Single Nucleotide Variants And Indels Identified From Whole-genome Re-sequencing Of Guzerat, Gyr, Girolando And Holstein Cattle Breeds

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. © 2017 Stafuzza et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.123Conselho Nacional de Desenvolvimento Científico e TecnológicoCAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorFAPEMIG, Fundação de Amparo à Pesquisa do Estado de Minas GeraisConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes)

African black-footed cats (Felis nigripes) are endangered wild felids. One male and full-sibling female African black-footed cat developed vision deficits and mydriasis as early as 3 months of age. The diagnosis of early-onset progressive retinal atrophy (PRA) was supported by reduced direct and consensual pupillary light reflexes, phenotypic presence of retinal degeneration, and a non-recordable electroretinogram with negligible amplitudes in both eyes. Whole genome sequencing, conducted on two unaffected parents and one affected offspring was compared to a variant database from 51 domestic cats and a Pallas cat, revealed 50 candidate variants that segregated concordantly with the PRA phenotype. Testing in additional affected cats confirmed that cats homozygous for a 2 base pair (bp) deletion within IQ calmodulin-binding motif-containing protein-1 (IQCB1), the gene that encodes for nephrocystin-5 (NPHP5), had vision loss. The variant segregated concordantly in other related individuals within the pedigree supporting the identification of a recessively inherited early-onset feline PRA. Analysis of the black-footed cat studbook suggests additional captive cats are at risk. Genetic testing for IQCB1 and avoidance of matings between carriers should be added to the species survival plan for captive management

Breeding objectives for three silvicultural regimes of radiata pine

A generic vertically integrated firm, comprising a production forest, a sawmill, and a pulp mill was modelled under three silvicultural regimes: direct to pulp, intermediate (includes production thinning), and intensive (includes production thinnings and pruning). The harvest age traits included in the breeding objective were total volume (m³/ha) and average wood density (kg/m³). Economic values for each trait were calculated as the difference in discounted profit for a unit marginal increase of volume or density, and expressed as relative weights to facilitate comparisons between the objectives. The methodology was applied to a Chilean case study using representative economic and production circumstances. The breeding objectives so derived were 1vol + 2.4den for pulp, 1vol + 1.1den for intermediate, and 1vol + 1.2den for the intensive regime, where vol and den are the breeding values for volume and density, respectively. The firm was profitable under all regimes. Genetic correlations between the objectives for each regime were higher than 0.9, indicating that a single breeding strategy with objective 1vol + 1.5den could be adopted, with almost no loss of genetic gain relative to selecting for a particular silvicultural regime

Accuracy of genetic prediction obtained using genetic relationships based on pedigree or marker information

The accuracy of genetic prediction when pedigree ( P A ) or pedigree and marker-based ( PM A ) relationships were used in mixed model equations was assessed. Daughter yield deviations (DYD) records for milk, fat and protein yields on Holstein sires (n = 1,811) with DNA marker information were analysed. Three sets of estimated breeding values (EBV) were obtained: (1) EBV-ALL (considered all sources of information and the inverse of), (2) EBV-PED (similar to EBV-ALL but the sire’s own DYD was excluded), and (3) EBV-MRK (similar to EBV-PED except that the inverse of was used). Linear and rank correlations were computed between EBV-ALL and EBVPED or EBV-MRK. The accuracy increased by 4.3% for milk yield but did not change for fat and protein yields when was replaced by for sires without sons. These results suggest that genetic markers may be used to enhance accuracy in genetic evaluation particularly for young animals

Effect of Live Weight and Differing Economic Values on Responses to Selection for Milk Fat, Protein, Volume, and Live Weight

Five traits of major economic importance in the New Zealand dairy industry are milk volume, milk fat, milk protein, live weight, and survival. This study evaluated the impact of live weight as a trait in the selection objectives for the New Zealand dairy industry. Live weight of the lactating cow is an important measure because it reflects feeding costs via maintenance feed and salvage values of cows to be culled. In addition, selection responses were evaluated for differing relative economic values for milk protein and milk fat, and selection indexes that included or excluded phenotypic and genotypic correlations between traits were compared. Inclusion of live weight, with a negative economic value in a four-trait selection index with milk, milk fat, and protein resulted in higher economic response. Protein response to selection was not more than 2% when the relative economic value for the ratio of protein to milk fat exceeded 5:1 in a two-trait model; however, milk fat response decreased by over 10%. When a negative relative economic value was assigned to milk fat, economic returns were lower because of lower milk fat responses and the lack of higher protein responses compared with the same ratio for relative economic value but a positive weight for milk fat. Accounting for phenotypic and genetic correlations in deriving selection index weight improved economic response 5%