scholarly journals A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

2014 ◽  
Author(s):  
Jennifer Lachowiec ◽  
Xia Shen ◽  
Christine Queitsch ◽  
Örjan Carlborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Candidate Genes ◽  
Root Length ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Broad Sense ◽  
Genome Wide Association ◽  
Broad Sense Heritability ◽  
Narrow Sense ◽  
Genome Wide

Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the narrow-sense heritability for this trait was statistically zero. This low additive genetic variance likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, the broad-sense heritability for root length was significantly larger, and we therefore also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. This analysis revealed four interacting pairs involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. Explorations of the genotype-phenotype maps for these pairs revealed that the detected epistasis cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. In summary, statistical epistatic analyses were found to be indispensable for confirming known, and identifying several new, functional candidate genes for root length using a population of wild-collected A. thaliana accessions. We also illustrated how epistatic cancellation of the additive genetic variance resulted in an insignificant narrow-sense, but significant broad-sense heritability that could be dissected into the contributions of several individual loci using a combination of careful statistical epistatic analyses and functional genetic experiments.

PSXI-4 Genome-Wide association study for muscle visual score in Nellore cattle raised in pasture-based systems

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 246-246
Author(s):  
Victor B Pedrosa ◽  
Pamela Machado ◽  
Rafaela Martins ◽  
Marcio Silva ◽  
Luis Fernando Pinto ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Additive Genetic Variance ◽  
Genome Wide Association ◽  
Zebu Cattle ◽  
Visual Score ◽  
Genome Wide ◽  
A Genome ◽  
Nellore Cattle

Abstract Visual scoring traits have been proposed as an alternative to evaluate body composition of Zebu cattle near the slaughter season when phenotyping technologies are not available. Considering the increased demand for high-quality animal protein in developing countries, there is a need to genetically improve body muscle (MUSC) in Zebu cattle (Bos taurus indicus), especially in animals raised in pasture-based systems. Therefore, our main objectives were to estimate genetic parameters, perform a genome-wide association study based on the single-step GBLUP approach (ssGWAS), and identify candidate genes and metabolic pathways related to MUSC in Nellore cattle. A total of 20,808 Nellore animals born between 2009 and 2018 were visually score at 18 months of age and 2,775 of these animals were also genotyped using the GGP-Indicus 35K SNP panel (33,247 SNPs after quality control). Heritability was estimated based on the REML approach and the model included the effects of age at measurement as covariable and the contemporary group (farm, birth season, management group and sex). The ssGWAS was performed using the BLUPF90 family programs. The identification of candidate genes was performed through the Ensembl database incorporated in the BioMart tool. MUSC is heritable (0.38) and can be improved through selection. Nineteen genomic regions (explaining 38.12% of the total additive genetic variance) located on BTA1, BTA7, BTA9, BTA16, and BTA21 and harboring 19 candidate genes were identified. The main genes identified were SEMA6A, TIAM2, UNC5A, and UIMC1, which are related to the metabolism of energy, growth, homeostasis and axonogenesis, and therefore, muscle development. These findings contribute to a better understanding of the molecular mechanisms over the gene expression of muscle visual score in Nellore cattle, and the polymorphisms located in these genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for body and carcass traits.

Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses

2021 ◽  
Author(s):  
Quanshun Mei ◽  
Chuanke Fu ◽  
Goutam Sahana ◽  
Yilong Chen ◽  
Lilin Yin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Sperm Concentration ◽  
Genome Wide Association ◽  
Pig Production ◽  
Network Analyses ◽  
Genetic Region ◽  
Genome Wide ◽  
A Genome

Abstract Semen traits are crucial in commercial pig production since semen from boars is widely used in artificial insemination for both purebred and crossbred pig production. Revealing the genetic architecture of semen traits potentially promotes the efficiencies of improving semen traits through artificial selection. This study is aimed to identify candidate genes related to the semen traits in Duroc boars. First, we identified the genes that were significantly associated with three semen traits, including sperm motility (MO), sperm concentration (CON), and semen volume (VOL) in a Duroc boar population through a genome wide association study (GWAS). Second, we performed a weighted gene co-expression network analysis (WGCNA). A total of 2, 3, and 20 SNPs were found to be significantly associated with MO, CON, and VOL, respectively. Based on the haplotype block analysis, we identified one genetic region associated with MO, which explained 6.15% of the genetic trait variance. ENSSSCG00000018823 located within this region was considered as the candidate gene for regulating MO. Another genetic region explaining 1.95% of CON genetic variance was identified, and in this region B9D2, PAFAH1B3, TMEM145, and CIC were detected as the CON-related candidate genes. Two genetic regions that accounted for 2.23% and 2.48% of VOL genetic variance were identified, and in these two regions, WWC2, CDKN2AIP, ING2, TRAPPC11, STOX2, and PELO were identified as VOL-related candidate genes. WGCNA analysis showed that among these candidate genes, B9D2, TMEM145, WWC2, CDKN2AIP, TRAPPC11, and PELO were located within the most significant module eigengenes, confirming these candidate genes’ role in regulating semen traits in Duroc boars. The identification of these candidate genes can help to better understand the genetic architecture of semen traits in boars. Our findings can be applied for semen traits improvement in Duroc boars.

scholarly journals Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1386
Author(s):  
Ana Paula Sbardella ◽  
Rafael Nakamura Watanabe ◽  
Rebeka Magalhães da Costa ◽  
Priscila Arrigucci Bernardes ◽  
Larissa Graciano Braga ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variability ◽  
Additive Genetic Variance ◽  
Reproductive Traits ◽  
Genome Wide Association ◽  
Gestation Length ◽  
Data Set ◽  
Breeding Programs ◽  
Genome Wide ◽  
Nelore Cattle

The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.

scholarly journals Single-step genome-wide association study for resistance toPiscirickettsia salmonisin rainbow trout (Oncorhynchus mykiss)

2019 ◽  
Author(s):  
Rodrigo Marín-Nahuelpi ◽  
Agustín Barría ◽  
Pablo Cáceres ◽  
María E. López ◽  
Liane N. Bassini ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Candidate Genes ◽  
Genetic Improvement ◽  
Genetic Variance ◽  
Snp Array ◽  
Single Step ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Genomic Regions

ABSTRACTOne of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteriaPiscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait. The objectives of this study were to i) identify the genomic regions associated with resistance toP. salmonis; and ii) identify candidate genes associated with the trait. We experimentally challenged 2,130 rainbow trout withP. salmonisand genotyped them with a 57 K SNP array. Resistance toP. salmoniswas defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located onOmy27was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited byP. salmonisduring infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance toP. salmonisthrough artificial selection in the current rainbow trout population. Furthermore, our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance toP. salmonisinO. mykiss.

scholarly journals Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

2018 ◽  
Author(s):  
Mohamed Salem ◽  
Rafet Al-Tobasei ◽  
Ali Ali ◽  
Daniela Lourenco ◽  
Guangtu Gao ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Muscle Development ◽  
Genetic Variance ◽  
Cold Water ◽  
Additive Genetic Variance ◽  
Genome Wide Association ◽  
Production Traits ◽  
Significant Qtls ◽  
Snp Chip ◽  
Genome Wide

AbstractDetection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ≥ 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

scholarly journals Genetic variance and heritability estimation of hybridized pepper plants (Capsicum annuum L.) F2 progeny for begomovirus resistance in growth stage

2022 ◽  
Vol 951 (1) ◽  
pp. 012103
Author(s):  
E Kesumawati ◽  
Sabaruddin ◽  
E Hayati ◽  
N Hadisah ◽  
R Hayati ◽  
...  
Keyword(s):  
Growth Stage ◽  
Genetic Variance ◽  
Broad Sense ◽  
Phenotypic Variance ◽  
Broad Sense Heritability ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Training Centre ◽  
Tertiary Branch ◽  
Heritability Estimation

Abstract Pepper is widely cultivated as a condiment and cash crop in Indonesia. However, Pepper yellow leaf curl disease (PepYLCD) caused by begomovirus is currently seriously affect the domestic pepper production. Breeding for begomovirus resistance material by crossing is currently necessary to overcome the constraint. The present study is aimed to determine the resistance of pepper (C. annuum) plants F2 progenies to begomovirus infection in the growth stage. Two local C. annuum accessions, BaPep-5 as a resistance donor for pepy-1 begomovirus resistance gene (locally called Perintis) and BaPep-4 as a susceptible parent (locally called Kencana) were crossed to generate F2 progenies. The research was conducted in Agricultural Extension Training Centre (BLPP) Saree and Horticulture Laboratory of Syiah Kuala University from February to July 2020. 500 F2 progenies were transplanted to the field along with 15 plants of each parent as control. The result suggested that plant height and crown width had the highest broad sense heritability value, whereas the dichotomous height, stem diameter, secondary branch, and tertiary branch had the lowest broad sense heritability value. Coefficient of genetic variance and coefficient of phenotypic variance from overall characteristics were relatively low which suggest the narrow sense to slightly narrow sense heritability.

scholarly journals Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 191
Author(s):  
Bandana Ghimire ◽  
Thangasamy Saminathan ◽  
Abiodun Bodunrin ◽  
Venkata Lakshmi Abburi ◽  
Arjun Ojha Kshetry ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Association Study ◽  
Root Length ◽  
Natural Variation ◽  
Genome Wide Association Study ◽  
Mine Drainage ◽  
The United States ◽  
Genome Wide Association ◽  
Acid Mine ◽  
Genome Wide

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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