Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays

Palombo, Valentino; Milanesi, Marco; Sgorlon, Sandy; Capomaccio, Stefano; Mele, Marcello; Nicolazzi, Ezequiel Luís; Ajmone‐Marsan, Paolo; Pilla, Fabio; Stefanon, Bruno; D’Andrea, Mariasilvia

doi:10.3168/jds.2018-14413

Cited by 62 publications

(50 citation statements)

References 77 publications

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“…Accordingly to the reference study [24], we also performed the enrichment analysis of KEGG pathways considering the 452 genes identified by the authors. The results obtained by PANEV enrichment function showed an over-representation of immune diseases and immune PANEV was already applied by Palombo and colleagues on genes significantly associated with milk fatty acid profiles in Italian Simmental and Holstein breeds [38]. A total of 47 and 165 significant positional candidate genes were detected in Italian Simmental and Holstein breeds, respectively.…”

Section: Resultsmentioning

confidence: 85%

PANEV: an R package for a pathway-based network visualization

et al. 2020

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Background: During the last decade, with the aim to solve the challenge of post-genomic and transcriptomic data mining, a plethora of tools have been developed to create, edit and analyze metabolic pathways. In particular, when a complex phenomenon is considered, the creation of a network of multiple interconnected pathways of interest could be useful to investigate the underlying biology and ultimately identify functional candidate genes affecting the trait under investigation. Results: PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes. Conclusions: The suite has no species constraints and it is ready to analyze genomic or transcriptomic outcomes. Users need to supply the list of candidate genes, specify the target pathway(s) and the number of interconnected downstream and upstream pathways (levels) required for the investigation. The package is available at https:// github.com/vpalombo/PANEV.

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Section: Resultsmentioning

confidence: 85%

PANEV: an R package for a pathway-based network visualization

et al. 2020

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“…Its expression increases the production of milk by secretory cells of the mammary gland at the beginning of lactation (Farhadian, Rafat, Hasanpur, Ebrahimi, & Ebrahimie, 2018). In addition, LZTS2 was found to be involved in milk fat composition in a study on Italian Holstein cows (Palombo et al, 2018). The SLC25A33 gene was identified on BTA16.…”

Section: Identification Of Candidate Genes Within Roh Islandsmentioning

confidence: 99%

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Ospina

Faria

Filho

et al. 2020

Reprod Domestic Animals

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Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1‐2 Mb) were observed between the two populations, while the number of long ROH (ROH>16 Mb) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

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“…The SNORA62 gene was identified on OAR3 as a candidate gene affecting LMWW trait. Recently, a GWAS of milk fatty acid composition identified the SNORA62 gene as a candidate gene affecting milk fatty acid content [38].…”

Section: Gwas and Gsa Of Maternal Composite Traits At Weaningmentioning

confidence: 99%

Maternal genes and pathways affecting birth weight and weaning weight traits in sheep: A GWAS and pathway enrichment analysis

Esmaeili-Fard

Hafezian

Gholizadeh

et al. 2020

Preprint

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Background Ewe productivity is considered as the most important economic trait in sheep meat production. Due to very limited reports, the objective of this study was the application of alternative GWAS approaches followed by gene set enrichment analysis (GSEA) on the maternal genome to unravel the genomic architecture underlying ewe productivity in Iranian Baluchi sheep. Six maternal composite traits including progeny birth weight (PBW), litter mean weight at birth (LMWB), total litter weight at birth (TLWB), progeny weaning weight (PWW), litter mean weight at weaning (LMWW) and total litter weight at weaning (TLWW) were studied. Results Genes such as RDX , FDX1 , ARHGAP20 , ZC3H12C , THBS1 , and EPG5 on OAR6, OAR7, OAR15, and OAR23 were identified for composite traits at birth. The genes are involved in pregnancy, including autophagy in the placenta, progesterone production by the placenta, maternal immune response and placenta formation. Some maternal pathways, related to calcium ion transport, signal transduction, neurogenesis, and immune response were also identified for birth weight traits. Moreover, many genes including NR2C1 , VEZT , HSD17B4 , RSU1 , CUBN , VIM , PRLR , and FTH1 were located on OAR2, OAR3, OAR5, OAR7, OAR13, OAR16, and OAR25 identified as maternal genes affecting weaning weight traits. Most of the identified genes were involved in mammary glands development and milk components production. Also, many GO terms related to protein processing and transport, ion transport and homeostasis, proteins and lipid phosphorylation, and phospholipid translocation were identified in association with weaning weight traits. Conclusions The results of the present study revealed that calcium ion homeostasis and transport and the maternal immune system could have an important role in progeny’s birth weight. Also, the results showed that genes and pathways affecting mammary glands development during pregnancy and milk components production have the most impact on lambs weaning weight. These findings contribute to a better understanding of the genetic architecture of the studied traits and providing opportunities for improving ewe productivity via marker-assisted selection.

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Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays

Cited by 62 publications

References 77 publications

PANEV: an R package for a pathway-based network visualization

PANEV: an R package for a pathway-based network visualization

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Maternal genes and pathways affecting birth weight and weaning weight traits in sheep: A GWAS and pathway enrichment analysis

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