RESUMO
The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.
Assuntos
Búfalos/genética , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Locos de Características Quantitativas , Animais , Bovinos/genéticaRESUMO
Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
Assuntos
Búfalos/genética , Genômica , Leite/metabolismo , Reprodução , Animais , Brasil , Búfalos/fisiologia , Feminino , Genótipo , Homozigoto , Endogamia , Masculino , Linhagem , Fenótipo , Locos de Características Quantitativas/genéticaRESUMO
The aim of this study was to evaluate a genome wide association study (GWAS) approach to identify single nucleotide polymorphisms (SNPs) associated with fertility traits (early puberty) in Nellore cattle (Bos indicus). Fifty-five Nellore cows were selected from a herd monitored for early puberty onset (positive pregnancy at 18 months of age). Extremes of this phenotype were selected; 30 and 25 individuals were pregnant and non-pregnant, respectively, at that age. DNA samples were genotyped using a high-density SNP chip (>777.000 SNP). GWAS using a case-control strategy highlighted a number of significant markers based on their proximity with the Bonferroni correction line. Results indicated that chromosomes 5, 6, 9, 10, and 22 were associated with the traits of interest. The most significant SNPs on these chromosomes were rs133039577, rs110013280, rs134702839, rs109551605, and rs41639155. Candidate genes, as well as quantitative trait loci (QTL) previously reported in the Ensembl and Cattle QTLdb databases, were further investigated. Analysis of the regions close to the SNP on chromosomes 9 and 10 revealed that four QTL had been previously classified under the reproduction category. In conclusion, we have identified SNPs in close proximity to genes associated with reproductive traits. Moreover, U6 spliceosomal RNA was present on three different chromosomes, which is possibly associated with age at first calving, suggesting that it might be a strong candidate for future studies.
Assuntos
Fertilidade/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Característica Quantitativa Herdável , Reprodução/genética , Maturidade Sexual/genética , Animais , Cruzamento , Bovinos , Cromossomos de Mamíferos/química , Feminino , Estudo de Associação Genômica Ampla , Genótipo , Masculino , Fenótipo , Gravidez , RNA Nuclear Pequeno/genética , Spliceossomos/genéticaRESUMO
Leaf samples of yellow passionfruit (Passiflora edulis f. flavicarpa) displaying fruit woodiness symptoms were collected in seven Brazilian states and the Federal District. Viral infection was confirmed by host range and ELISA, and fourteen viral isolates were obtained. All isolates were capable of infecting several leguminous host species, although differences in symptom severity were noticeable. Woodiness symptoms were reproduced in yellow passionfruit, and mosaic symptoms were induced in common bean. All isolates infected cowpea, reported as a non-host of passion fruit woodiness virus (PWV). Indirect ELISA demonstrated that all isolates were serologically related to each other and also to cowpea aphid-borne mosaic virus (CABMV). The complete sequence of the capsid protein was determined for all isolates. Comparison of these sequences with those of other potyviruses indicated the highest identity with CABMV isolates (85 to 94%). Identity with PWV isolates ranged from 54 to 70%. Phylogenetic analysis grouped all of the Brazilian isolates in a monophyletic cluster with the CABMV isolates, clearly distinct from the PWV isolates. Furthermore, this analysis demonstrated that a group of previously characterized isolates from Brazil that had been designated as PWV should be reclassified as CABMV. Together, these results provide unequivocal evidence that, in Brazil, passionfruit woodiness disease is primarily caused by CABMV. The presence of PWV in Brazil has yet to be confirmed.