This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

The objective of this study was to describe the runs of homozygosity (ROH) detected in the Mexican Holstein population and to associate them with milk, fat and protein yields, and conformation final score. After imputation and genomic quality control, 4,227 genotyped animals with 100,806 SNPs markers each were used. ROH with a minimum length of 1 Mb and a minimum of 10 SNPs were included in the analysis. One heterozygous SNP marker and five missing genotypes per ROH were allowed. A total of 425,098 ROH were found in the studied population (71.83 ± 10.73 ROH per animal), with an average length and coverage of 4.80 ± 0.77 Mb, and 276.89 Mb, respectively. The average chromosome length covered by ROH was 10.40 ± 3.70 Mb. ROH between 1 and 2 Mb were the most frequent in the population (51.33%) while those between 14 and 16 Mb were the least frequent (1.20%). Long chromosomes showed a larger number of ROH. Chromosomes 10 and 20, had a greater percentage of their length covered by ROH because they presented a largest number of long ROH (>8 Mb). From the total ROH, 17 were detected in 1,847 animals and distributed among different chromosomes, and were associated with milk, fat and protein yield and percentage, and conformation final score. Of the ROH with effects on production traits, the majority were found with a length between 1 and 4 Mb. These results show evidence of genomic regions preserved by genetic selection and associated with the improvement of the productivity and functionality of dairy cattle.

El objetivo del presente estudio fue calcular los niveles de consanguinidad en la población Holstein de México y evaluar su efecto sobre la producción de leche, grasa, proteína y puntos finales de conformación. La información de pedigrí constó de 326,238 animales, a los cuales se les calculó la consanguinidad a través del algoritmo recursivo modificado (INBUPGF90). Se obtuvieron tendencias de consanguinidad de animales nacidos de 1990 a 2018 a través de un análisis de regresión, y se evaluó el efecto de la consanguinidad sobre caracteres productivos con un análisis de varianzas, para lo cual se incluyó información fenotípica de 68,779 animales. Se formaron seis grupos de acuerdo al nivel de consanguinidad (1= <1%, 2= ≥1 y <2%, 3= ≥2 y <3%, 4= ≥3 y <4%, 5= ≥4 y <5%, y 6= ≥5%). Los resultados mostraron que, por cada punto porcentual de aumento en la consanguinidad, se disminuye la producción de leche, grasa y proteína en 88, 3.16 y 2.57 kg (P<0.0001). A niveles bajos de consanguinidad (<5%), no se detectó ningún efecto sobre la producción de grasa y proteína. Sin embargo, cuando la consanguinidad aumentó a más de 5%, la pérdida en producción fue de 12 kg de grasa y de 9 kg en proteína. También se observó que los animales con menor promedio de conformación, presentan bajos niveles de consanguinidad (<1%) y los niveles más elevados, no mostraron diferencias significativas entre ellos; lo que ratifica que la conformación funcional es menos sensible a los efectos de la consanguinidad que otras características de interés económico. Se recomienda promover programas de selección basados en contribuciones óptimas para maximizar las ganancias genéticas y controlar los niveles de consanguinidad.

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