RESUMEN
BACKGROUND: The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. RESULTS: We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. CONCLUSION: The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.
Asunto(s)
Selección Genética , Pavos/crecimiento & desarrollo , Pavos/genética , Agricultura , Animales , Evolución Biológica , Cromosomas , Genética de Población , Estudio de Asociación del Genoma Completo , Secuenciación de Nucleótidos de Alto Rendimiento , Morfogénesis , Análisis de Secuencia de ADN , Pavos/clasificaciónRESUMEN
Two clinically healthy mature Pakistani Bos indicus × Bos taurus cattle were genotyped as homozygous affected for the lethal immunodeficiency disorder bovine leukocyte adhesion deficiency (BLAD) using previously described PCR-RFLP based DNA tests which was confirmed by sequencing. Sequencing of Bos taurus and B. indicus × B. taurus genomic DNA surrounding the disease causing mutation (c.383A > G) in the ITGB2 gene identified numerous variations in exonic and intronic regions within and between species, including substantial variation in primer annealing sites for three PCR-RFLP tests for one of the B. indicus allelic variants. These variations in the primer annealing sites resulted in a null allele in the DNA tests causing the misdiagnosis of some heterozygous B. taurus × B. indicus cattle to be classified as homozygous affected. New primers were designed and a modified test was developed which simultaneously identified the disease mutation and the Pakistani B. indicus allelic variant associated with the null allele in the previous test.
Asunto(s)
Enfermedades de los Bovinos/genética , Pruebas Genéticas , Síndrome de Deficiencia de Adhesión del Leucocito/veterinaria , Alelos , Análisis del Polimorfismo de Longitud de Fragmentos Amplificados , Animales , Secuencia de Bases , Antígenos CD18/genética , Bovinos , Enfermedades de los Bovinos/diagnóstico , Estudios de Asociación Genética , Síndrome de Deficiencia de Adhesión del Leucocito/diagnóstico , Síndrome de Deficiencia de Adhesión del Leucocito/genética , Masculino , Técnicas de Diagnóstico Molecular , Datos de Secuencia Molecular , Pakistán , Análisis de Secuencia de ADNRESUMEN
Bovine leukocyte adhesion deficiency (BLAD) is an autosomal recessive disease. Affected animals die because of extreme susceptibility to infections caused by the lack of a membrane glycoprotein called the leukocyte integrin beta-2 subunit of CD18. The present study was planned to standardize a technique for the diagnosis of BLAD and to get an estimation of BLAD allele in the Pakistani cattle population. The study was performed on 700 animals including Holstein-Friesian (HF) (n=280), Friesian-Sahiwal (FS) (n=120) Sahiwal (n=100) cows and HF calves (n=59) from Government as well as private farms. Similarly 141 bulls of Sahiwal (n=100), HF (n=18) and FS (n=23) from the Semen Production Unit Qadirabad and Kherimorat were also sampled. The identification of normal, carrier and affected animals were made by the PCR-RFLP method. No animal was found homozygous for BLAD while 10 animals including HF calve (n=1), FS bull (n=1), HF (n=6) and FS (n=2) cows were BLAD carrier. The Hardy-Weinberg frequency of the mutant allele in HF and FS population in Pakistan was calculated to 0.01. Thus there is a need of regular screening of the bulls used for artificial insemination to avoid the risk of spreading BLAD in the cattle population of Pakistan.