scholarly journals Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice

2020 ◽  
Vol 10 (7) ◽  
pp. 2435-2443 ◽  
Author(s):  
Nicholas G. Karavolias ◽  
Anthony J. Greenberg ◽  
Luz S. Barrero ◽  
Lyza G. Maron ◽  
Yuxin Shi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Root Growth ◽  
Low Frequency ◽  
Phenotypic Variance ◽  
Single Nucleotide ◽  
Additional Advantage ◽  
Fundamental Interest ◽  
Additive Genetic Variation ◽  
Snp Map ◽  
Dense Single Nucleotide Polymorphism

Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additional advantage because phenotypes of genetically identical individuals can be measured in replicate. This makes it possible to estimate marker effects separately from the contribution of the genetic background not captured by genotyped loci. We focused on root growth in domesticated rice, Oryza sativa, under normal and aluminum (Al) stress conditions, a trait under recent selection because it correlates with survival under drought. A dense single nucleotide polymorphism (SNP) map is available for all accessions studied. Taking advantage of this map and a set of Bayesian models, we assessed additive marker effects. While total genetic variation accounted for a large proportion of phenotypic variance, marker effects contributed little information, particularly in the Al-tolerant tropical japonica population of rice. We were unable to identify any loci associated with root growth in this population. Models estimating the aggregate effects of all measured genotypes likewise produced low estimates of marker heritability and were unable to predict total genetic values accurately. Our results support the long-standing conjecture that additive genetic variation is depleted in traits under selection. We further provide evidence that this depletion is due to the prevalence of low-frequency alleles that underlie the trait.

scholarly journals Low additive genetic variation in a trait under selection in domesticated rice

2019 ◽  
Author(s):  
Nicholas G. Karavolias ◽  
Anthony J. Greenberg ◽  
Luz S. Barrero ◽  
Lyza G. Maron ◽  
Yuxin Shi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Root Growth ◽  
Low Frequency ◽  
Phenotypic Variance ◽  
Single Nucleotide ◽  
Additional Advantage ◽  
Fundamental Interest ◽  
Additive Genetic Variation ◽  
Snp Map ◽  
Dense Single Nucleotide Polymorphism

AbstractQuantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additional advantage because phenotypes of genetically identical individuals can be measured in replicate. This makes it possible to estimate marker effects separately from the contribution of the genetic background. We focused on root growth in domesticated rice,Oryza sativa, under normal and aluminum (Al) stress conditions, a trait under recent selection because it correlates with survival under drought. A dense single nucleotide polymorphism (SNP) map is available for all accessions studied. Taking advantage of this map and a set of Bayesian models, we assessed additive marker effects. While total genetic variation accounted for a large proportion of phenotypic variance, marker effects contributed little information, particularly in the Al-toleranttropical japonicapopulation of rice. We were unable to identify any loci associated with root growth in this population. Models estimating the aggregate effects of all measured genotypes like-wise produced low estimates of marker heritability and were unable to predict total genetic values accurately. Our results support the long-standing conjecture that additive genetic variation is depleted in traits under selection. We further provide evidence that this depletion is due to the prevalence of low-frequency alleles that underlie the trait.

scholarly journals Association mapping and genetic dissection of drought-induced canopy temperature differences in rice

2019 ◽  
Vol 71 (4) ◽  
pp. 1614-1627 ◽  
Author(s):  
Giovanni Melandri ◽  
Ankush Prashar ◽  
Susan R McCouch ◽  
Gerard van der Linden ◽  
Hamlyn G Jones ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Canopy Temperature ◽  
Leaf Temperature ◽  
Genetic Dissection ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Snp Map ◽  
Trait Locus

Abstract Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.

Genetic variation for rate of establishment in caucasian clover

1998 ◽  
pp. 213-217
Author(s):  
K.H. Widdup ◽  
T.L. Knight ◽  
C.J. Waters
Keyword(s):  
Genetic Variation ◽  
Root Growth ◽  
Seedling Growth ◽  
White Clover ◽  
Seedling Emergence ◽  
Red Clover ◽  
Dry Weight ◽  
Cool Season ◽  
Trifolium Ambiguum ◽  
Root Dry Weight

Slow establishment of caucasian clover (Trifolium ambiguum L.) is hindering the use of this legume in pasture mixtures. Improved genetic material is one strategy of correcting the problem. Newly harvested seed of hexaploid caucasian clover germplasm covering a range of origins, together with white and red clover and lucerne, were sown in 1 m rows in a Wakanui soil at Lincoln in November 1995. After 21 days, the caucasian clover material as a group had similar numbers of emerged seedlings as white clover and lucerne, but was inferior to red clover. There was wide variation among caucasian clover lines (48-70% seedling emergence), with the cool-season selection from cv. Monaro ranked the highest. Recurrent selection at low temperatures could be used to select material with improved rates of seedling emergence. Red clover and lucerne seedlings produced significantly greater shoot and root dry weight than caucasian and white clover seedlings. Initially, caucasian clover seedlings partitioned 1:1 shoot to root dry weight compared with 3:1 for white clover. After 2 months, caucasian clover seedlings had similar shoot growth but 3 times the root growth of white clover. Between 2 and 5 months, caucasian clover partitioned more to root and rhizome growth, resulting in a 0.3:1 shoot:root ratio compared with 2:1 for white clover. Both clover species had similar total dry weight after 5 months. Unhindered root/ rhizome devel-opment is very important to hasten the establishment phase of caucasian clover. The caucasian clover lines KZ3 and cool-season, both selections from Monaro, developed seedlings with greater shoot and root growth than cv. Monaro. KZ3 continued to produce greater root growth after 5 months, indicating the genetic potential for improvement in seedling growth rate. Different pasture estab-lishment techniques are proposed that take account of the seedling growth characteristics of caucasian clover. Keywords: establishment, genetic variation, growth, seedling emergence, Trifolium ambiguum

scholarly journals Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 363
Author(s):  
Sulochana K. Wasala ◽  
Dana K. Howe ◽  
Louise-Marie Dandurand ◽  
Inga A. Zasada ◽  
Dee R. Denver
Keyword(s):  
Genetic Variation ◽  
Potato Production ◽  
Globodera Pallida ◽  
Fixation Index ◽  
Parasitic Nematodes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Field Samples ◽  
Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

scholarly journals Pleiotropy and multilocus polymorphisms.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 223-227
Author(s):  
A Gimelfarb
Keyword(s):  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Stabilizing Selection ◽  
Additive Genetic Variation ◽  
Very High

Abstract It is demonstrated that systems of two pleiotropically related characters controlled by additive diallelic loci can maintain under Gaussian stabilizing selection a stable polymorphism in more than two loci. It is also shown that such systems may have multiple stable polymorphic equilibria. Stabilizing selection generates negative linkage disequilibrium, as a result of which the equilibrium phenotypic variances are quite low, even though the level of allelic polymorphisms can be very high. Consequently, large amounts of additive genetic variation can be hidden in populations at equilibrium under stabilizing selection on pleiotropically related characters.

scholarly journals A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Evangelina López de Maturana ◽  
◽  
Juan Antonio Rodríguez ◽  
Lola Alonso ◽  
Oscar Lao ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Functional Analysis ◽  
Genetic Susceptibility ◽  
In Silico ◽  
Complex Disease ◽  
Meta Analysis ◽  
Low Frequency ◽  
Acinar Cells ◽  
Pancreatic Acinar Cells ◽  
Phenotypic Variance

Abstract Background Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% of the phenotypic variance. Methods We complemented a new conventional PC GWAS (1D) with genome spatial autocorrelation analysis (2D) permitting to prioritize low frequency variants not detected by GWAS. These were further expanded via Hi-C map (3D) interactions to gain additional insight into the inherited basis of PC. In silico functional analysis of public genomic information allowed prioritization of potentially relevant candidate variants. Results We identified several new variants located in genes for which there is experimental evidence of their implication in the biology and function of pancreatic acinar cells. Among them is a novel independent variant in NR5A2 (rs3790840) with a meta-analysis p value = 5.91E−06 in 1D approach and a Local Moran’s Index (LMI) = 7.76 in 2D approach. We also identified a multi-hit region in CASC8—a lncRNA associated with pancreatic carcinogenesis—with a lowest p value = 6.91E−05. Importantly, two new PC loci were identified both by 2D and 3D approaches: SIAH3 (LMI = 18.24), CTRB2/BCAR1 (LMI = 6.03), in addition to a chromatin interacting region in XBP1—a major regulator of the ER stress and unfolded protein responses in acinar cells—identified by 3D; all of them with a strong in silico functional support. Conclusions This multi-step strategy, combined with an in-depth in silico functional analysis, offers a comprehensive approach to advance the study of PC genetic susceptibility and could be applied to other diseases.

scholarly journals Biomarkers for Lifetime Caries-Free Status

2020 ◽  
Vol 11 (1) ◽  
pp. 23
Author(s):  
Ariana M. Kelly ◽  
Mariana Bezamat ◽  
Adriana Modesto ◽  
Alexandre R. Vieira
Keyword(s):  
Genetic Variation ◽  
Dental Caries ◽  
Protective Effect ◽  
Permanent Teeth ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Interacting Protein ◽  
Mandibular Molars ◽  
Matrix Metallopeptidase ◽  
Free Status

The purpose of this study was to address the hypothesis that extreme outcomes of dental caries, such as edentulism or prematurely losing permanent teeth are associated with genetic variation in enamel-formation genes. After scanning 6206 individuals, samples of 330 were selected for this study. Tested phenotypes included patients who were edentulous by age 30, patients with missing first molars by age 30, patients with missing second molars by age 30, and caries-free patients. Fourteen single nucleotide polymorphisms were genotyped by TaqMan chemistry. The analyses of each phenotype were performed using the software PLINK with an alpha of 0.05. Nominal associations were found between rs12640848 in enamelin (p = 0.05), rs1784418 in matrix metallopeptidase 20 (p = 0.02), and rs5997096 in the tuftelin interacting protein 11 and being caries-free at the age of 60. When combining patients that were missing both first mandibular molars and missing both second mandibular molars, no associations were found. Matrix metallopeptidase 20, and tuftelin interacting protein 11 also showed trends for association with being caries-free. Genetic variation in TFIP11, MMP20, and ENAM may have a protective effect increasing the chances of individuals preserving their teeth caries-free over a lifetime.

scholarly journals Genome-wide single nucleotide polymorphism heritability of nicotine dependence as a multidimensional phenotype

2016 ◽  
Vol 46 (10) ◽  
pp. 2059-2069 ◽  
Author(s):  
L. C. Bidwell ◽  
R. H. C. Palmer ◽  
L. Brick ◽  
J. E. McGeary ◽  
V. S. Knopik
Keyword(s):  
Nicotine Dependence ◽  
Twin Studies ◽  
Factor Models ◽  
Genetic Effects ◽  
European Ancestry ◽  
Relationship Matrix ◽  
Phenotypic Variance ◽  
Single Nucleotide ◽  
Common Genetic Variants ◽  
Dsm Iv

BackgroundHeritability estimates from twin studies of the multi-faceted phenotype of nicotine dependence (ND) range from moderate to high (31–60%), but vary substantially based on the specific ND-related construct examined. The current study estimated the aggregate role of common genetic variants on key ND constructs.MethodGenomic-relationship-matrix restricted maximum likelihood (GREML) was used to decompose phenotypic variance across multiple ND indices using 796 125 polymorphisms from 2346 unrelated ‘lifetime ever smokers’ of European ancestry. Measures included DSM-IV ND and Fagerström Test for Nicotine Dependence (FTND) summary measures and constituent constructs (e.g. withdrawal severity, tolerance, heaviness of smoking and time spent smoking). Exploratory and confirmatory factor models were used to describe the covariance structure across ND measures; resulting factor(s) were the subject(s) of GREML analyses.ResultsFactor models indicated highly correlated DSM-IV and FTND factors for ND (0.545, 95% confidence interval 0.50–0.60) that could be represented as a higher-order factor (NIC DEP). Additive genetic influence on NIC DEP was 33% (s.e. = 0.14, p = 0.009). Post-hoc analyses indicated moderate genetic effects on the DSM-IV (34%, s.e. = 0.14, p = 0.008) and FTND (26%, s.e. = 0.14, p = 0.032) factors, both of which were influenced by the same genetic effects (rG-SNP = 1.00, s.e. = 0.09, p < 0.00001).ConclusionsOverall, common single nucleotide polymorphisms accounted for a large proportion of the genetic influences on ND-related phenotypes that have been observed in twin studies. Genetic contributions across distinct ND scales were largely influenced by shared genetic factors.

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