivax en toros asintomáticos de distintas razas y edades (n=85), y comparar niveles séricos promedios de testosterona en animales infectados y no-infectados. La mayor prevalencia obtenida por la reacción en cadena de la polimerasa (PCR) fue 46% para A. marginale, 34% para Babesia spp. y 60% para T. vivax. El porcentaje más alto de toros infectados con A. marginale y Babesia spp. fue encontrado en la raza Holstein (75,0 y 66,7%, respectivamente) y el más bajo en la raza Carora (35,7 y 14,2%, respectivamente) con valores de P<0,001. El porcentaje de toros infectados con T. vivax fue más alto en las razas Holstein, Carora y en los mestizos (75,0; 71,4 y 76,5%) que en la raza Brahman (38,1%). Se encontró un porcentaje mayor de infección con A. marginale y con Babesia spp. en el grupo etario de 10-19 meses y en los toros menores de 29 meses de edad, respectivamente, mientras que el mayor porcentaje de infección con T. vivax fue observado en el grupo etario de 40-49 meses. Estos resultados mostraron la importancia de la raza y la edad en la selección de individuos para estudios de prevalencia, tratamientos y control epidemiológico. Los hematocritos fueron estadísticamente menores en los animales infectados con A. marginale comparado con los no-infectados (P<0,02). Los toros infectados con T. vivax presentaron niveles inferiores de testosterone sérica, mientras que los toros asintomáticos bien sea con A. marginale o con Babesia spp. como los no infectados, no mostraron diferencias significativas en los niveles en esta hormona. La disminución en los niveles de testosterona en toros parece correlacionarse con la infección crónica con T. vivax, lo cual sugiere una conexión entre la presencia de este patógeno y los niveles de esta hormona.13 - [email protected] bovine hemotropic infections are associated with decreased reproductive potential in bulls, but the underlying mechanisms involved are poorly understood. The main objective of this transversal study was to determine Anaplasma marginale, Babesia spp., and Trypanosoma vivax infections in asymptomatic bulls (n=85) of various breeds and ages, and to compare serum average testosterone levels in infected and non-infected animals. The highest prevalence by Polymerase Chain Reaction (PCR) was 46% for A. marginale, 34% for Babesia spp. and 60% for T. vivax. The greatest percentages of bulls infected with A. marginale and Babesia spp. were found in the Holstein breed (75.0 and 66.7%, respectively), and the lowest in the Carora breed (35.7 and 14.2%, respectively) with values of P<0.001. The percentage of bulls infected with T. vivax was higher in the Holstein, Carora and Mixed Breeds (75.0, 71.4 and 76.5%) as compared to the Brahman breed (38.1%). The highest percentages of infection with A. marginale and Babesia spp. were found in animals 10- 19 months old and less than 29 months old, respectively, while the highest percentage of infection with T. vivax was observed in 40-49 months old animals. These results show the importance of the breed and age in the selection of individuals for studies of prevalence, treatment and epidemiological control. Hematocrit values were statistically lower in animals infected with A. marginale as compared to the non-infected group (P<0.02). Bulls infected with T. vivax presented lower levels of serum testosterone, while bulls either infected with A. marginale or Babesia spp. or noninfected, showed no differences in this hormone. The decrease in testosterone levels in bulls appears to correlate with T. vivax chronic infection, suggesting a link between the presence of this pathogen and hormonal levels

A proline racemase based PCR for identification of Trypanosoma vivax in cattle blood.

A study was conducted to develop a Trypanosoma vivax (T. vivax) specific PCR based on the T. vivax proline racemase (TvPRAC) gene. Forward and reverse primers were designed that bind at 764-783 bp and 983-1002 bp of the gene. To assess its specificity, TvPRAC PCR was conducted on DNA extracted from different haemotropic pathogens: T. vivax from Nigeria, Ethiopia and Venezuela, T. congolense Savannah type, T. brucei brucei, T. evansi, T. equiperdum, T. theileri, Theileria parva, Anaplasma marginale, Babesia bovis and Babesia bigemina and from bovine, goat, mouse, camel and human blood. The analytical sensitivity of the TvPRAC PCR was compared with that of the ITS-1 PCR and the 18S PCR-RFLP on a dilution series of T. vivax DNA in water. The diagnostic performance of the three PCRs was compared on 411 Ethiopian bovine blood specimens collected in a former study. TvPRAC PCR proved to be fully specific for T. vivax, irrespective of its geographical origin. Its analytical sensitivity was lower than that of ITS-1 PCR. On these bovine specimens, TvPRAC PCR detected 8.3% T. vivax infections while ITS-1 PCR and 18S PCR-RFLP detected respectively 22.6 and 6.1% T. vivax infections. The study demonstrates that a proline racemase based PCR could be used, preferably in combination with ITS-1 PCR, as a species-specific diagnostic test for T. vivax infections worldwide

Chromosomal regions under selection.

<p>Chromosomal regions under selection.</p

Details of the haplotype structure within the four significant footprints of selection identified.

<p>For each of the four regions, the decays of EHH (SEN ancestral and derived allele) and EHHS (for SEN, EUT and ZEB populations) from the core SNP located under the peak position are plotted in the leftmost panel. Haplotype bifurcation diagrams for both the ancestral (in red in the center panel) and derived allele (in blue in the rightmost panel) are also represented.</p

Heterozygosity (HZ), inbreeding coefficient (F_IS) for each breed and differentiation (F_ST) of SEN vs other breeds.

<p>Heterozygosity (HZ), inbreeding coefficient (F_IS) for each breed and differentiation (F_ST) of SEN vs other breeds.</p

Amplicons generated with ITS-1 PCR on DNA of different trypanosome taxa at 1 ng/µl, except for lanes 4, 8 and 9 where the specimen contains also host DNA.

<p>Lanes 1 and 16 = 100 bp marker, lane 2 = <i>T. vivax</i> Y486, lane 3 = <i>T. vivax</i> Fc, lane 4 = <i>T. vivax</i> Sh, lane 5 = <i>T. vivax</i> 4337, lane 6 = <i>T. vivax</i> 4338, lane 7 = <i>T. vivax</i> Di, lanes 8 & 9 <i>T. vivax</i> LIEM 176, lane 10 = <i>T. congolense</i>, lane 11 = <i>T. brucei brucei</i>, lane 12 = <i>T. evansi</i>, lane 13 = <i>T. equiperdum</i>, lane 14 = <i>T. theileri</i>, lane 15 = negative extraction control.</p

Lower detection limits expressed as pg/µl of <i>Tv</i>PRAC PCR, ITS-1 PCR and 18S PCR-RFLP assessed on DNA dilutions of four Ethiopian <i>T. vivax</i> isolates.

<p>Lower detection limits expressed as pg/µl of <i>Tv</i>PRAC PCR, ITS-1 PCR and 18S PCR-RFLP assessed on DNA dilutions of four Ethiopian <i>T. vivax</i> isolates.</p

Amplicons generated with <i>Tv</i>PRAC PCR on DNA of different trypanosome taxa at 1 ng/µl, except for lanes 4, 8 and 9 where the specimen contains also host DNA.

<p>Lanes 1 and 16 = 100 bp marker, lane 2 = <i>T. vivax</i> Y486, lane 3 = <i>T. vivax</i> Fc, lane 4 = <i>T. vivax</i> Sh, lane 5 = <i>T. vivax</i> 4337, lane 6 = <i>T. vivax</i> 4338, lane 7 = <i>T. vivax</i> Di, lanes 8 & 9 <i>T. vivax</i> LIEM 176, lane 10 = <i>T. congolense</i>, lane 11 = <i>T. brucei brucei</i>, lane 12 = <i>T. evansi</i>, lane 13 = <i>T. equiperdum</i>, lane 14 = <i>T. theileri</i>, lane 15 = negative extraction control.</p

Plots over the genome of the SEN iHS (a) and ZEB/SEN (b) and EUT/CGU (c) Rsb scores for each SNP.

<p>Plots over the genome of the SEN iHS (a) and ZEB/SEN (b) and EUT/CGU (c) Rsb scores for each SNP.</p