Phenotypic Variance Research Articles

Prevalence and correlates of frailty among older people with and without HIV in rural Uganda.

The relationship between HIV and frailty, a predictor of poor outcomes in the face of stressors, remains unknown in older people in sub-Saharan Africa. We analysed data from the Quality of Life and Ageing with HIV in Rural Uganda cohort study to estimate the prevalence and correlates of frailty among older people with HIV (PWH) on long-term antiretroviral therapy and among age and sex-similar HIV-uninfected comparators. Frailty was defined as a self-report of 3 or 4 (and pre-frailty as 1 or 2) of the following phenotypic variables: weight loss, exhaustion, low activity, and slowness. We estimated the prevalence of frailty and pre-frailty and fitted logistic regression models to estimate the association between HIV and frailty, adjusting for sociodemographic factors, depression, and other comorbidities. We enrolled 599 participants (49% women) with a mean age of 58 years. PWH had a similar prevalence of frailty (8.1% vs. 10.9%, p=0.24) but a lower prevalence of pre-frailty (54.2% vs. 63.2%, p=0.03) compared with their HIV-uninfected comparators. In multivariable regression models, people with depression (AOR 7.52 [95% CI: 3.67-15.40], p<0.001) and those with ≥1 comorbidities (AOR 3.15 [95% CI: 1.71-3.82], p<0.001) were more likely to be frail. HIV serostatus was not significantly associated with frailty (AOR 0.71 [95% CI: 0.37-1.34], p=0.29). Older PWH had a similar prevalence of frailty as those without HIV. These findings call for additional study of the factors that contribute to the robustness of older PWH in sub-Saharan Africa.

Experimental unbalance: reflections on genetic parameters and corn selection gain

Genetic progress depends on the components of variance and genetic parameters. In this context, the objective of this work was to identify the maximum allowed percentage of experimental imbalance in the estimation of variance components, genetic parameters and selection gain in intervarietal corn hybrids. The experimental design used was randomized blocks, with 60 corn hybrids with three replications. Random subsets of data were created in order to express unbalance scenarios of the phenotypic matrix, we obtained 9 scenarios (0, 10, 20, 30, 40, 50, 60, 70 and 80% unbalance).Thus, the genetic variance of the paternal genitor, the genetic variance of the maternal genitor, additive variance, individual phenotypic variance, narrow-sense heritability of intervarietal additive effects for the paternal genitor were estimated, narrow-sense heritability of intervarietal additive effects for the maternal genitor, narrow-sense heritability, broad-sense heritability, genotypic variation coefficient between progenies and variation coefficient residual. Narrow sense heritability reveals high magnitude for the characters cob mass and hundred grain mass. Maternal effect is expressed through ear insertion height, ear grain mass, cob mass and diameter, number of rows, ear mass and length, and grain yield. The imbalance inflates the variance components and genetic parameters for the highlighted characters. It supports 10% imbalance in the data matrix without compromising the reliability of the estimates. Pronounceable selection gains are obtained for grain yield based on pressures of 1 and 5%. An unbalance of 10% is supported in the selection gain for cob mass, ear length and hundred grain mass.

Fine Mapping and Candidate Gene Analysis of Two Major Quantitative Trait Loci, qFW2.1 and qFW3.1, Controlling Fruit Weight in Pepper (Capsicum annuum).

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, "129-1" (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F2 generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F2 generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC2S2 and BC2S3 populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper.

Evaluation of Turfgrasses for Qualitative and Quantitative Traits in Varanasi Region of India

The present experiment was conducted at Horticulture Research Farm, Department of Horticulture, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi. This study was carried out to evaluate performance of eleven turfgrass genotypes for qualitative traits, quantitative traits and their genetic variability under same climatic condition. The experimental design was a Randomized Block Design (RBD) with three replications. Eleven genotypes consist of Bermuda grass, Centipede grass, Panama grass, Bargusto grass, Tiftdwarf 419 grass, Local grass, Palma grass, Bahia grass, Manila grass, Crow Foot grass and Tanu Variant grass. These were assessed for their suitability to be used as turfgrass under Varanasi region. All the grasses exhibited semi prostrate growth habit except local grass having upright growth habit. Panama and Local grass showed fine leaf texture whereas, Manila grass exhibited coarse texture. Dark green colour was observed in Local, Crow Foot and Panama grass whereas, Centipede grass showed light green colour. Local grass exhibited maximum canopy height, leaf length, leaf width, chlorophyll content, stolen internode diameter, culm length, shoot length and shoot diameter. The maximum genotypic (187.22) and phenotypic variance (197.80) was observed for parameters like fresh weight. Canopy height showed maximum phenotypic coefficient of variation (47.04) and genotypic coefficient of variation (46.16) over all the parameters. Genetic advance maximum (27.49) for parameter fresh weight and genetic advance as a percentage of mean was maximum also for fresh weight (93.30). The maximum heritability at broad sense was observed for the parameter dry weight (98.25).

Association mapping of important agronomic traits in Mucuna pruriens (L.) DC.

BackgroundThe tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model.ResultsThe results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon’s information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83.ConclusionFifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.

Bread wheat cultivar Popo harbors QTLs for seedling and adult plant resistance to leaf rust in South African and Argentine environments

Leaf rust, caused by the fungus Puccinia triticina Eriks (Pt), is a destructive disease affecting wheat (Triticum aestivum L.) production in many countries, and a serious threat to food security. As a result, several breeding programs have included leaf rust resistance as an important trait. The discovery and identification of new resistance genes that could aid in incorporating durable or long-lasting leaf rust resistance into wheat is fundamental in these breeding programs. The present study aimed to identify quantitative trait loci (QTLs) for leaf rust resistance in 127 recombinant inbred lines (RIL) developed from the cross between the resistant wheat cultivar Popo and the susceptible cultivar Kariega. The RIL population and parental lines were phenotyped for leaf rust infection type and severity at seedling and adult plant stage, respectively. The former in the greenhouse (in Argentina) and the latter in multiple field test environments comprising 3 locations in South Africa (in Tygerhoek in the Western Cape Province during the 2014, 2015, 2017 and 2018 cropping seasons; Clarens during 2014, 2016 and 2017 cropping seasons and in Bethlehem in the Free State Province during 2017 cropping season) and in 1 location in Argentina (during the 2017 and 2018 cropping seasons in Marcos Juárez, Córdoba Province). The population was genotyped using genotyping-by-sequencing. A total of 12,080 silicoDArT and 2,669 SNP markers were used for QTL analysis. In total, 25 putative QTLs for resistance to leaf rust at seedling and adult plant stages were identified, including 5 QTLs for seedling and 20 QTLs for adult plant resistance (APR). Interestingly, both Popo and Kariega contributed with alleles for resistance. Significant loci for reducing leaf rust infection at seedling stage were designated QLr.arc-1A, QLr.arc-2B, QLr.arc-5B, QLr.arc-6A and QLr.arc-6D. Three minor QTLs derived from Popo designated as QLr.arc-1B1, QLr.arc-2D and QLr.arc-3D were also detected from the field tests, explaining 5–10%, 10–16% and 5–7% of the phenotypic variance, respectively. The identified QTLs and their closely linked silicoDArT and SNP-based markers can be used for fine mapping and candidate gene discovery in wheat breeding programs targeting durable leaf rust resistance.

Brain transcriptomic signatures for mood disorders and suicide phenotypes: an anterior insula and subgenual ACC network postmortem study.

Mood disorders affect over ten percent of humans, but studies dissecting the brain anatomical and molecular neurobiological mechanisms underlying mood (dys)functions have not consistently identified the patterns of pathological changes in relevant brain regions. Recent studies have identified pathological changes in the anterior insula (Ant-Ins) and subgenual anterior cingulate (sgACC) brain network in mood disorders, in line with this network's role in regulating mood/affective feeling states. Here, we applied whole-tissue RNA-sequencing measures of differentially expressed genes (DEGs) in mood disorders versus (vs.) psychiatrically unaffected controls (controls) to identify postmortem molecular pathological markers for mood disorder phenotypes. Using data-driven factor analysis of the postmortem phenotypic variables to determine relevant sources of population variances, we identified DEGs associated with mood disorder-related diagnostic phenotypes by combining gene co-expression, differential gene expression, and pathway-enrichment analyses. We found downregulation/under expression of inflammatory, and protein synthesis-related genes associated with psychiatric morbidity (i.e., all co-occurring mental disorders and suicide outcomes/death by suicide) in Ant-Ins, in contrasts to upregulation of synaptic membrane and ion channel-related genes with increased psychiatric morbidity in sgACC. Our results identified a preponderance of downregulated metabolic, protein synthesis, inflammatory, and synaptic membrane DEGs associated with suicide outcomes in relation to a factor representing longevity in the Ant-Ins and sgACC (AIAC) network. Our study revealed a critical brain network molecular repertoire for mood disorder phenotypes, including suicide outcomes and longevity, and provides a framework for defining dosage-sensitive (i.e., downregulated vs. upregulated) molecular signatures for mood disorder phenotypic complexity and pathological outcomes.

Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries.

Subcortical brain structures are involved in developmental, psychiatric and neurological disorders. We performed GWAS meta-analyses of intracranial and nine subcortical brain volumes (brainstem, caudate nucleus, putamen, hippocampus, globus pallidus, thalamus, nucleus accumbens, amygdala and, for the first time, the ventral diencephalon) in 74,898 participants of European ancestry. We identified 254 independent loci associated with these brain volumes, explaining up to 35% of phenotypic variance. We observed gene expression in specific neural cell types across differentiation time points, including genes involved in intracellular signalling and brain ageing-related processes. Polygenic scores for brain volumes showed predictive ability when applied to individuals of diverse ancestries. We observed causal genetic effects of brain volumes with Parkinson's disease and ADHD. Findings implicate specific gene expression patterns in brain development and genetic variants in comorbid neuropsychiatric disorders, which could point to a brain substrate and region of action for risk genes implicated in brain diseases.

Modeling embryo survival: Genetic and environmental influences on eye-up rate in a north American Atlantic salmon selective breeding program

Selective breeding programs improve target traits but can also unintentionally change genetically correlated traits in the selected strain. The U.S. Department of Agriculture–Agricultural Research Service National Cold Water Marine Aquaculture Center (NCWMAC) in Franklin, Maine maintains a North American Atlantic salmon selective breeding program focused on improving commercially important traits (e.g., carcass weight). However, the program has experienced a significant decline in the percent of eyed embryos over its 14 years of operation, leading to concerns that reproductive performance was being unintentionally changed by selection for the target traits. The aims of this study were to 1) model eye up success as a potentially heritable trait utilizing the recorded pedigree and 2) assess the relationship between eye-up rate and environmental conditions experienced by the broodstock. Over 14 years of data encompassing 1537 full-sib families produced by 1537 dams and 885 sires was analyzed. Counts of eyed embryos and carcass weight were analyzed with a linear multi-trait trait model that included maternal genetic effects and a spawn year effect to determine the strength of genetic and environmental influences on the eyed embryo rate. To investigate the environmental influences in more detail, we assessed the correlation between water quality parameters in the broodstock rearing system observed over the same 14-year time period and the estimated spawn year effects. There was small heritability of the direct genetic effect (0.059 ± 0.009) and the maternal genetic effect (0.039 ± 0.013). Comparatively, the proportion of phenotypic variance explained by the maternal environmental effect was moderate (0.165 ± 0.012). The genetic correlations between carcass weight and eye up rate were very small and had a large amount of uncertainty. The correlation between the direct genetic effects on eye-up and carcass weight was −0.0528 ± 0.1469 while the correlation between the maternal genetic effect on eye-up and the direct genetic effect on carcass weight was 0.2030 ± 0.1791. The correlation between maternal common environmental effects on the two traits was also low at 0.0676 ± −0.0804. The effect of spawn year was statistically significant (p < 0.01), and the values were negatively correlated with mean un-ionized ammonia (mg/L, −0.56, p = 0.04,), nitrate concentrations (mg/L r = −0.65, p = 0.01) and temperature (°C, r = −0.61, p = 0.02) experienced by the broodstock prior to spawning. Overall, the results suggest that the decrease in eyed embryos over time was not caused by inadvertent selection but instead due to increases in water temperature and/or nitrogenous waste concentrations in the broodstock rearing system. Further investigation of the mechanisms behind these apparent environmentally induced declines and potential mitigation measures to prevent decreases in eye-up rates are needed.

Two dwarfing genes Rht-B1b and Rht-D1b show pleiotropic effects on grain protein content in bread wheat (Triticum aestivum L.).

Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.

High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing.

Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Genetic Architecture of Neurological Disorders and Their Endophenotypes: Insights from Genetic Association Studies.

Population-scale genetic association studies of complex neurologic diseases have identified the underlying genetic architecture as multifactorial. Despite the study sample sizes reaching the millions, the identified disease-related genes explain only a small fraction of the phenotypic variance. Notable advancements in statistical methods now enable researchers to gain insights even from genomic regions where genotype-phenotype associations do not reach statistical significance. Such studies confirm a highly interconnected molecular network comprising a core group of genes directly involved in the disease process, alongside an expanded peripheral network, each contributing a small but potentially important (modulatory) effect. Additionally, causal inference methods, utilizing genetic instruments, have shed light on putative causal links between risk factors and clinical endpoints. In light of the pervasive genetic overlap or pleiotropy, however, caution is warranted in interpreting causal relationships inferred from these analyses. In this chapter, I will introduce the genetic association model, provide insights into the current state of genetic association studies, and discuss potential future directions.

Exploration and genetic analyses of canopy leaf pigmentation changes in soybean (Glycine max L.): unveiling a novel phenotype

Key messagePigmentation changes in canopy leaves were first reported, and subsequent genetic analyses identified a major QTL associated with levels of pigmentation changes, suggesting Glyma.06G202300 as a candidate gene.An unexpected reddish-purple pigmentation in upper canopy leaves was discovered during the late reproductive stages in soybean (Glycine max L.) genotypes. Two sensitive genotypes, ‘Uram’ and PI 96983, exhibited anomalous canopy leaf pigmentation changes (CLPC), while ‘Daepung’ did not. The objectives of this study were to: (i) characterize the physiological features of pigmented canopy leaves compared with non-pigmented leaves, (ii) evaluate phenotypic variation in a combined recombinant inbred line (RIL) population (N = 169 RILs) under field conditions, and (iii) genetically identify quantitative trait loci (QTL) for CLPC via joint population linkage analysis. Comparison between pigmented and normal leaves revealed different Fv/Fm of photosystem II, hyperspectral reflectance, and cellular properties, suggesting the pigmentation changes occur in response to an undefined abiotic stress. A highly significant QTL was identified on chromosome 6, explaining ~ 62.8% of phenotypic variance. Based on the QTL result, Glyma.06G202300 encoding flavonoid 3′-hydroxylase (F3′H) was identified as a candidate gene. In both Uram and PI 96983, a 1-bp deletion was confirmed in the third exon of Glyma.06G202300 that results in a premature stop codon in both Uram and PI 96983 and a truncated F3′H protein lacking important domains. Additionally, gene expression analyses uncovered significant differences between pigmented and non-pigmented leaves. This is the first report of a novel symptom and an associated major QTL. These results will provide soybean geneticists and breeders with valuable knowledge regarding physiological changes that may affect soybean production. Further studies are required to elucidate the causal environmental stress and the underlying molecular mechanisms.

Identification of QTLs and candidate genes for water-soluble protein content in soybean seeds

Soybean represents a vital source of premium plant-based proteins for human nutrition. Importantly, the level of water-soluble protein (WSP) is crucial for determining the overall quality and nutritional value of such crops. Enhancing WSP levels in soybean plants is a high-priority goal in crop improvement. This study aimed to elucidate the genetic basis of WSP content in soybean seeds by identifying quantitative trait loci (QTLs) and set the foundation for subsequent gene cloning and functional analysis. Using 180 F10 recombinant inbred lines generated by crossing the high-protein soybean cultivar JiDou 12 with the wild variety Ye 9, our researcher team mapped the QTLs influencing protein levels, integrating Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene expression profiling to identify candidate genes. During the 2020 and 2022 growing seasons, a standard bell-shaped distribution of protein content trait data was observed in these soybean lines. Eight QTLs affecting protein content were found across eight chromosomes, with LOD scores ranging from 2.59 to 7.30, explaining 4.15–11.74% of the phenotypic variance. Notably, two QTLs were newly discovered, one with a elite allele at qWSPC-15 from Ye 9. The major QTL, qWSPC-19, on chromosome 19 was stable across conditions and contained genes involved in nitrogen metabolism, amino acid biosynthesis, and signaling. Two genes from this QTL, Glyma.19G185700 and Glyma.19G186000, exhibited distinct expression patterns at maturity, highlighting the influence of these genes on protein content. This research revealed eight QTLs for WSP content in soybean seeds and proposed a gene for the key QTL qWSPC-19, laying groundwork for gene isolation and enhanced soybean breeding through the use of molecular markers. These insights are instrumental for developing protein-rich soybean cultivars.

Identifying Genetic Loci Determining Grain Yield Under Drought Stress in Rice (Oryza sativa L.)

ABSTRACTIdentifying the genomic regions (quantitative trait loci (QTL)) significantly linked to grain yield under drought stress could expedite the development of novel rice cultivars suited for rainfed areas through marker‐assisted breeding. This study identified QTL regions linked to plant phenology and production traits by evaluating 122 recombinant inbred lines (RILs) of Danteshwari × Daggaddeshi under different environmental conditions. A consistent QTL region associated with grain yield under water stress (60.4 Mbp) was mapped on chromosome 1 between RM428 and RM24 with an LOD score of 4.0. Another QTL region (9.4 Mbp) linked to plant height under all environmental conditions was mapped on chromosome 1 between RM1‐HvSSR1‐87 with a LOD score of 7.5 and phenotypic variance of 25%. A core set of 402 diverse rice accessions was also evaluated under water stress conditions and subjected to genome‐wide association analysis. Twelve markers linked to grain yield under drought were identified, out of which five were significantly associated with grain yield and days to flowering under drought. The markers linked to grain yield were compared between the bi‐parental population and germplasm accessions to identify the common markers. Three markers (RM1, RM259 and RM201) were found to be consistently linked to drought stress across the seasons in both bi‐parental population and germplasm accessions studied and could be potential candidates for application in marker‐assisted selection for improving grain yield under drought stress in rice.

Assessing genetic and environmental components for pterygium: a nationwide study in Taiwan

This study aims to estimate the familial risks of pterygium and assess its relative contributions to environmental and genetic factors using the 2000–2017 Taiwan National Health Insurance Research Database. The marginal Cox's model and the polygenic liability model were made. In Taiwan, the prevalence rate of pterygium in 2017 was 1.64% for individuals with affected first-degree relatives, higher than the general population (1.34%). The adjusted relative risk (RR) for pterygium was highest for twins of the same sex (15.54), followed by siblings of the same sex (4.69), offsprings (3.39), siblings of the different sex (2.88), spouse (2.12), parents (1.86), twins of the different sex (1.57), respectively. The phenotypic variance of pterygium was 21.6% from additive genetic variance, 24.3% from common environmental factors shared by family members, and 54.1% from non-shared environmental factors, respectively. Sensitivity analysis by restricting those with surgical pterygium reveals that aRRs and the three components were similar to those of the overall pterygium. In summary, the prevalence rate of pterygium was higher for individuals with affected first-degree relatives than for the general population. The non-shared environmental factors account for half of the phenotypic variance of pterygium; genetic and shared environmental factors explain the rest.

Longitudinal changes in brain asymmetry track lifestyle and disease.

Human beings may have evolved the largest asymmetries of brain organization in the animal kingdom. Hemispheric left-vs-right specialization is especially pronounced in our species-unique capacities. Yet, brain asymmetry features appear to be strongly shaped by non-genetic influences. We hence charted the largest longitudinal brain-imaging adult resource, yielding evidence that brain asymmetry changes continuously in a manner suggestive of neural plasticity. In the UK Biobank population cohort, we demonstrate that asymmetry changes show robust associations across 959 distinct phenotypic variables spanning 11 categories. We also find that changes in brain asymmetry over years co-occur with changes among specific lifestyle markers. Finally, we reveal relevance of brain asymmetry changes to major disease categories across thousands of medical diagnoses. Our results challenge the tacit assumption that asymmetrical neural systems are highly conserved throughout adulthood.

Leaf Membrane Stability under High Temperatures as an Indicator of Heat Tolerance in Potatoes and Genome-Wide Association Studies to Understand the Underlying Genetics.

High temperatures during the crop growing season are becoming more frequent and unpredictable, resulting in reduced crop productivity and quality. Heat stress disrupts plant metabolic processes that affect cell membrane composition and integrity. Cell membrane permeability, ion leakage, and heat shock proteins have been evaluated to screen for heat tolerance in plants. In potatoes, it is unclear whether leaf membrane stability under heat stress is correlated with underground tuber productivity and quality. The main goal of this study was to evaluate if leaf membrane relative electrolyte conductivity (REC) under high temperatures could be used to identify heat-tolerant potato genotypes. Electrolyte leakage assays, correlation estimations, and genome-wide association studies were carried out in 215 genotypes. Expression levels of small heat shock protein 18 (sHSP18) were evaluated in the heat-sensitive potato variety Russet Burbank and compared with those of the heat-tolerant variety Vanguard Russet using Western blotting. Significant differences were observed among genotypes for leaf membrane REC under extreme heat (50°C); REC values ranged from 47.0-99.5%. Leaf membrane REC was positively correlated with tuber external and internal defects and negatively correlated with yield. REC was negatively correlated with the content of several tuber minerals, such as nitrogen, magnesium, and manganese. Eleven quantitative trait loci (QTLs) were identified for leaf membrane REC, explaining up to 13.8% of the phenotypic variance. Gene annotation in QTL areas indicated associations with genes controlling membrane solute transport and plant responses to abiotic stresses. Vanguard Russet had lower leaf REC and higher expression of sHSP18 under high-temperature stress. Our findings indicate that leaf membrane REC under high temperatures can be used as an indicator of potato heat tolerance.

Interpreting SNP heritability in admixed populations.

SNP heritability is defined as the proportion of phenotypic variance explained by genotyped SNPs and is believed to be a lower bound of heritability ( ), being equal to it if all causal variants are known. Despite the simple intuition behind , its interpretation and equivalence to is unclear, particularly in the presence of population structure and assortative mating. It is well known that population structure can lead to inflation in estimates because of confounding due to linkage disequilibrium (LD) or shared environment. Here we use analytical theory and simulations to demonstrate that estimates can be biased in admixed populations, even in the absence of confounding and even if all causal variants are known. This is because admixture generates LD, which contributes to the genetic variance, and therefore to heritability. Genome-wide restricted maximum likelihood (GREML) does not capture this contribution leading to under- or over-estimates of relative to , depending on the genetic architecture. In contrast, Haseman-Elston (HE) regression exaggerates the LD contribution leading to biases in the opposite direction. For the same reason, GREML and HE estimates of local ancestry heritability are also biased. We describe this bias in and as a function of admixture history and the genetic architecture of the trait and show that it can be recovered under some conditions. We clarify the interpretation of in admixed populations and discuss its implication for genome-wide association studies and polygenic prediction.

Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India

BackgroundIn the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie resistance to MLB in maize by employing a diverse panel comprising 336 lines. The panel was screening for MLB across four environments, employing standard artificial inoculation techniques. Genome-wide association studies (GWAS) and haplotype analysis were conducted utilizing a total of 128,490 SNPs obtained from genotyping-by-sequencing (GBS).ResultsGWAS identified 26 highly significant SNPs associated with MLB resistance, among the markers examined. Seven of these SNPs, reported in novel chromosomal bins (9.06, 5.01, 9.01, 7.04, 4.06, 1.04, and 6.05) were associated with genes: bzip23, NAGS1, CDPK7, aspartic proteinase NEP-2, VQ4, and Wun1, which were characterized for their roles in diminishing fungal activity, fortifying defence mechanisms against necrotrophic pathogens, modulating phyto-hormone signalling, and orchestrating oxidative burst responses. Gene mining approach identified 22 potential candidate genes associated with SNPs due to their functional relevance to resistance against necrotrophic pathogens. Notably, bin 8.06, which hosts five SNPs, showed a connection to defense-regulating genes against MLB, indicating the potential formation of a functional gene cluster that triggers a cascade of reactions against MLB. In silico studies revealed gene expression levels exceeding ten fragments per kilobase million (FPKM) for most genes and demonstrated coexpression among all candidate genes in the coexpression network. Haplotype regression analysis revealed the association of 13 common significant haplotypes at Bonferroni ≤ 0.05. The phenotypic variance explained by these significant haplotypes ranged from low to moderate, suggesting a breeding strategy that combines multiple resistance alleles to enhance resistance to MLB. Additionally, one particular haplotype block (Hap_8.3) was found to consist of two SNPs (S8_152715134, S8_152460815) identified in GWAS with 9.45% variation explained (PVE).ConclusionThe identified SNPs/ haplotypes associated with the trait of interest contribute to the enrichment of allelic diversity and hold direct applicability in Genomics Assisted Breeding for enhancing MLB resistance in maize.