Single-step genome-wide association studies (GWAS) and post-GWAS analyses to identify genomic regions and candidate genes for milk yield in Brazilian Girolando cattle

Otto, Pamela Itajara; Guimarães, Simone Eliza Facioni; Calus, M.P.L.; Vandenplas, Jérémie; Machado, M. A.; Panetto, J. C. do C.; Silva, Marcos Vinícius Gualberto Barbosa da

doi:10.3168/jds.2019-17890

Cited by 20 publications

(15 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Various genes in this pathway were previously associated with important traits in cattle. For example, the STAT gene family (signal transducer and transcription activator) is responsible for the development and differentiation of mammary gland cells in different life stages [ 51 ]. The MAPK10 gene (mitogen-activated protein kinase 10) is linked with the inflammatory response and immunity of epithelial cells in the mammary gland.…”

Section: Discussionmentioning

confidence: 99%

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

et al. 2022

View full text Add to dashboard Cite

Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

show abstract

Section: Discussionmentioning

confidence: 99%

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Some genes in this pathway were previously associated with some traits in cattle. For example, the STAT gene family (signal transducer and transcription activator) is responsible for the development and differentiation of mammary gland cells in the different life phases [50]. The MAPK10 gene (mitogen-activated protein kinase 10) is linked with the in ammatory response and immunity of epithelial cells in the mammary gland.…”

Section: Homozygosity Islandsmentioning

confidence: 99%

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Mulim

Brito

Pinto

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: A decline in the level of genetic diversity can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, some metrics have been proposed to assess the levels of populational genetic diversity in selected populations. The main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results: A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3,576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.Conclusions: The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

show abstract

“…From this standpoint, animal genotyping using medium-or high-density SNP panels followed by GWAS has been presented as a powerful approach to reconnect phenotypes of interest back to their underlying genetics in livestock species (Korte and Farlow, 2013). To complement GWAS, post-GWAS analyses, such as gene prioritization analyses, gene set enrichment, or pathway analyses, have been increasingly used over the past few years to better understand the molecular mechanisms involved in the different traits of interest (Otto et al, 2020). Such new approaches help to solve GWAS limitations, such as by taking into account that genes work together in networks across the different biological pathways, thus generating the complex control of quantitative traits (Dadousis et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…In the dairy industry, milk yield and milk solids, referred to here as "milk traits," are major goals for selection. Accordingly, a large number of studies have implemented QTL mapping and GWAS to identify QTL with effects on milk traits in dairy cattle (Li et al, 2020b;Otto et al, 2020), goats (Mucha et al, 2018;Guan et al, 2020), andsheep (García-Gámez et al, 2012a;Li et al, 2020a). Moreover, in recent years, an increasing number of studies have successfully applied post-GWAS analyses to determine those genes potentially involved in controlling milk traits (Sanchez et al, 2019;Otto et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

Marina

Pelayo

Suárez-Vega

et al. 2021

Journal of Dairy Science

View full text Add to dashboard Cite

This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.

show abstract

Single-step genome-wide association studies (GWAS) and post-GWAS analyses to identify genomic regions and candidate genes for milk yield in Brazilian Girolando cattle

Cited by 20 publications

References 101 publications

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

Contact Info

Product

Resources

About