scholarly journals Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

PLoS ONE ◽  
2017 ◽  
Vol 12 (6) ◽  
pp. e0173482 ◽  
Author(s):  
Justyna Horodyska ◽  
Ruth M. Hamill ◽  
Patrick F. Varley ◽  
Henry Reyer ◽  
Klaus Wimmers
Keyword(s):  
Growth Rate ◽  
Candidate Genes ◽  
Association Analysis ◽  
Conversion Efficiency ◽  
Functional Annotation ◽  
Genome Wide Association ◽  
Feed Conversion ◽  
Positional Candidate ◽  
Feed Conversion Efficiency ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

scholarly journals Identification of Novel Genome-Wide Associations for Oral Inflammatory Traits

2020 ◽  
Author(s):  
Yanjiao Jin ◽  
Jie Yang ◽  
Shuyue Zhang ◽  
Jin Li ◽  
Songlin Wang
Keyword(s):  
Candidate Genes ◽  
Immune Regulation ◽  
Functional Annotation ◽  
Inflammatory Diseases ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Causal Variants

Abstract Background: Oral diseases impact the majority of the world’s population. The following traits are common in oral inflammatory diseases: mouth ulcers, painful gums, bleeding gums, loose teeth, and toothache. Despite the prevalence of genome-wide association studies, the associations between these traits and common genomic variants, and whether pleiotropic loci are shared by some of these traits remain poorly understood. Methods: In this work, we conducted multi-trait joint analyses based on the summary statistics of genome-wide association studies of these five oral inflammatory traits from the UK Biobank, each of which is comprised of over 10,000 cases and over 300,000 controls. We estimated the genetic correlations between the five traits. We conducted fine-mapping and functional annotation based on multi-omics data to better understand the biological functions of the potential causal variants at each locus. To identify the pathways in which the candidate genes were mainly involved, we applied gene-set enrichment analysis, and further performed protein-protein interaction (PPI) analyses.Results: We identified 39 association signals that surpassed genome-wide significance, including three that were shared between two or more oral inflammatory traits, consistent with a strong correlation. Among these genome-wide significant loci, two were novel for both painful gums and toothache. We performed fine-mapping and identified causal variants at each novel locus. Further functional annotation based on multi-omics data suggested IL10 and IL12A/TRIM59 as potential candidate genes at the novel pleiotropic loci, respectively. Subsequent analyses of pathway enrichment and protein-protein interaction networks suggested the involvement of candidate genes at genome-wide significant loci in immune regulation.Conclusions: Our results highlighted the importance of immune regulation in the pathogenesis of oral inflammatory diseases. Some common immune-related pleiotropic loci or genetic variants are shared by multiple oral inflammatory traits. These findings will be beneficial for risk prediction, prevention, and therapy of oral inflammatory diseases.

scholarly journals Effect of Diatomaceous Earth on Growth Rate, Egg Production, Feed Conversion Efficiency and Parasitic Load in Hens Raised on Deep Litter

2021 ◽  
Vol 3 (1) ◽  
pp. 97-103
Author(s):  
Robert Alex Isabirye ◽  
Savino Biryomumaisho ◽  
James Okwee-Acai ◽  
Samuel Okello ◽  
George William Nasinyama
Keyword(s):  
Growth Rate ◽  
Conversion Efficiency ◽  
Egg Production ◽  
Diatomaceous Earth ◽  
Agricultural Research ◽  
Ascaridia Galli ◽  
Feed Conversion ◽  
Indigenous Chicken ◽  
Feed Conversion Efficiency ◽  
Treatment Groups

The efficacy of diatomaceous earth (DE) on growth rate, egg production and on increasing feed conversion efficiency in deep litter raised layer hens was evaluated. The study was conducted at Mukono Zonal Agricultural Research and Development Institute (MUZARDI) in Uganda. Worms were collected from fresh intestines of indigenous chicken obtained from Kalerwe chicken market near Kampala. The DE was mined in Pakwach (formerly Nebbi) district in Northern Uganda. Chickens of the Lohmann Brown breed raised on deep litter were studied. At 7 weeks the birds were divided into 5 treatment groups, A, B, C, D and E each composed of 40 birds. Groups C, D and E were given an oral dose containing 250 embryonated eggs of A. galli while groups A and B were not infected. The chicks were weighed; and subjected to feeding trials as arranged below: A – Non-infected birds on DE (4%) supplemented diet; B –non-infected birds on neither piperazine (a conventional de-wormer) nor DE; C – infected birds on DE supplemented diet; D – infected birds on piperazine; and group E – infected birds on neither DE nor piperazine applied. Fecal samples were collected and analysed in the laboratory biweekly at week 16 till week 22 respectively for fecal egg counts. In a subsequent experiment, day-old layer chicks from Lohmann Brown strain but different from those used in earlier experiments, were used to assess the effect of DE on egg production. At 17 weeks of age the 420 were divided as follows: 6 treatment groups each having 7 replicates and each replicate having 10 birds. This study showed that DE can be used successfully in growing pullet diets to correct nutritional mineral imbalance since it supplies more than 14 trace elements and other elements. Diatomaceous earth also enables pullets to cope with Ascaridia galli load; and 2% DE supplementation did not have significant improvement on egg production as compared to no supplementation at all. However, reduction in egg production was experienced when supplementation with levels of DE higher that 2% was applied. Results from biweekly fecal analyses showed significant differences in fecal egg counts (p<0.05); and treatment by group (p<0.05).

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

2022 ◽  
Author(s):  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Yibin Qiu ◽  
Donglin Ruan ◽  
Jie Wu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Large Scale ◽  
Major Gene ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Backfat Thickness ◽  
Lean Meat ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Effects of castration on growth rate, feed conversion efficiency and carcass quality in Damascus goats

1977 ◽  
Vol 24 (3) ◽  
pp. 387-391 ◽  
Author(s):  
A. Louca ◽  
S. Economides ◽  
J. Hancock
Keyword(s):  
Growth Rate ◽  
Sexual Activity ◽  
Conversion Efficiency ◽  
Live Weight ◽  
Carcass Quality ◽  
Feed Conversion ◽  
Intact Male ◽  
Goat Meat ◽  
Feed Conversion Efficiency

SUMMARYOne hundred and forty-two kids of the Damascus breed of goat were used over a 10½-mo period to study the effects of early castration (at 7 days of age) on growth, feed conversion efficiency and carcass quality and late castration (at 7½ mo of age) on the presence or absence of taint in goat meat.Intact male kids grew faster and used feed more efficiently than castrates until they were about 9 mo old (56 kg live weight). There- after intact kids exhibited strong sexual activity and as a result their growth ceased completely whereas castrates continued growing. Early castrates produced fatter carcasses than those of intact kids. Castration of male kids at the age of about 7½ mo (44 kg live weight) was not successful in this trial and the kids performed very poorly. A taint of varying intensity was present in the meat of intact goats but not in that from any of the early or late castrates.

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