The objective of this study was to perform a genomewide association study (GWAS) for growth traits in Charolais beef cattle and to identify SNP markers and genes associated with these traits. Our study included 855 animals genotyped using 76,883 SNP from the GeneSeek Genomic Profiler Bovine HD panel. The examined phenotypic data included birth, weaning, and yearling weights as well as pre- and postweaning ADG. After quality control, 68,337 SNP and 823 animals were retained in the analysis. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. Eighteen SNP located in 13 BTA were associated with growth traits ( < 5 × 10). The most important genes in these genomic regions were (), (), (), (), and ( [angiotensinase C]), due to their relationships with perinatal and postnatal survival, bone growth, cell adhesion, regulation of adipogenesis, and appetite. In conclusion, this study is the first to describe a GWAS conducted in beef cattle in Mexico and represents a basis for further and future research. This study detected new QTL associated with growth traits and identified 5 positional and functional candidate genes that are potentially involved in variations of the analyzed traits. Future analyses of these regions could help to identify useful markers for marker-assisted selection and will contribute to the knowledge of the genetic basis of growth in cattle and be a foundation for genomic predictions in Mexican Charolais cattle.
El objetivo fue comparar los efectos de una metodología para la clasificación de épocas climáticas, que tradicionalmente son utilizadas para establecer épocas de nacimiento (EN) en estudios y experimentos estadísticos. Esta metodología se basa en un índice de aridez (IA) para clasificar las EN utilizando información meteorológica histórica. Se trabajó una base de datos con un pedigrí de 7,460 animales, se ajustaron dos modelos para peso al nacimiento y peso al destete en bovinos Charolais manejados en pastoreo extensivo. Los modelos incluyeron el efecto fijo de grupo contemporáneo (GC= subclase de hato, sexo, año y EN) y edad de la madre. Los mismos modelos se compararon utilizando una clasificación tradicional de estaciones del año para clasificar las EN. Al estimar los componentes de varianza y valores genéticos (DEP) con sus exactitudes, los modelos fueron diferentes de acuerdo a la prueba de razón de verosimilitudes (P<0.01). El número de GC se redujo en 25 % para la EN basada en el IA, con GC con mayor número de individuos. El principal efecto observado en los modelos analizados fue el cambio en la jerarquización de las DEP para ambas características. Este método de clasificación de épocas de nacimiento, puede ayudar a mejorar el ajuste de modelos estadísticos en los sistemas ganaderos manejados en pastoreo extensivo.
Charolais cattle are one of the most important breeds for meat production worldwide;in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8-59.3 Mb on BTA 4; 67.5-69.3 on BTA 5; 39.5-41.0 Mb on BTA 6; and 26.4-29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits. K E Y W O R D S Charolais, integrated haplotype score, signatures of selection, single nucleotide polymorphism | 379 JAHUEY-MARTÍNEZ ET Al.
A genome-wide association study (GWAS) was performed to elucidate genetic architecture of growth traits in Braunvieh cattle. Methods: The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth (BW), weaning (WW), and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with BW, and two SNPs were associated with WW, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), related to embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico providing evidence for genetic architecture of assessed growth traits. Further specific analysis of found associated genes and regions will clarify its contribution to the genetic basis of growth-related traits.
Reports in the literature suggest that a transient surge of ghrelin secretion (TSGS) just before a scheduled meal may be triggered by an appetite mechanism. Also, it is known that circulating ghrelin concentrations fluctuate relative to nutritional status and influence feeding behavior. The aim of the present study was to search for genetic variants in five selected genes (GHRL, GHSR1a, MBOAT4, NPY and AgRP) within the ghrelin gene (GHRL) interaction network. gDNA was extracted from the six highest- and six lowest-RFI Hampshire non-castrated male lambs, out of a total of 25 lambs in a 56-d GrowSafe SystemsÒ feeding trial and the complete genes were amplified by PCR. Libraries were prepared and sequenced in the ILLUMINA platform MiniSeq Sequencing System. Variations were identified using the genomic variant call format (GVCF) workflow with HaplotypeCaller using the reference genome oviAri 4 - Oar_v4 (GCA_000298732.2). One hundred and ninety-two SNPs were found in the five analyzed genes. Most of them had been reported in the SNPs data base. Linear models including each SNP genotype at a time as fixed effects, in addition to ADG and mid test metabolic body weight as covariates for some variables, were adjusted. Forty-three of these SNPs had different genotype frequencies in the two RFI groups, and appear to be associated (p < 0.05) with traits such as RFI, feed intake (FI), feed conversion (FC) and ghrelin hormone concentration in plasma (GHRL) at the TSGS; especially SNPs rs399405301, rs421869734, rs604106535, rs417836509, rs600356564, rs590893697 at the MBOAT4 gene which resulted highly significant (p < 0.01) for RFI and GHRL. The SNP rs423156356 at the GHSR1a gene was highly significant (p < 0.01) for FI and FC. These SNPs (Table 1) have the potential to be used as genetic markers for improvement of feed efficiency in Hampshire sheep, but validation on a larger sample deserves further research efforts.
The aim was to explore potential differences on ghrelin plasm concentrations between efficient and inefficient lambs within a transient surge of ghrelin secretion just before a scheduled meal feeding. Six high- (256±19 g) and six low-RFI (-242±19 g) Hampshire entire male lambs (Age=168±2 d and BW=63±5 kg) were taken out of 25 individuals in a 56-d GrowSafe SystemsÒ feeding trial. After a 10-d adaptation to a once-daily ad-libitum feed offering (0900 h), at d11 three lambs from each RFI group continued the once-daily feeding schedule (FED), whereas feed was withheld from the other three lambs (FAST) from each RFI group for 24-h (d11 to d12). Blood samples were collected via indwelling jugular catheter. In d11, ghrelin plasm concentrations were determined by ELISA in all animals at 0800, 0840, 0900, 1000 and 1100, and d12 at 0900, 1000 and 1100 in the FAST group. A linear model for repeated measures was adjusted with PROC MIXED of SAS. Plasm ghrelin levels began to increase at 0800, and RFI groups reached significant difference (P < 0.05) within both FED and FAST groups at 0840, with the greatest difference at peak concentrations at 0900 h (3.9±0.2 vs 2.4±0.2 and 3.9±0.2 vs 3.0±0.2 ng/ml for high vs low RFI, respectively). In the descendent phase of the curve for the FED group, one hour after feeding, ghrelin plasm concentration levels continued to be greater (P < 0.05) for high RFI vs low RFI animals and reached basal levels by 1100 h. For the FAST group, ghrelin concentrations continued to increase averaging maximum concentrations at the end of feed restriction, 0900 h of d12, being 4.9±0.2 ng/mL for the high RFI animals and 3.5±0.2 ng/mL for the low RFI ones. In conclusion, high RFI lambs show more pronounced transient surge of ghrelin secretion just before a scheduled meal feeding than low RFI lambs.
Con el objetivo de definir el panel de polimorfismos de nucleótido simple (SNP) para pruebas de paternidad en bovinos, se analizaron los genotipos en tres razas (número de SNP evaluados e individuos muestreados): Hereford (HER; 202; 1317), Brangus (BRA; 217; 3431) y Limousin (LIM; 151; 8205). Dentro de raza, se descartó los SNP con porcentaje de individuos genotipados (PIG) menor a 90 %, con desequilibrio Hardy Weinberg (HW; P<0.05), con frecuencia de alelo menor de 0.10 o menos y con desequilibrio de ligamiento, donde la correlación entre frecuencias genotípicas fue superior a 0.25. Se estimó los niveles de heterocigosis esperada (He) y observada (Ho), contenido de información polimórfica (CIP); así como, el índice de Shannon, el índice de fijación y tamaño efectivo de población (Ne). Se calculó la probabilidad de exclusión (PEC) y de identidad combinada (PIC). El panel final fue de 121, 188 y 113 SNP en HER, BRA y LIM, respectivamente; la principal fuente de descarte fue HW seguido de PIG. Los niveles de Ho y He fueron superior a 0.40; el PIC fue mayor a 0.32 y Ne presentó estimaciones por arriba de 181.3. Los resultados para la PEC fueron superiores a 0.999999; para la PIC, estuvieron por debajo de 1 x 10-20.
The scrotal circumference is one of the main characteristics related to fertility of the bovine male and female. Its study through genetic and genomic tools would help to the discovery of favorable variation and genetic architecture to promote its selection. The aim of this work was to carry out a genome- wide association study using a large microarray of SNPs, to identify variations and candidate genes associated with the studied trait, for which information from 141 Charolais bulls was used. Four markers found, rs110416965, rs110130953, rs43423602 and rs29003417, showed significant association at the genome level. Three of them are found within candidate genes (RBFOX2, TTF2 and CXCL2). This information contributes to the understanding of the genetic architecture of this trait.
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