Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency

Davoudi, Pourya; Ngoc, Duy; Colombo, Stefanie M.; Rathgeber, Bruce; Miar, Younes

doi:10.3389/fgene.2022.903733

Cited by 10 publications

(4 citation statements)

References 189 publications

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“…In the past few decades, researchers have made great efforts in functional genomics research of pigs and accumulate valuable omics data [46]. Compared to earlier released databases for pigs, such as IAnimal [20], ISwine [21], and AOD [47], PIGOME contains the most data types and the most up-to-date multi-omics datasets covering comprehensive meta-information (Table 2).…”

Section: Discussionmentioning

confidence: 99%

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

Han,

Yang,

Zhang

et al. 2024

Preprint

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In addition to being a major source of animal protein, pigs are important model for the study of development and diseases in humans. During the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, the multi-omics database specifically used for pig functional genomic research is still limited. Here, we present a user-friendly database of pig multi-omics named PIGOME. PIGOME contains seven types of pig omics datasets, including whole-genome sequencing, RNA-seq, miRNA-seq, ChIP-seq, ATAC-seq, bisulfite-seq, and MeRIP-seq, from 6,901 samples and 392 projects with manually curated metadata, integrated gene annotation, and quantitative trait locus information. Furthermore, various 'explore and browse' functions have been established for user-friendly access to omics information. PIGOME implemented several tools to visualize genomic variants, gene expression, and epigenetic signals of a given gene in the pig genome, enabling efficient exploration of spatial-temporal expression/epigenetic pattern, function, regulatory mechanism, and associated economic traits. Collectively, PIGOME provides valuable resources for pig breeding and is helpful for human biomedical research. PIGOME is available at https://pigome.com.

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Section: Discussionmentioning

confidence: 99%

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

Han,

Yang,

Zhang

et al. 2024

Preprint

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“…One approach is to increase the efficiency with which animals convert feed into meat and other products, such as eggs or milk. A commonly used metric for measuring this trait, called feed efficiency, is the feed conversion ratio (FCR), which is calculated as the ratio of feed intake to weight gain [2,3]. The FCR is also positively correlated with average daily gain [4].…”

Section: Introductionmentioning

confidence: 99%

Integrating Multi-Omics Data to Identify Key Functional Variants Affecting Feed Efficiency in Large White Boars

Xiang,

Sun,

et al. 2024

Genes

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Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single-nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.

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“…The aim of the livestock industry is to reach high productivity and good quality at the lowest possible cost. This is why poultry, pigs and ruminants are genetically selected to gain the maximum weight in the minimum possible time with the minimum required feed [ 1 , 2 , 3 ]. This phenotype is mainly characterised by the Feed Conversion Ratio (FCR), representing the efficiency with which the animal converts feed into increased body mass.…”

Section: Introductionmentioning

confidence: 99%

Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach

et al. 2023

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Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on the gastrointestinal microbiota of poultry, pigs and ruminants and their consequences on host physiology. To this end, 65, 32 and 4 controlled trials or systematic reviews were selected from PubMed for poultry, pigs and ruminants, respectively. Microorganisms and their derivatives were the most studied modulator family in poultry, while in pigs, the micronutrient family was the most investigated. With only four controlled trials selected for ruminants, it was difficult to conclude on the modulators of interest for this species. For some modulators, most studies showed a beneficial effect on both the phenotype and the microbiota. This was the case for probiotics and plants in poultry and minerals and probiotics in pigs. These modulators seem to be a good way for improving animal performance.

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Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency

Cited by 10 publications

References 189 publications

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

Integrating Multi-Omics Data to Identify Key Functional Variants Affecting Feed Efficiency in Large White Boars

Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach

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