Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram...

The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree ($F_{Ped}$), the genomic relationship matrix ($F_{GRM}$), and runs of homozygosity ($F_{ROH}$) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for $F_{PED}$, $F_{GRM}$, and $F_{ROH}$, respectively. Correlation between $F_{PED}$ and $F_{ROH}$ was significant only for runs of homozygosity > 4 Mb, indicating the $F_{PED}$ of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program.

The Sardo Negro cattle (SN) is the only zebu cattle breed developed in Mexico. Since its development, the selection could have led to an increase in the homozygosity level in some regions of the genome and made differentiation with other cattle populations. We aimed to identify and characterize selection signatures in SN using medium-density SNP data using four approaches: 1) Runs of homozygosity (ROH) 2) Nucleotide Diversity 3) Tajima’s D and 4) the Wright’s fixation index (F_ST). A sample of 555 SN animals genotyped for 65k SNPs was used to obtain ROH segments considered regions under selection. The F_ST values were estimated by comparing the sample of genotyped SN animals with samples of genotyped animals from the Gir, Brahman, and Ongole breeds. Only one region mapped to 35.78–42.51 Mb on BTA6 was considered a selection signature by the ROH method. This selection signature overlapped with the lowest diversity, negative values of Tajima’s D and a diversification region between SN and the other Zebu breeds by F_ST. We found several candidate genes (LCORL, NCAPG, and SLIT2) related to growth and other economically important productive traits in this common region. Using the F_ST method, different regions, such as regions on BTA8 (8:93.4–93.9 Mb), BTA11 (11:99.2–99.7), and BTA14 (14: 26.1–26.8) related to growth and milk traits also were defined as candidate selection signatures. The selective signals identified in this study reflected the direction of the selection pressure that primarily involves the increase of live weight traits in the Sardo Negro cattle breeding program.

Objetivo. Caracterizar las curvas de crecimiento y el comportamiento reproductivo de vacas Romosinuano en México. Materiales y métodos. Se analizaron 928 registros de peso y edad de 127 hembras para características de crecimiento, y 459 registros de partos de 113 vacas para características reproductivas. Se ajustaron cuatro modelos no lineales mixtos para describir la curva de crecimiento, y se estimaron los indicadores de edad al 50% de madurez (E50M) y porcentaje de madurez a los 18 meses de edad (PM18). Para evaluar el comportamiento reproductivo se estimó la edad al primer parto (EPP), intervalo entre partos (IEP), y tasa de pariciones (TP). Resultados. El modelo de Brody fue el que mejor ajustó la curva de crecimiento. El parámetro A, que estima el peso maduro, osciló entre 430.2 y 466.2 kg; el b entre 0.94 y 5.45; y el k entre 0.001 y 0.002; dependiendo del modelo utilizado. La E50M varió entre 20 y 21 meses, y el PM18 entre 44.5 y 45.5%. Las medias de EPP, IEP, y TP a los 550 d fueron 1059±282 d, 553±68 d, y 74±19%, y mejorando (p<0.05) cuando las hembras presentan mayor porcentaje de su peso maduro, dependiendo de la época de parto. Conclusiones. El peso maduro estimado indica que el ganado Romosinuano puede considerarse como una raza de tamaño pequeño o mediano, con aceptable aptitud reproductiva. Las hembras con menor tamaño maduro estimado presentaron edades al primer parto más temprano que vacas más pesadas.

Romosinuano is a tropically adapted Bos taurus breed, and some Mexican breeders aim to improve it genetically. The aim was to estimate allelic and genotypic frequencies for SNPs associated with meat quality in a Mexican Romosinuano population. Four hundred ninety-six animals were genotyped using the Axiom©BovMDv3 array. Only SNPs related to meat quality in this array were studied in this analysis. The Calpain, Calpastatin, and Melanocortin-4 receptor alleles were considered. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium were estimated with the PLINK software. Alleles associated with meat tenderness and higher marbling scores were found in the Romosinuano cattle population. CAPN1_4751 was not found in Hardy-Weinberg equilibrium. The rest of the markers could not be affected by selection and inbreeding. Romosinuano cattle in Mexico have similar genotypic frequencies in markers related to meat quality to Bos taurus breeds known for their meat tenderness. Breeders can choose a marker-assisted selection to improve meat quality characteristics.