Genealogical structure of the Colombian Romosinuano Creole cattle

Tropical Animal Health and Production (2023) 55:292 https://doi.org/10.1007/s11250-023-03694-1 REGULAR ARTICLES Genealogical structure of the Colombian Romosinuano Creole cattle Jhon Jacobo Cañas–Álvarez1 · Gustavo Alfonso Ossa‑Saraz2 · Jorge Luis Garcés‑Blanquiceth2 · William Orlando Burgos–Paz3 Received: 16 October 2022 / Accepted: 19 July 2023 © The Author(s) 2023 Abstract The Romosinuano cattle breed is one of the most important Creole genetic resources in Colombia, and interesting traits like adaptation or reproductive efficiency have promoted its use in different countries in America. To consolidate the genealogical historical records, the review of very first yield records in this population was used to reconstruct the genealogy of the breed since the first animals incorporated to the in vivo germplasm bank and estimate different demographic parameters. The complete genealogy comprises 17,136 animals with 5.8 years of generation interval for two pathways. The estimated average inbreeding for the population and inbred animals was 2.53% and 6.32% respectively, with a progressive increase of inbred animals across the generations. Almost 48% of the total animals presented some level of consanguinity. Effective population size (Ne) based on the inbreeding rate estimated by regression in all generations was 120 animals whereas Ne estimated by equivalent generations was 69 animals. Effective number of founders (Fe), effective number of ancestors (Fa), and ancestors explaining 50% of variability were 75, 48, and 22, respectively. The relation between Fa/Fe of 64% indicates a genetic bottleneck effect in the population studied. Keywords Effective population size · Genealogy · Genetic diversity · Inbreeding Introduction The origin of the Romosinuano cattle (ROM) is traced to the very first cattle introduced to America, with a close relationship with Iberian cattle (Ginja et al. 2019). This hornless breed (“romo” is the term used for this phenotype in Colombia) has been traditionally maintained in the north coast of Colombia, particularly in the “Sinú Valley,” from where it adopted its name. Nowadays, ROM is the most important Creole beef cattle in Colombia due to adaptation to the tropical environment and the meat quality production (Flórez et al. 2014). * William Orlando Burgos–Paz 1 Corporación Colombiana de Investigación AgropecuariaAgrosavia, Centro de Investigación Motilonia, Km 5 Vía Becerril, Cesar, Agustín Codazzi, Colombia 2 Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Turipaná, Km 13 Vía Montería‑Cereté, Córdoba, Colombia 3 Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Tibaitatá, Km 14 Vía Mosquera‑Bogotá, Cundinamarca, Colombia The very first government effort to promote the ROM conservation was the establishment of the breed germplasm bank in 1936, with 258 females (42.6% individuals belong to “El Torno” herd) and 12 males from different breeders (Ossa et al. 2013). Once the herd was created, a productive and genealogical data recording program was implemented. By 1963, the entire herd was transferred to the Turipaná Research Centre where it is maintained until today. Since 1994, a permanent monitoring of diversity was implemented using the circular mating system (Martínez et al. 2008). Recently, some individuals from the germplasm bank have been selected to establish a genetic improvement program where growth and reproductive traits have been used as selection criteria (Ossa et al. 2008). Genealogical and productive information collected from 1980 has supported the genetic diversity management as well as the genetic evaluations, that alongside performance testing of young bulls has increased the inventory of this breed in Colombia. In 2010, historical herd records were recovered from the AGROSAVIA files (Ossa et al. 2013) containing the very first herd records of the population. This data allowed to connect the pedigree until its conformation in 1936. However, issues like different animal identification patterns or 13 Vol.:(0123456789) 292 Page 2 of 8 discrepancies between dates limited the use of this data until today. Because of the relevance of the pedigree data for support either genetic information of the herd or developing new strategies for animal selection, the objective of this work was to validate the individual relationships and reconstruct the pedigree data in order to revisit the genetic diversity and demography status of Colombian Romosinuano Creole cattle breed. Materials and methods Genealogical data preparation The ROM population is maintained in the Turipaná Research Centre of the Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA (www.agrosavia.co), located at the Sinú Valley in Cereté, Córdoba (8°50′15.2″ North and 75°47′33.9″ West). The center is around 14 m above sea level with average annual temperature of 28 °C, relative humidity ranged from 79 to 87%, and precipitation of 1200 mm. Pedigree and productive performance were continuously updated since 1980, but previous pedigree records were only available in herd recording cards. Therefore, the first step was to include genealogical, growth, and reproductive data from cards into the breed database. Subsequently, a random sample of 10% of cards were reviewed manually to check typing errors or miscoding data. Furthermore, pedigree records review was performed with Python and R (R Core Team, 2020) scripts that validated parentage relationships, bisexualities, and other mistakes in the pedigree consolidation. Main routine of data validation included (1) coherence between individual date of birth and weights at different ages; (2) validation age of dam at individual birth date, considering at least 22 months dam age at first parity; and (3) validation dam parity interval ranged from 380 to 440 days. Because some bulls were sire at most 14 years, special attention was required to validate heifer incorporation in the pedigree. Finally, historical data validation allowed to obtain 17,136 pedigree records between 1936 and 2019. Pedigree analyses Once pedigree relationships, birth dates, and concordance between age of dams and parities were validated, numerous demography, structure, and genetic status parameters based on pedigree information were estimated: Breed censuses Correspond to the number of sires and dams with offspring in a given year. The parents of animals born 13 Tropical Animal Health and Production (2023) 55:292 in a given year are entered into the equation used to calculate the effective population size ( Ne ) for each reporting year according to Falconer and Macky (1996): Ne = 4Nm Nf Nm + Nf where Nm and Nf are the number of male and female parents, respectively. The above formula refers to the number of breeding males and females in a population with discrete generations. Generation interval Defined as the average age of parents at the birth of their progen (...truncated)