Evolution of phenotypic variance in response to a novel hot environment

This Research Communication describes the association between genetic variation within the prolactin (PRL) gene and the milk production traits of Italian Mediterranean river buffalo (Bufala mediterranea Italiana). High resolution melting (HRM) techniques were developed for genotyping 465 buffaloes. The association of genetic polymorphism with milk production traits was performed and subsequently the effects of parity and calving season were evaluated. Single nucleotide polymorphisms (SNPs) were identified at exons 2 and 5 and at introns 1 and 2. All the SNPs were in Hardy–Weinberg equilibrium, and statistical analysis showed that the polymorphism of intron1 was significantly (P < 0·05) associated with milk yield, milk protein content and peak milk yield. The average contribution of the intron1 genotype (r2intron1) to total phenotypic variance in milk production traits was 0·09, and the TT genotype showed lower values than CC and CT genotypes. A nonsynonymous SNP was identified in exon 2, which resulted in an amino acid change from arginine to cysteine. Moreover, the polymorphism of exon 2 was associated significantly with milk fat content (P < 0·05), and the buffaloes with TT genotype showed higher total fat content than the buffaloes with CT genotype. These findings provide evidence that polymorphisms of the buffalo PRL gene are associated with milk production traits and PRL can be used as a candidate gene for marker-assisted selection in Italian Mediterranean river buffalo breeding.

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Phenotypic and genetic variation of ultraviolet–visible-infrared spectral wavelengths of bovine meat

Scientific Reports ◽

10.1038/s41598-021-93457-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Giovanni Bittante ◽

Simone Savoia ◽

Alessio Cecchinato ◽

Sara Pegolo ◽

Andrea Albera

Keyword(s):

Meat Quality ◽

Genetic Improvement ◽

Near Infrared ◽

Infrared Region ◽

Phenotypic Variance ◽

Quality Traits ◽

Meat Quality Traits ◽

Infrared Spectral ◽

Portable Spectrometers ◽

Absorbance Spectra

AbstractSpectroscopic predictions can be used for the genetic improvement of meat quality traits in cattle. No information is however available on the genetics of meat absorbance spectra. This research investigated the phenotypic variation and the heritability of meat absorbance spectra at individual wavelengths in the ultraviolet–visible and near-infrared region (UV–Vis-NIR) obtained with portable spectrometers. Five spectra per instrument were taken on the ribeye surface of 1185 Piemontese young bulls from 93 farms (13,182 Herd-Book pedigree relatives). Linear animal model analyses of 1481 single-wavelengths from UV–Vis-NIRS and 125 from Micro-NIRS were carried out separately. In the overlapping regions, the proportions of phenotypic variance explained by batch/date of slaughter (14 ± 6% and 17 ± 7%,), rearing farm (6 ± 2% and 5 ± 3%), and the residual variances (72 ± 10% and 72 ± 5%) were similar for the UV–Vis-NIRS and Micro-NIRS, but additive genetics (7 ± 2% and 4 ± 2%) and heritability (8.3 ± 2.3% vs 5.1 ± 0.6%) were greater with the Micro-NIRS. Heritability was much greater for the visible fraction (25.2 ± 11.4%), especially the violet, blue and green colors, than for the NIR fraction (5.0 ± 8.0%). These results allow a better understanding of the possibility of using the absorbance of visible and infrared wavelengths correlated with meat quality traits for the genetic improvement in beef cattle.

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Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽

10.1093/genetics/156.1.457 ◽

2000 ◽

Vol 156 (1) ◽

pp. 457-467 ◽

Cited By ~ 1

Author(s):

Z W Luo ◽

S H Tao ◽

Z-B Zeng

Keyword(s):

Linkage Disequilibrium ◽

Allele Frequency ◽

Random Mating ◽

Natural Populations ◽

Polymorphic Marker ◽

Marker Locus ◽

Model Parameters ◽

Phenotypic Variance ◽

Wide Range ◽

Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

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Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

Scientific Reports ◽

10.1038/s41598-020-80473-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jonathan Brassac ◽

Quddoos H. Muqaddasi ◽

Jörg Plieske ◽

Martin W. Ganal ◽

Marion S. Röder

Keyword(s):

Flowering Time ◽

Aspartic Acid ◽

Synonymous Substitution ◽

Minor Effect ◽

Phenotypic Variance ◽

Spikelet Number ◽

Wheat Varieties ◽

Trait Locus ◽

A Minor ◽

Spikelet Number Per Spike

AbstractTotal spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

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Genome-Wide Association and Prediction of Male and Female Floral Hybrid Potential Traits in Elite Spring Bread Wheat Genotypes

Plants ◽

10.3390/plants10050895 ◽

2021 ◽

Vol 10 (5) ◽

pp. 895

Author(s):

Samira El Hanafi ◽

Souad Cherkaoui ◽

Zakaria Kehel ◽

Ayed Al-Abdallat ◽

Wuletaw Tadesse

Keyword(s):

Genomic Selection ◽

Bread Wheat ◽

Genome Wide Association ◽

Hybrid Breeding ◽

Floral Traits ◽

Phenotypic Variance ◽

Spring Bread Wheat ◽

Genome Wide ◽

Anther Length ◽

Anther Extrusion

Hybrid wheat breeding is one of the most promising technologies for further sustainable yield increases. However, the cleistogamous nature of wheat displays a major bottleneck for a successful hybrid breeding program. Thus, an optimized breeding strategy by developing appropriate parental lines with favorable floral trait combinations is the best way to enhance the outcrossing ability. This study, therefore, aimed to dissect the genetic basis of various floral traits using genome-wide association study (GWAS) and to assess the potential of genome-wide prediction (GP) for anther extrusion (AE), visual anther extrusion (VAE), pollen mass (PM), pollen shedding (PSH), pollen viability (PV), anther length (AL), openness of the flower (OPF), duration of floret opening (DFO) and stigma length. To this end, we employed 196 ICARDA spring bread wheat lines evaluated for three years and genotyped with 10,477 polymorphic SNP. In total, 70 significant markers were identified associated to the various assessed traits at FDR ≤ 0.05 contributing a minor to large proportion of the phenotypic variance (8–26.9%), affecting the traits either positively or negatively. GWAS revealed multi-marker-based associations among AE, VAE, PM, OPF and DFO, most likely linked markers, suggesting a potential genomic region controlling the genetic association of these complex traits. Of these markers, Kukri_rep_c103359_233 and wsnp_Ex_rep_c107911_91350930 deserve particular attention. The consistently significant markers with large effect could be useful for marker-assisted selection. Genomic selection revealed medium to high prediction accuracy ranging between 52% and 92% for the assessed traits with the least and maximum value observed for stigma length and visual anther extrusion, respectively. This indicates the feasibility to implement genomic selection to predict the performance of hybrid floral traits with high reliability.

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The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults

Metabolites ◽

10.3390/metabo11010006 ◽

2020 ◽

Vol 11 (1) ◽

pp. 6

Author(s):

Eun Pyo Hong ◽

Seong Gu Heo ◽

Ji Wan Park

Keyword(s):

Type 2 Diabetes ◽

Cardiovascular Disease ◽

Risk Prediction ◽

Linear Mixed Model ◽

Threshold Model ◽

Snp Markers ◽

Polygenic Risk Score ◽

Phenotypic Variance ◽

Prediction Approach

Personalized risk prediction for diabetic cardiovascular disease (DCVD) is at the core of precision medicine in type 2 diabetes (T2D). We first identified three marker sets consisting of 15, 47, and 231 tagging single nucleotide polymorphisms (tSNPs) associated with DCVD using a linear mixed model in 2378 T2D patients obtained from four population-based Korean cohorts. Using the genetic variants with even modest effects on phenotypic variance, we observed improved risk stratification accuracy beyond traditional risk factors (AUC, 0.63 to 0.97). With a cutoff point of 0.21, the discrete genetic liability threshold model consisting of 231 SNPs (GLT231) correctly classified 87.7% of 2378 T2D patients as high or low risk of DCVD. For the same set of SNP markers, the GLT and polygenic risk score (PRS) models showed similar predictive performance, and we observed consistency between the GLT and PRS models in that the model based on a larger number of SNP markers showed much-improved predictability. In silico gene expression analysis, additional information was provided on the functional role of the genes identified in this study. In particular, HDAC4, CDKN2B, CELSR2, and MRAS appear to be major hubs in the functional gene network for DCVD. The proposed risk prediction approach based on the liability threshold model may help identify T2D patients at high CVD risk in East Asian populations with further external validations.

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Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽

10.3390/agronomy11010118 ◽

2021 ◽

Vol 11 (1) ◽

pp. 118

Author(s):

Ljiljana Brbaklić ◽

Dragana Trkulja ◽

Sanja Mikić ◽

Milan Mirosavljević ◽

Vojislava Momčilović ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Hordeum Vulgare ◽

Crop Improvement ◽

Genetic Erosion ◽

Breeding Period ◽

Phenotypic Variance ◽

Hordeum Vulgare L ◽

Phenotypic Data ◽

Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

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Genetically Raised Circulating Bilirubin Levels and Risk of Ten Cancers: A Mendelian Randomization Study

Cells ◽

10.3390/cells10020394 ◽

2021 ◽

Vol 10 (2) ◽

pp. 394

Author(s):

Nazlisadat Seyed Seyed Khoei ◽

Robert Carreras-Torres ◽

Neil Murphy ◽

Marc J. Gunter ◽

Paul Brennan ◽

...

Keyword(s):

Breast Cancer ◽

Lung Cancer ◽

Squamous Cell ◽

Cell Lung Cancer ◽

Hodgkin’S Lymphoma ◽

Mendelian Randomization ◽

Hodgkin's Lymphoma ◽

Squamous Cell Lung Cancer ◽

Phenotypic Variance ◽

A Genome

Bilirubin, an endogenous antioxidant, may play a protective role in cancer development. We applied two-sample Mendelian randomization to investigate whether genetically raised bilirubin levels are causally associated with the risk of ten cancers (pancreas, kidney, endometrium, ovary, breast, prostate, lung, Hodgkin’s lymphoma, melanoma, and neuroblastoma). The number of cases and their matched controls of European descent ranged from 122,977 and 105,974 for breast cancer to 1200 and 6417 for Hodgkin’s lymphoma, respectively. A total of 115 single-nucleotide polymorphisms (SNPs) associated (p < 5 × 10−8) with circulating total bilirubin, extracted from a genome-wide association study in the UK Biobank, were used as instrumental variables. One SNP (rs6431625) in the promoter region of the uridine-diphosphoglucuronate glucuronosyltransferase1A1 (UGT1A1) gene explained 16.9% and the remaining 114 SNPs (non-UGT1A1 SNPs) explained 3.1% of phenotypic variance in circulating bilirubin levels. A one-standarddeviation increment in circulating bilirubin (≈ 4.4 µmol/L), predicted by non-UGT1A1 SNPs, was inversely associated with risk of squamous cell lung cancer and Hodgkin’s lymphoma (odds ratio (OR) 0.85, 95% confidence interval (CI) 0.73–0.99, P 0.04 and OR 0.64, 95% CI 0.42–0.99, p 0.04, respectively), which was confirmed after removing potential pleiotropic SNPs. In contrast, a positive association was observed with the risk of breast cancer after removing potential pleiotropic SNPs (OR 1.12, 95% CI 1.04–1.20, p 0.002). There was little evidence for robust associations with the other seven cancers investigated. Genetically raised bilirubin levels were inversely associated with risk of squamous cell lung cancer as well as Hodgkin’s lymphoma and positively associated with risk of breast cancer. Further studies are required to investigate the utility of bilirubin as a low-cost clinical marker to improve risk prediction for certain cancers.

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Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽

10.1093/genetics/165.3.1307 ◽

2003 ◽

Vol 165 (3) ◽

pp. 1307-1315

Author(s):

Daibin Zhong ◽

Aditi Pai ◽

Guiyun Yan

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Life Cycles ◽

Red Flour Beetle ◽

Phenotypic Variance ◽

Flour Beetle ◽

Trait Loci ◽

Host Ecology ◽

Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

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