scholarly journals Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats

2021 ◽  
Vol 8 ◽  
Author(s):  
Lei Zhang ◽  
Fenghong Wang ◽  
Gong Gao ◽  
Xiaochun Yan ◽  
Hongfu Liu ◽  
...  
Keyword(s):  
Body Weight ◽  
Association Study ◽  
Inner Mongolia ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Mitogen Activated Protein Kinase ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Cashmere Goats

Objective: Body weight is an important economic trait for a goat, which greatly affects animal growth and survival. The purpose of this study was to identify genes associated with birth weight (BW), weaning weight (WW), and yearling weight (YW).Materials and Methods: In this study, a genome-wide association study (GWAS) of BW, WW, and YW was determined using the GGP_Goat_70K single-nucleotide polymorphism (SNP) chip in 1,920 Inner Mongolia cashmere goats.Results: We discovered that 21 SNPs were significantly associated with BW on the genome-wide levels. These SNPs were located in 10 genes, e.g., Mitogen-Activated Protein Kinase 3 (MAPK3), LIM domain binding 2 (LDB2), and low-density lipoprotein receptor-related protein 1B (LRP1B), which may be related to muscle growth and development in Inner Mongolia Cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these genes were significantly enriched in the regulation of actin cytoskeleton and phospholipase D signaling pathway etc.Conclusion: In summary, this study will improve the marker-assisted breeding of Inner Mongolia cashmere goats and the molecular mechanisms of important economic traits.

scholarly journals Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

scholarly journals SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1583-1589 ◽  
Author(s):  
Qiang Yang ◽  
Pingxian Wu ◽  
Kai Wang ◽  
Dejuan Chen ◽  
Jie Zhou ◽  
...  
Keyword(s):  
Body Weight ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Backfat Thickness ◽  
Pig Breeds ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1170
Author(s):  
Jihye Cha ◽  
Hyojun Choo ◽  
Krishnamoorthy Srikanth ◽  
Seung-Hwan Lee ◽  
Ju-Whan Son ◽  
...  
Keyword(s):  
Body Weight ◽  
Association Study ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Gene Set Enrichment Analysis ◽  
Mitogen Activated Protein Kinase ◽  
Genome Wide Association ◽  
Regulation Of Transcription ◽  
Genome Wide ◽  
Native Chickens

Meat from Korean native chickens (KNCs) has high consumer demand; however, slow growth performance and high variation in body weight (BW) of KNCs remain an issue. Genome-wide association study (GWAS) is a powerful method to identify quantitative trait-associated genomic loci. A GWAS, based on a large-scale KNC population, is needed to identify underlying genetic mechanisms related to its growth traits. To identify BW-associated genomic regions, we performed a GWAS using the chicken 60K single nucleotide polymorphism (SNP) panel for 1328 KNCs. BW was measured at 8 weeks of age, from 2018 to 2020. Twelve SNPs were associated with BW at the suggestive significance level (p < 2.95 × 10−5) and located near or within 11 candidate genes, including WDR37, KCNIP4, SLIT2, PPARGC1A, MYOCD and ADGRA3. Gene set enrichment analysis based on the GWAS results at p < 0.05 (1680 SNPs) showed that 32 Gene Ontology terms and two Kyoto Encyclopedia of Genes and Genomes pathways, including regulation of transcription, motor activity, the mitogen-activated protein kinase signaling pathway, and tight junction, were significantly enriched (p < 0.05) for BW-associated genes. These pathways are involved in cell growth and development, related to BW gain. The identified SNPs are potential biomarkers in KNC breeding.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

scholarly journals Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

2020 ◽  
Author(s):  
Rhonda C. Meyer ◽  
Kathleen Weigelt-Fischer ◽  
Dominic Knoch ◽  
Marc Heuermann ◽  
Yusheng Zhao ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

scholarly journals Genome-wide association study of delay discounting in 23,217 adult research participants of European ancestry

2017 ◽  
Author(s):  
Sandra Sanchez-Roige ◽  
Pierre Fontanillas ◽  
Sarah L. Elson ◽  
Anita Pandit ◽  
Ellen M. Schmidt ◽  
...  
Keyword(s):  
Body Weight ◽  
Association Study ◽  
Delay Discounting ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
European Ancestry ◽  
Research Participants ◽  
Hyperactivity Disorder ◽  
Genome Wide ◽  
A Genome

ABSTRACTDelay discounting (DD), which is the tendency to discount the value of delayed versus current rewards, is elevated in a constellation of diseases and behavioral conditions. We performed a genome-wide association study of DD using 23,127 research participants of European ancestry. The most significantly associated SNP was rs6528024 (P = 2.40 × 10−8), which is located in an intron of the gene GPM6B. We also showed that 12% of the variance in DD was accounted for by genotype, and that the genetic signature of DD overlapped with attention-deficit/hyperactivity disorder, schizophrenia, major depression, smoking, personality, cognition, and body weight.

scholarly journals Genome-Wide Association Study of Weaning Traits in Lori-Bakhtiari Sheep

2020 ◽  
Vol 20 (3) ◽  
pp. 811-824
Author(s):  
Mohammad Almasi ◽  
Pouya Zamani ◽  
Seyed Ziaeddin Mirhoseini ◽  
Mohammad Hossein Moradi
Keyword(s):  
Body Weight ◽  
Association Study ◽  
Growth Performance ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Values ◽  
Genome Wide ◽  
A Genome ◽  
Meat Type

AbstractWeaning traits, including preweaning daily gain (PWDG) and weaning weight (WW) are important economic traits, especially for meat type mammals, with high impacts on growth performance and survival rate in higher ages. This study was conducted to perform a genome-wide association study (GWAS) on weaning traits in a meat type breed of sheep. Body weight records of 7557 Lori-Bakhtiari sheep with PWDG and WW records were used to estimate breeding values (EBVs) using an animal mixed model. A total of 132 animals were selected by two-tailed selection strategy, based on EBVs for body weight and then were genotyped using Illumina 50k Ovine SNP chip. After quality control, a total of 130 animals and 41323 SNPs were remained for further analyses. De-regressed estimates of breeding values were used as a pseudo-phenotype in GWAS analysis. Based on Bonferroni-adjusted p-values, five SNPs, located on chromosomes 2, 3, 4, 12 and 22 were significantly (p < 0.05) associated with weaning traits and accounted for 5.06% and 0.37% of total genetic variations of PWDG and WW, respectively. Two SNPs on chromosomes 2 and 3 were located near to previously reported QTLs for weaning traits. Three genes, including ANGPTL7, mTOR and WDR11, were found within 50 kbp distances from the significant SNPs and thus could be considered as candidate genes for weaning traits. The detected QTLs and candidate genes could be studied for construction of breeding programs for genetic improvement of growth performance in meat type sheep.

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