Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

Lam, Stephanie; Miglior, F.; Fonseca, Pablo A S; Gómez-Redondo, Isabel; Zeidan, J.; Suárez-Vega, Aroa; Schenkel, F.S.; Guan, Le Luo; Waters, Sinéad M.; Stothard, Paul; Cánovas, Ángela

doi:10.3168/jds.2020-18241

Cited by 22 publications

(15 citation statements)

References 72 publications

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“…A recent transcriptome study of the liver in Jersey and Holstein cattle selected for RFI was designed to identify genetic variants from expressed genes in RNA-sequencing data. A polymorphism in KAT2B , a gene involved in the Notch signaling pathway, was identified that segregated with the same RFI phenotypes in both breeds of cattle [ 23 ]. The identification of KAT2B genetic variant associated with RFI, along with the correlation of KAT2B expression with RFI in this study, suggest that KAT2B may be of particular importance for feed efficiency in cattle.…”

Section: Discussionmentioning

confidence: 99%

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

Lindholm‐Perry

Meyer

Kern-Lunbery³

et al. 2022

Animals

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In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging. The purpose of this study was to perform a meta-analysis of the ruminal transcriptome of two unrelated populations of animals to identify genes that are involved in feed efficiency across populations. RNA-seq data from animals with high and low residual feed intake (RFI) from a United States population of cattle (eight high and eight low RFI) and a Canadian population of cattle (nine high and nine low RFI) were analyzed for differences in gene expression. A total of 83 differentially expressed genes were identified. Some of these genes have been previously identified in other feed efficiency studies. These genes included ATP6AP1, BAG6, RHOG, and YPEL3. Differentially expressed genes involved in the Notch signaling pathway and in protein turnover were also identified. This study, combining two unrelated populations of cattle in a meta-analysis, produced several candidate genes for feed efficiency that may be more robust indicators of feed efficiency than those identified from single populations of animals.

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Section: Discussionmentioning

confidence: 99%

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

Lindholm‐Perry

Meyer

Kern-Lunbery³

et al. 2022

Animals

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“…Lastly, QTL annotation analysis was performed using the R package: Genomic functional Annotation in Livestock for positional candidate LOci (GALLO) ( https://CRAN.R-project.org/package=GALLO; [ 67 ]). The genome coordinates of the DE transcripts were used, as well as the QTL .gff annotation file retrieved from the cattle QTL Database ( https://www.animalgenome.org/cgi-bin/QTLdb/index [ 49 , 68 ]). We used windows of 1000 bp to account for 100 upstream and 100 downstream of each DE transcript [ 69 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of novel alternative splicing associated with mastitis disease in Holstein dairy cows using large gap read mapping

2022

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Background Mastitis is a very common disease in the dairy industry that producers encounter daily. Transcriptomics, using RNA-Sequencing (RNA - Seq) technology, can be used to study the functional aspect of mastitis resistance to identify animals that have a better immune response to mastitis. When the cow has mastitis, not only genes but also specific mRNA isoforms generated via alternative splicing (AS) could be differentially expressed (DE), leading to the phenotypic variation observed. Therefore, the objective of this study was to use large gap read mapping to identify mRNA isoforms DE between healthy and mastitic milk somatic cell samples (N = 12). These mRNA isoforms were then categorized based on being 1) annotated mRNA isoforms for gene name and length, 2) annotated mRNA isoforms with different transcript length and 3) novel mRNA isoforms of non - annotated genes. Results Analysis identified 333 DE transcripts (with at least 2 mRNA isoforms annotated, with at least one being DE) between healthy and mastitic samples corresponding to 303 unique genes. Of these 333 DE transcripts between healthy and mastitic samples, 68 mRNA isoforms are annotated in the bovine genome reference (ARS.UCD.1.2), 249 mRNA isoforms had novel transcript lengths of known genes and 16 were novel transcript lengths of non - annotated genes in the bovine genome reference (ARS.UCD.1.2). Functional analysis including gene ontology, gene network and metabolic pathway analysis was performed on the list of 288 annotated and unique DE mRNA isoforms. In total, 67 significant metabolic pathways were identified including positive regulation of cytokine secretion and immune response. Additionally, numerous DE novel mRNA isoforms showed potential involvement with the immune system or mastitis. Lastly, QTL annotation analysis was performed on coding regions of the DE mRNA isoforms, identifying overlapping QTLs associated with clinical mastitis and somatic cell score. Conclusion This study identified novel mRNA isoforms generated via AS that could lead to differences in the immune response of Holstein dairy cows and be potentially implemented in future breeding programs.

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“…The QTL enrichment analysis was performed using GALLO as described by Fonseca et al (2020a). A guilt-by-association approach was performed to identify potential functional candidate genes (Fonseca et al, 2020b;Martins de Carvalho et al, 2020;Sweett et al, 2020;Lam et al, 2021). Briefly, a trained list containing genes associated with stillbirth and pregnancy persistence was obtained from GUILDify (Guney et al, 2014), using the following list of keywords: stillbirth, pregnancy, and pregnancy loss.…”

Section: Functional Candidate Genes Searchmentioning

confidence: 99%

Genome-wide association study using haplotype libraries and repeated-measures model to identify candidate genomic regions for stillbirth in Holstein cattle

Fonseca

Schenkel

Cánovas

2022

Journal of Dairy Science

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Reduced fertility is one of the main causes of economic losses on dairy farms, resulting in economic losses estimated at $938 per stillbirth case in Holstein herds. The identification of genomic regions associated with stillbirth could help to develop better management and breeding strategies aimed to reduce the frequency of undesirable gestation outcomes. Here, 10,570 cows and 50,541 birth records were used to perform a haplotypebased GWAS. A total of 41 significantly associated pseudo-SNPs (haplotypes within haplotype blocks converted to a binary classification) were identified after Bonferroni adjustment for multiple tests. A total of 117 positional candidate genes were annotated within or close (in a 200-kb interval) to significant pseudo-SNPs (haplotype blocks). The guilt-by-association functional prioritization identified 31 potential functional candidate genes for reproductive performance out of the 117 positional candidate genes annotated. These genes play crucial roles in biological processes associated with pregnancy persistence, fetus development, immune response, among others. These results helped us to better understand the genetic basis of stillbirth in dairy cattle and may be useful for the prediction of stillbirth in Holstein cattle, helping to reduce the related economic losses caused by this phenotype.

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Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

Cited by 22 publications

References 72 publications

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

Identification of novel alternative splicing associated with mastitis disease in Holstein dairy cows using large gap read mapping

Genome-wide association study using haplotype libraries and repeated-measures model to identify candidate genomic regions for stillbirth in Holstein cattle

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