scholarly journals New insights from genome-wide association analysis using imputed whole-genome sequence: the genetic mechanisms underlying residual feed intake in chickens

2019 ◽  
Author(s):  
Shaopan Ye ◽  
Zitao Chen ◽  
Rongrong Zheng ◽  
Shuqi Diao ◽  
Jinyan Teng ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Significant Snps ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Environmental Footprint ◽  
Genome Wide ◽  
Component Traits ◽  
Genetic Mechanisms

Abstract Background: Poultry feed occupies the largest cost of poultry production, which is estimated up to 70%. Moreover, it is pressure on the agricultural industry to reduce emissions and improve its environmental footprint, simultaneously increasing output to meet the growing demand for protein worldwide. Therefore, improving feed efficiency (FE) play an important role to improve profits and their environmental footprint in broiler production. In this study, using imputed whole genome sequencing (WGS) data, genome-wide association analysis (GWAS) was performed to identify SNPs and genes associated with residual feed intake (RFI) and its component traits. Furthermore, transcriptomic analysis between high- and low-RFI groups was performed to validate candidate genes from GWAS. Results: Results showed that heritability estimates of average daily gain (ADG), average daily feed intake (ADFI) , and RFI were 0.29 (0.004), 0.37 (0.005), and 0.38 (0.004), respectively. Using imputed sequence-based GWAS, we identified seven significant SNPs and five candidate genes ( MTSS I-BAR domain containing 1, MTSS1; folliculin, FLCN; COP9 signalosome subunit 3, COPS3; 5',3'-nucleotidase, mitochondrial, NT5M; and gametocyte specific factor 1, GTSF1) associated with RFI, twenty significant SNPs and one candidate gene ( inositol polyphosphate multikinase, IPMK ) associated with ADG, and one significant SNP and one candidate gene ( coatomer protein complex subunit alpha, COPA ) associated with ADFI. After performing transcriptomic analysis between high- and low-RFI groups, both 38 up-regulated and 26 down-regulated genes were identified in high-RFI group. Furthermore, integrating regional conditional GWAS and transcriptome analysis, ras related dexamethasone induced 1 (RASD1) was the only one overlapped gene associated with RFI, which also suggested that the region (GGA14: 4767015 -4882318) is a new quantitative trait locus (QTL) associated with RFI. Conclusions: In conclusions, using imputed sequence-based GWAS is an efficient method to identify significant SNPs and candidate genes in chicken. Our results provide valuable insights into the genetic mechanisms of RFI and component traits, which would further improve the genetic gain of feed efficiency rapidly and cost-effectively in the context of marker-assisted breeding selection. Keywords: Whole genome sequence, GWAS, transcriptome analysis, feed efficiency, chickens.

scholarly journals Identification of QTL regions and candidate genes for growth and feed efficiency in broilers

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Wei Li ◽  
Maiqing Zheng ◽  
Guiping Zhao ◽  
Jie Wang ◽  
Jie Liu ◽  
...  
Keyword(s):  
Body Weight ◽  
Candidate Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Genetic Variance ◽  
Significant Snps ◽  
Abdominal Fat ◽  
Chromosome 1 ◽  
Thigh Muscle ◽  
Genome Wide

Abstract Background Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. Results Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34–2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27–92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. Conclusions We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

scholarly journals Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants

2018 ◽  
Vol 50 (1) ◽  
Author(s):  
Chunyan Zhang ◽  
Robert Alan Kemp ◽  
Paul Stothard ◽  
Zhiquan Wang ◽  
Nicholas Boddicker ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Feed Efficiency ◽  
Whole Genome Sequence ◽  
Sequence Variants ◽  
Whole Genome ◽  
Genomic Evaluation ◽  
Component Traits

scholarly journals Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiyuan Li ◽  
Robert Mukiibi ◽  
Yining Wang ◽  
Graham S. Plastow ◽  
Changxi Li
Keyword(s):  
Citric Acid ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Feed Efficiency ◽  
Plasma Metabolites ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Biological Functions ◽  
Dna Variants ◽  
Component Traits

Abstract Background Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. Results Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10−5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. Conclusions This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.

scholarly journals Whole Genome Sequence Data From Captive Baboons Implicate RBFOX1 in Epileptic Seizure Risk

2021 ◽  
Vol 12 ◽  
Author(s):  
Mark Z. Kos ◽  
Melanie A. Carless ◽  
Lucy Blondell ◽  
M. Michelle Leland ◽  
Koyle D. Knape ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Sequence ◽  
Epileptic Seizure ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Ppi Network ◽  
Genetic Etiology ◽  
Human Epilepsy ◽  
Genome Wide

In this study, we investigate the genetic determinants that underlie epilepsy in a captive baboon pedigree and evaluate the potential suitability of this non-human primate model for understanding the genetic etiology of human epilepsy. Archived whole-genome sequence data were analyzed using both a candidate gene approach that targeted variants in baboon homologs of 19 genes (n = 20,881 SNPs) previously implicated in genetic generalized epilepsy (GGE) and a more agnostic approach that examined protein-altering mutations genome-wide as assessed by snpEff (n = 36,169). Measured genotype association tests for baboon cases of epileptic seizure were performed using SOLAR, as well as gene set enrichment analyses (GSEA) and protein–protein interaction (PPI) network construction of top association hits genome-wide (p &lt; 0.01; n = 441 genes). The maximum likelihood estimate of heritability for epileptic seizure in the pedigreed baboon sample is 0.76 (SE = 0.77; p = 0.07). Among candidate genes for GGE, a significant association was detected for an intronic SNP in RBFOX1 (p = 5.92 × 10–6; adjusted p = 0.016). For protein-altering variants, no genome-wide significant results were observed for epilepsy status. However, GSEA revealed significant positive enrichment for genes involved in the extracellular matrix structure (ECM; FDR = 0.0072) and collagen formation (FDR = 0.017), which was reflected in a major PPI network cluster. This preliminary study highlights the potential role of RBFOX1 in the epileptic baboon, a protein involved in transcriptomic regulation of multiple epilepsy candidate genes in humans and itself previously implicated in human epilepsy, both focal and generalized. Moreover, protein-damaging variants from across the genome exhibit a pattern of association that links collagen-containing ECM to epilepsy risk. These findings suggest a shared genetic etiology between baboon and human forms of GGE and lay the foundation for follow-up research.

scholarly journals Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1163
Author(s):  
Manuel J. Wolf ◽  
Tong Yin ◽  
Guilherme B. Neumann ◽  
Paula Korkuć ◽  
Gudrun A. Brockmann ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Sequence ◽  
Genome Wide Association Study ◽  
Fasciola Hepatica ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Potential Candidate ◽  
Genome Wide

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

scholarly journals PSXI-24 Rumen temperature, fermentation and microbial signatures are poorly associated with steer feed-efficiency profiles

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 382-382
Author(s):  
Obioha N Durunna ◽  
Daalkhaijav Damiran ◽  
John R Campbell ◽  
Jeffery A Carroll ◽  
Bart Lardner
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Screening Tool ◽  
Rumen Fluid ◽  
Microbial Populations ◽  
Environmental Footprint ◽  
Rumen Temperature ◽  
Potential Applications ◽  
Cost Implications ◽  
The Relationship

Abstract Breeding feed-efficient cattle can reduce the environmental footprint of beef operations but assessing all replacement candidates for feed-intake is not practical due to cost implications. The main objectives of this study were to evaluate if rumen temperature (RumT), measured with wireless rumen Thermobolus® can distinguish steers with different feed-efficiency profiles and whether steers with divergent efficiency profiles have different nutrient fermentation signatures. The study also validated the relationship between rectal temperature (RecT) and RumT measured with automatic thermistors. Residual feed intake (RFI) profiles of 160 steers were measured over two years. All steers were assessed for RFI profiles using high and moderate forage diets, respectively, over two successive periods each year. Each steer was fitted with a rumen Thermobolus® throughout each ~80-d test period while half of the steers wore an automatic temperature-logger rectal device for ~30d. The devices recorded the RumT and RecT every 5 minutes, respectively. Rumen fluid samples were collected from high-RFI (n = 5) and low-RFI (n = 5) steers to assess if differences in rumen fermentation and microbial profiles exist. Circadian-adjusted RumT and RecT for each steer were used for analysis. The within-period correlations between RumT and RecT ranged between 49 and 77%. There was a trend (P = 0.08) that differences exist for rhythm-adjusted temperatures among different RFI profiles with low-RFI steers (39.72±0.01oC) having lower average RumT than those in high (39.75±0.01oC) or medium (39.74±0.01oC) classes. The correlation between the two test-periods for rhythm-adjusted RumT was 65% while the correlation between RFI from both periods was 47%. There was no difference (P &gt; 0.30) between high- and low-RFI animals for the total or individual volatile fatty acid fractions or microbial populations. The narrow temperature variation among RFI classes limits its use as screening tool but the higher across-period correlation encourages the need for further studies into alternative potential applications.

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