Genotypic and phenotypic data of 1,562 animals were analyzed to find genomic regions
that potentially influence the birth weight (BW), weaning weight at seven months of
age (WW) and yearling weight (YW) of Colombian Brahman cattle, with genotyping
conducted using Illumina Bead chip array with 74,669 SNPs. A Single Step Genomic BLUP
(ssGBLP), approach was used to estimate the proportion of variance explained by each
marker. Multiple regions scattered across the genome were found to influence weights
at different ages, also dependent on the trait component (direct or maternal). The
most interesting regions were connected to previously identified QTLs and genes, such
as ADAMTSL3, CAPN2, CAPN2, FABP6, ZEB2 influencing growth and weight traits. The
identified regions will contribute to the development and refinement of genomic
selection programs for Zebu Brahman cattle in Colombia.
Pseudomonas fluorescens is a well-known plant growth-promoting rhizobacterium (PGPR). We report here the first whole-genome sequence of PGPR P. fluorescens evaluated in Colombian banana plants. The genome sequences contains genes involved in plant growth and defense, including bacteriocins, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and genes that provide resistance to toxic compounds.
Salmonella enterica is a pathogen of significant public health importance that is frequently associated with foodborne illness. We report the whole-genome sequences of four multidrug-resistant Salmonella enterica serovar Paratyphi B and Heidelberg strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, β-lactams, fluoroquinolones, sulfonamides, tetracycline, and trimethoprim.
The linkage disequilibrium (LD) between molecular markers affects the accuracy of
genome-wide association studies and genomic selection application. High-density
genotyping platforms allow identifying the genotype of thousands of single
nucleotide polymorphisms (SNPs) distributed throughout the animal genomes, which
increases the resolution of LD evaluations. This study evaluated the
distribution of minor allele frequencies (MAF) and the level of LD in the
Colombian Creole cattle breeds Blanco Orejinegro (BON) and Romosinuano (ROMO)
using a medium density SNP panel (BovineSNP50K_v2). The LD decay in these breeds
was lower than those reported for other taurine breeds, achieving optimal LD
values (r2 ≥ 0.3) up to a distance of 70 kb in BON and 100 kb in
ROMO, which is possibly associated with the conservation status of these cattle
populations and their effective population size. The average MAF for both breeds
was 0.27 ± 0.14 with a higher SNP proportion having high MAF values (≥ 0.3). The
LD levels and distribution of allele frequencies found in this study suggest
that it is possible to have adequate coverage throughout the genome of these
breeds using the BovineSNP50K_v2, capturing the effect of most QTL related with
productive traits, and ensuring an adequate prediction capacity in genomic
analysis.
ABSTRACT. Whole genome selection represents an important tool for improving parameters related to the production of livestock. In order to build genomic selection indexes within a particular breed, it is important to identify polymorphisms that have the most significant association with a desired trait. A genome-wide marker association approach based on the Illumina BovineSNP50 BeadChip TM was used to identify genomic regions affecting birth weight (BW), weaning weight (WW), and daily weight gain (DWG) in purebred and crossbred creole cattle populations. We genotyped 654 individuals of Blanco Orejinegro (BON), Romosinuano (ROMO) and Cebú breeds and the crossbreeds BON x Cebú and ROMO x Cebú, and tested 5 genetic control models. In total, 85 single nucleotide polymorphisms (SNPs) were related (P < 0.05) to the 3 evaluated traits; BW was associated with the highest number of SNPs. For statistical falsepositive correction, Bonferroni correction was used. From the results, we identified 7, 6, and 4 SNPs with strong associations with BW, WW, and DWG, respectively. Many of these SNPs were located Genome-wide association studies in Colombian creole cattle on important coding regions of the bovine genome; their ontology and interactions are discussed herein. The results could contribute to the identification of genes involved in the physiology of beef cattle growth and the development of new strategies for breeding management via genomic selection to improve the productivity of creole cattle herds.
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