Population structure and inbreeding of Holstein cattle in southern Brazil

Breeding and genetics Population structure and inbreeding of Holstein cattle in southern Brazil Michelli de Fátima Sieklicki1  Henrique Alberto Mulim1  http://orcid.org/0000-0001-8798-8899 Luís Fernando Batista Pinto2  http://orcid.org/0000-0002-0831-3293 Altair Antônio Valloto3  http://orcid.org/0000-0001-8956-0685 Victor Breno Pedrosa1  *  http://orcid.org/0000-0001-8966-2227 1Universidade Estadual de Ponta Grossa, Departamento de Zootecnia, Ponta Grossa, PR, Brasil. 2Universidade Federal da Bahia, Departamento de Zootecnia, Salvador, BA, Brasil. 3Associação Paranaense de Criadores de Bovinos da Raça Holandesa, Curitiba, PR, Brasil. ABSTRACT The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average relatedness coefficient. POPREP and ENDOG v.4.5 software packages were employed to estimate these parameters. Based on the data set, the mean generation interval was found to be 6.3 years, and the average inbreeding coefficient, related to inbred animals, was 4.99%. Furthermore, the realized effective population size varied throughout the time period, ranging from 22 to 114, whereas the rate of inbreeding in this same period showed a decreasing trend towards the later years in the period until 2014. Upon evaluation, average relatedness coefficient was estimated to be 0.71%. Moreover, the effective number of founders and ancestors were estimated as 418 and 400 animals, respectively. According to the level of inbreeding observed, it could be noticed that genetic diversity remains elevated, which will be important to the genetic progress in the Holstein breeding program in Southern Brazil. Key words: effective population size; founders; generation interval Introduction Data monitoring is beneficial for maximizing profits and improving the application of selection methods to provide genetic progress in dairy herds ( Silva et al., 2016 ). In addition, rigorous pedigree control is essential for the correct identification of relationships between the animals, which will help prevent possible high rates of inbreeding in the long term. Inbreeding is caused by the mating of individuals that share one or more common ancestors. High inbreeding rates cause undesirable outcomes, such as a decrease in genetic variance and, therefore, should be avoided ( Hinrichs and Thaller, 2011 ). Since the adoption of large-scale reproductive biotechnologies, the probability of producing inbred animals has increased considerably because of the diffusion of genetic material from specific breeding herds. Thus, more careful analyses of the structural genealogy of populations are required ( Pedrosa et al., 2010 ). The population structure is typically determined by calculating the allelic frequencies of the different individuals. To prevent inbreeding, possible changes in the distribution of genetic variability should be constantly monitored ( Barros et al., 2017 ). Many dairy herds utilize imported genetic material, often collected from proven bulls from various countries. In 2017, Brazil imported 2.4 million doses of semen from the Holstein breed alone ( ASBIA, 2018 ). As a result of these high importation rates, males that become distinctive internationally tend to become progenitors in several countries, which leads to the dissemination of their genetic material worldwide. Thus, in a relatively short period, many progenies are produced from a small number of bulls, leading to a significant increase in the likelihood of inbreeding ( Hammami et al., 2009 ). The Holstein breed is recognized globally for its high milk production rates and availability of its genetic material on all continents. The breed is a product of intensive artificial selection, which has resulted in increased milk production ( Rodríguez-Ramilo et al., 2015 ). Furthermore, many studies have demonstrated the genetic gain obtained in this breed ( Stachowicz et al., 2011 ; García-Ruiz et al., 2016 ). However, only a few scientific papers have focused on the population structure of the Holstein breed and the effects of possible inbreeding in the herds of South America, which are important factors that can potentially interfere with the genetic gain over generations. Therefore, the present study aimed to evaluate the population structure and inbreeding rates of Holstein herds in southern Brazil to determine the process of gene distribution over the years. Material and Methods To carry out the present investigation, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which primarily consisted of information about Holstein animals from herds located in southern Brazil. A complete pedigree file, which included the identification of the animal, sire, dam, and birth year, was created, consisting of 206,796 animals (200,856 females and 5,940 males) born between 1970 and 2014. Of these animals, one or both parents of 45,905 animals were unidentified. These animals were excluded from the study, resulting in a reference population of 160,891 animals. To determine the genetic structure of the population and the level of inbreeding, the following parameters were considered: pedigree integrity, effective number of founders (fe), effective number of ancestors (fa), generation interval (GI), inbreeding coefficient (F), realized effective population size (Nē), and average relatedness coefficient (AR). All population parameters and inbreeding rates were estimated using the software packages POPREP ( Groeneveld et al., 2009 ) and ENDOG v.4.5 ( Gutiérrez and Goyache, 2005 ). The integrity of the pedigree was examined, which was essential for the complete evaluation of the available data. The number of known generations was determined, and the proportion of known ancestors from several previous generations was calculated. Generation equivalents were calculated by averaging the sum of (1/2)n, in which n is the number of generations that separates the individual from each known ancestor ( Sargolzaei et al., 2006 ). Additionally, detailed information regarding the ancestry of each individual was generated using complete pedigree knowledge. The pedigree integrity for each generation was estimated according to the methods proposed by MacCluer et al. (1983) , in which the proportion of individuals with parental information is estimated. Estimates of gene dissemination over time were determined by calculating fe and fa. Esse (...truncated)