Retelling the recent evolution of genetic diversity for Guzerá: Inferences from LD decay, runs of homozygosity and Ne over the generations

[EN] Genetic diversity is the one of the most important issues in conservation studies of livestock breeds or endangered species. In the present study, we tested the feasibility of describing the recent evolution in genetic diversity through genome-wide SNP genotyping and estimates of linkage disequilibrium decay patterns, effective population size, inbreeding coefficient based on runs of homozygosity and population structure. We choose the bovine indicine breed Guzerá because it has suffered recent bottlenecks which have been registered historically. A sample of 1036 females was genotyped using Illumina BovineSNP50. A resampling strategy was applied to correct for sampling biases caused by the population structure in herds, and by the extensive use of some sires for artificial reproduction. A subsample of 210 animals and 32,806 markers with MAF > 0.01 was used. Very low linkage disequilibrium was detected for distances greater than 120 Kb between two markers. Furthermore, three points of decrease in effective population size between generations were detected, which coincide with the historically registered bottlenecks. The inbreeding coefficient, based on runs of homozygosity, confirmed a strong contribution of the last 20–30 generations to current inbreeding. In the population structure analysis, the most probable number of sub-populations is 2, reflecting selection purpose (beef or dual-purpose). Taken together, these results allow a retelling of the recent evolution of this breed. The strategy described here will be useful for other breeds or even species for which a careful historical registry is not available for conservation proposals.SIWe thank to the farmers, who allowed the development of this project in their farms. We thank to Mr. Peter Laspina for reviewing language review and valuable comments. This study was supported by Fundação de Amparo a Pesquisa de Minas Gerais (FAPEMIG), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Marcos V. B. Silva was supported by the Embrapa – SEG 02.09.07.008.00.00 “Genomic Selection in Dairy Cattle in Brazil”, CNPq PVE 407246/2013-4 “Genomic Selection in Dairy Gyr and Girolando Breeds”, and FAPEMIG CVZ PPM 00395/14 “Genomic Selection in Brazilian Dairy Breeds” appropriated projects. MRSC has a fellowship from the CNPq – 307975/2010-0 and was supported by CNPq – 505338/2008-A and 481018/2008-5 projects. MGCDP, RVV, MAM have fellowships from FAPEMIG. PASF, FCS and ICR have CAPES fellowships

Identification of Candidate Genes for Reactivity in Guzerat (Bos indicus) Cattle: A Genome-Wide Association Study

[EN] Temperament is fundamental to animal production due to its direct influence on the animalherdsman relationship. When compared to calm animals, the aggressive, anxious or fearful ones exhibit less weight gain, lower reproductive efficiency, decreased milk production and higher herd maintenance costs, all of which contribute to reduced profits. However, temperament is a trait that is complex and difficult to assess. Recently, a new quantitative system, REATEST®, for assessing reactivity, a phenotype of temperament, was developed. Herein, we describe the results of a Genome-wide association study for reactivity, assessed using REATEST® with a sample of 754 females from five dual-purpose (milk and meat production) Guzerat (Bos indicus) herds. Genotyping was performed using a 50k SNP chip and a twostep mixed model approach (Grammar-Gamma) with a one-by-one marker regression was used to identify QTLs. QTLs for reactivity were identified on chromosomes BTA1, BTA5, BTA14, and BTA25. Five intronic and two intergenic markers were significantly associated with reactivity. POU1F1, DRD3, VWA3A, ZBTB20, EPHA6, SNRPF and NTN4 were identified as candidate genes. Previous QTL reports for temperament traits, covering areas surrounding the SNPs/genes identified here, further corroborate these associations. The seven genes identified in the present study explain 20.5% of reactivity variance and give a better understanding of temperament biology. IntroductionSIWe thank the farmers, who allowed the development of this project in their facilities. We thank to Mr. Peter Laspina for performing language review and for the valuable comments. This study was supported by Fundação de Amparo à Pesquisa de Minas Gerais (FAPEMIG), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Maria Gabriela Campolina Diniz Peixoto was supported by the Fapemig—CVZ APQ 01353 e CVZ APQ 3182–5.04/07. MRSC has a fellowship from the CNPq– 307975/2010-0 and was supported by CNPq– 312068/2015-8 and 481018/2008-5 projects. MGCDP, RVV, MAM have fellowships from FAPEMIG. PASF has CNPq fellowship, FCS and ICR have CAPES fellowships

Aplicação marcadores moleculares para análise de diversidade genética no cromossoma Y de bovinos da raça Guzerá

Exportado OPUSMade available in DSpace on 2019-08-14T22:07:50Z (GMT). No. of bitstreams: 1 disserta__o_izinara_pg_gen_tica_ufmg_2011.pdf: 818402 bytes, checksum: 441e7e7e01b89b7ff487bbb1dcfa6d5c (MD5) Previous issue date: 15O Brasil possui um dos maiores rebanhos de bovinos do mundo e é considerado o sexto maior produtor de leite mundial. O agronegócio do leite no país gera emprego e renda para mais de 3,6 milhões de pessoas e responde por 9% do PIB. Programas de melhoramento genético têm conseguido aumentar consideravelmente a produção leiteira dos rebanhos a partir de pequeno número de animais de maior valor genético para as características de interesse. Os touros com DEP elevada são intensivamente utilizados nos sistemas de reprodução assistida e muito pouco se sabe sobre o grau de diversidade genética ainda existente nos plantéis. Com o objetivo de analisar a diversidade genética dos touros da raça Guzerá avaliados nos programas de melhoramento genético da raça, uma amostra de 54 touros foi genotipada, utilizando-se quatro microssatélites Y-específicos INRA198, BYM-1, BM861 e UMN0307. Os microssatélites foram genotipados por amplificação por PCR e separação por eletroforese capilar. Frequências alélicas foram estabelecidas por contagem gênica. A diversidade haplotípica foi calculada com a fórmula de Nei. Os alelos identificados na raça foram INRA18982bp, INRA18990pb, UMN0307151pb, BM861158pb, BYM-1258pb, BYM-1260pb. O marcador INRA189 apresentou distúrbios de segregação e foi descartado da análise. O marcador BYM-1 foi bi-alélico e os demais foram monomórficos. Com base nos marcadores BYM-1, BM861 e UMN0307 foi possível identificar dois haplótipos. Os marcadores foram combinados em haplótipos (H1: UMN0307151pb, BM861158pb, BYM-1258pb e H2: UMN0307151pb, BM861158pb, BYM-1260pb). H1 foi o mais frequente, estando presente em 83% dos animais genotipados. A baixa diversidade haplotípica observada (0,28 ± 0,07) está de acordo com outros estudos na literatura, que também averiguaram pequeno número de haplótipos em raças zebuínas. Além disto, estudos de diversidade genética baseados na análise dos dados de registro genealógico da raça Guzerá no Brasil também indicam baixa diversidade genética e pequeno tamanho efetivo de população. Entretanto, estes resultados devem ser interpretados cautelosamente, uma vez que o sistema de haplotipagem precisa ser ampliado com a inclusão de mais marcadores genéticos.Brazil has one at the largest cattle population in the world and is sthe sixth largest milk producer worldwide. Dairy agribusiness generates jobs and income for more than 3.6 million people in the country and accounts for 9% of national annual internal product. Breeding programs have been able to significantly increase milk production of herds based on a small number of animals with high genetic merit for traits of interest. Bulls with the highest DEP are extensively used in mating systems, and very little is known about the degree of genetic diversity still existing in the herds. In order to characterizing genetic diversity among Guzerat bulls evaluated the breeding programs for this breed in Brazil, a sample of 54 bulls were genotyped for the Y-chromosome specific microsatellites INRA198, BYM-1, BM861 e UMN0307. These genetic markers were genotyped by PCR amplification and capillary electrophoresis separation. Allele frequencies were obtained by gene counting. Haplotype diversity was calculated using Neis formula. Alleles identified in Guzerat bulls were INRA18982bp, INRA18990bp, UMN0307151bp, BM861158bp, BYM-1258bp, BYM-1260bp. The genetic marker INRA189 presented segregation disturbances and was excluded from the analysis. BYM-1 presented two alleles while the two other markers were monomorphic. With the markers BYM-1, BM861 e UMN0307, it was possible to identify two haplotypes (H1: UMN0307151pb, BM861158pb, BYM-1258pb e H2: UMN0307151pb, BM861158pb, BYM-1260pb). Haplotype 1 was present in 83% of the animals. The low haplotype diversity observed (0,28 ± 0,07) is in good agreement with other studies in literature, that ascertained a small number of haplotypes in indicus breeds. Besides, that genetic diversity studies based on genealogical register of the Guzerat breed in Brazil have also pointed out the low genetic diversity, as well as the low effective population size. However, these results should be caustiously interpreted since the system must be improved by the association of aditional genetic markers

Evidence for a role of ACTN3 R577X polymorphism in football player?s career progression.

The aim was to investigate a possible role of the ACTN3 R577X polymorphism in a Brazilian football player?s career progression. 2 questions were formulated: 1. Does ACTN3 polymorphism affect the probability of an individual being a professional football player? 2. Does this polymorphism affect the progression of the athlete throughout his career? The study included 353 players from first division Brazilian football clubs in the following categories: under-14 (U-14), U-15, U-17, U-20, and professional (PRO). The control group (CON) was composed of 100 healthy non-athletes. The chi-squared test was used to assess differences between the allele and genotype frequencies. Comparing football categories, the XX genotype was less frequent among professional players than in the U-20 (p<0.05) or the U-15 category (p<0.05). The RX genotype also presented more frequently in the PRO category than the U-14 category (p < 0.05). Moreover, a trend towards a higher frequency of the RX genotype and a lower frequency of the XX genotype was observed in the professional category compared to U-20. These results suggest that the genotype in the ACTN3 polymorphism affects the probability of a football player progressing throughout his career and becoming professional, meaning that playing football selects against the ACTN3 XX genotype

Alpha-actinin-3 R577X polymorphism influences muscle damage and hormonal responses after a soccer game.

The purpose of this study was to evaluate indicators of muscle damage and hormonal responses after soccer matches and its relation to alpha-actinin-3 (ACTN3) gene expression (XX vs. RR/RX), considering that the R allele produces alpha-actinin-3 and provides greater muscle strength and power. Thirty players (10 XX and 20 RR/RX) younger than 16 years were evaluated in this study. Blood samples were collected immediately before, after, 2, and 4 hours after the games to assess muscle damage (creatine kinase [CK] and alpha-actin) and hormonal responses (interleukin-6 [IL-6], cortisol, and testosterone). Postgame CK was higher as compared to the pregame values in both groups and it was also higher in the RR/ RX (p , 0.05) than in the XX. The concentrations of alpha-actin and IL-6 were similar for both groups and did not change over time. Testosterone was increased after the game only in the RR/ RX group (p , 0.05). Cortisol concentrations in group RR/RX were higher immediately after the game than before the game, and 2 and 4 hours after the game the concentration decreased (p , 0.05). The RR and RX individuals presented higher markers of muscle microtrauma and hormonal stress, probably because they performed more speed and power actions during the game, which is a self-regulated activity. From the different responses presented by RR/RX and XX genotypes, we conclude that the genotypic profile should be taken into account when planning training workloads and recovery of athlete

The alpha-actinin-3 R577X polymorphism and physical performance in soccer players.

BACKGROUND: The aim of this study was to investigate the association between AC TN3 genotype (RR , RX, and XX) and physical performance of 138 adult, professional, U-20 and U-17 years Brazilian first-division soccer players. METHODS: The following three parameters were investigated: first, speed, using a 30-meter sprint test with speed measured at 10 meters, 20 meters, and 30 meters; second, muscular strength, using counter-movement-jump and squat jump tests; and third, aerobic endurance using the Yo-Yo endurance test. The athletes were ranked in ascending order according to their performance in each test. after which they were divided into quartiles and clustered according to genotype and allele frequency. The ?2 was used to compare the genotype frequencies (RR , RX and RR ) and allele frequencies (R and X) within and between the different quartiles of performance rating. RESULTS: No significant differences were observed in genotypic or allelic frequencies between different performance ratings. The AC TN3 genotype was not associated to any of the physical performance parameters. CONCLUSION: This information should be noted with care, because, besides physical capacity, there are other factors, like tactical knowledge, that interfere with performance in sport, considering that expertise is multifactorial

Effect of ACTN3 gene on strength and endurance in soccer players.

Sports efficiency in activities in which strength and speed are the determining factors has been associated to the ACTN3 gene, which is responsible for the expression of a-actinin-3. Soccer is a mainly aerobic sport because of its long duration, but the acute actions that define the game demand a lot of strength and speed. The purpose of the present study was to compare the performance capacity of soccer players with different genotype groups of ACTN3 (XX, RX, and RR) in strength, speed, and endurance tests. Two hundred professional players of Brazilian soccer first division teams participated in this study. Speed, jump, and endurance test results were compared with the polymorphisms of the ACTN3 gene. It was noticed that RR individuals spent less time to run a 10-m path, compared with XX individuals (p , 0.05). The RR individuals also presented lower time rates at the 20- and 30-m path, compared with RX and XX individuals (p , 0.05). In jump tests, RR individuals presented higher rates, compared with RX and XX individuals (p , 0.05). As for aerobic tests, the XX individuals presented higher rates of V_ O2 max, compared with the RR group (p , 0.05), and did not differ from the RX group. The main conclusion of this study is that soccer players of genotype ACTN3/RR are the fastest in short distances and present higher jump potential. ACTN3/XX individuals presented the highest aerobic capacity. These findings can be used in training load adjustment and can influence the development of tactical schemes in soccer matches

Significantly associated SNPs for REACT^adj in Guzerat obtained by the GRAMMAR-Gamma method.

<p>Significantly associated SNPs for REACT^adj in Guzerat obtained by the GRAMMAR-Gamma method.</p

Manhattan plot of the -log10(p-values) for genome-wide association of REACT^adj.

<p>The continuous line represents the 5% Bonferroni threshold (1.59 x 10⁻⁶) and the dashed line represents the 5% FDR threshold.</p

Heritability and descriptive statistics for REACT and REACT^adj.

<p>Heritability and descriptive statistics for REACT and REACT^adj.</p