Phenotypic Values Research Articles

A new allele PEL9 GG identified by genome-wide association study increases panicle elongation length in rice (Oryza sativa L.).

Considering the male sterile line has the phenomenon of panicle enclosure, panicle elongation length (PEL) plays an important role in hybrid rice seed production. However, the molecular mechanism underlying this process is poorly understood. In this study, we investigated the PEL phenotypic values of 353 rice accessions across six environments, which shows abundant phenotypic variation. Combining the 1.3 million single-nucleotide polymorphisms, we performed a genome-wide association study on PEL. Three quantitative trait loci (QTL) qPEL4, qPEL6, and qPEL9 were identified as significantly associated with PEL, of which qPEL4 and qPEL6 were previously reported QTLs and qPEL9 was novel. One causal gene locus, PEL9, was identified and validated. The PEL of accessions carrying allele PEL9 GG was significantly longer than that of those carrying allele PEL9 TT. We also demonstrated that the outcrossing rate of female parents carrying allele PEL9 GG increased by 14.81% compared with that of the isogenic line carrying allele PEL9 TT in an F1 hybrid seed production field. The allele frequency of PEL9GG increased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement of the PEL of the female parent of hybrid rice.

Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping

BackgroundRice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method.ResultsAmong the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (rGCC−FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC.ConclusionNot every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.

Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data

Longitudinal traits, such as milk production traits in dairy cattle, are featured by having phenotypic values at multiple time points, which change dynamically over time. In this study, we first imputed SNP chip (50-100K) data to whole-genome sequence (WGS) data in a Chinese Holstein population consisting of 6,470 cows. The imputation accuracies were 0.88 to 0.97 on average after quality control. We then performed longitudinal GWAS in this population based on a random regression test-day model using the imputed WGS data. The longitudinal GWAS revealed 16, 39, and 75 quantitative trait locus regions associated with milk yield, fat percentage, and protein percentage, respectively. We estimated the 95% confidence intervals (CI) for these quantitative trait locus regions using the logP drop method and identified 581 genes involved in these CI. Further, we focused on the CI that covered or overlapped with only 1 gene or the CI that contained an extremely significant top SNP. Twenty-eight candidate genes were identified in these CI. Most of them have been reported in the literature to be associated with milk production traits, such as DGAT1, HSF1, MGST1, GHR, ABCG2, ADCK5, and CSN1S1. Among the unreported novel genes, some also showed good potential as candidate genes, such as CCSER1, CUX2, SNTB1, RGS7, OSR2, and STK3, and are worth being further investigated. Our study provided not only new insights into the candidate genes for milk production traits, but also a general framework for longitudinal GWAS based on random regression test-day model using WGS data.

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex

Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.

The Relation Between InDel Genetic Distance and Heterosis in Rice

Heterosis is a common phenomenon in plant species, which has been extensively utilized in different crops. Genetic distance is one of important basis for selecting parents in hybrid breeding. There is a relation between the genetic distance and heterosis and hybrid rice combinations usually show a stronger heterosis with larger genetic distance between parental lines. In this study, 160 hybrid rice combinations were made by incomplete duallel cross using 10 sterile lines and 16 self-bred restorer lines. Moreover, the indica-japonica gene frequencies of 26 lines were identified by 20 pairs of the InDel markers. The relationships between the InDel genetic distance and the phenotype heterosis were analyzed. Here, the results showed that the InDel genetic distance between parents could be used to predict phenotype value of effective panicle per plant and control heterosis of yield per plant and seed setting rate of the tested rice combinations. The optimal distance between the parents was in the interval 0.1-0.55 for the control heterosis of several main yield traits including effective panicle per plant, filled grains per panicle and yield per plant of combinations. The present result will provide a useful reference for hybrid rice parents selection in breeding.

Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance.

Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g-1 FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g-1 FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.

Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis.

Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.

A linear profit function for economic weights of linear phenotypic selection indices in plant breeding

AbstractThe profit function (net returns minus costs) allows breeders to derive trait economic weights to predict the net genetic merit (H) using the linear phenotypic selection index (LPSI). Economic weight is the increase in profit achieved by improving a particular trait by one unit and should reflect the market situation and not only preferences or arbitrary values. In maize (Zea mays L.) and wheat (Triticum aestivum) breeding programs, only grain yield has a specific market price, which makes application of a profit function difficult. Assuming the traits’ phenotypic values have multivariate normal distribution, we used the market price of grain yield and its conditional expectation given all the traits of interest to construct a profit function and derive trait economic weights in maize and wheat breeding. Using simulated and real maize and wheat datasets, we validated the profit function by comparing its results with the results obtained from a set of economic weights from the literature. The criteria to validate the function were the estimated values of the LPSI selection response and the correlation between LPSI and H. For our approach, the maize and wheat selection responses were 1,567.13 and 1,291.5, whereas the correlations were .87 and .85, respectively. For the other economic weights, the selection responses were 0.79 and 2.67, whereas the correlations were .58 and .82, respectively. The simulated dataset results were similar. Thus, the profit function is a good option to assign economic weights in plant breeding.

The Relation between Genetic Difference for Parents of Hybrid Rice and Heterosis

Exploring the indica-japonica differentiation in parents of hybridization can provide theoretical bases for utilizing inter-subspecific heterosis. In this study, 5 sterile lines and 18 self-bred restorer lines were used as female parents and male parents respectively. Then 90 combinations were constructed by incomplete diallel cross followed by relationship analysis between parental Cheng’s index difference value and Euclidean distance and heterosis. The results showed a significant correlation between several phenotype values, super male parent heterosis and control heterosis and Euclidean distance or Cheng’s index difference value. However, it was no significant correlation for yield. Further analysis found a common interval, 3.41 - 3.46 for Euclidean distance and 3 - 4 for cheng’s index difference value of parents, which was significant or high significant positive correlated with phenotype value, super male parent and control heterosis of main yield traits. This illustrates that the larger the genetic difference of parents was, the stronger the heterosis combinations were, when the genetic differences of parents were in an appropriate range.

Productivity assessment of common bean (Phaseolus vulgaris) germplasm from Serbia

Context In Serbia, common bean (Phaseolus vulgaris L.) production largely relies on improved commercial cultivars; however, many farmers still grow and maintain landraces. Productivity assessment of common bean landraces from Serbia may enrich knowledge of bean diversity from Western Balkans, Europe and worldwide. Aims The study aims were to describe the underlying structure of a selected set of landraces and commercial cultivars of common bean, identify relatedness of accessions, and determine breeding values. Methods and key results Overall productivity was assessed through main yield components during a 2-year field trial. Average seed yield per plant was 7.9 g, with 1000-seed weight 425 g, 7.4 pods per plant and 22.9 seeds per plant. Accessions were classified according to seed colour and shape, with the Albus group generally showing highest productivity traits. Phenotypic and genotypic variability of the selected set was previously determined. Principal component analysis was used to assess bean germplasm structure, revealing subdivisions partially according to gene pool (Mesoamerican or Andean), evident through the existence of one larger Andean group. Relatedness of genotypes was assessed by hierarchical cluster analysis. Additional variation concentrated within the Andean gene pool was detected. Positive correlations were observed among numbers of pods and seeds per plant, yield per plant and plant height. According to the Mantel test, positive associations were observed among productivity trait distance, genetic distance and descriptive trait distance. Conclusions Substantial variation in productivity was observed for bean landraces, with differences among gene pools and seed forms, revealing their agronomic value. Acknowledged structure of agronomic traits and recognised stratification will assist in multilevel organisation of common bean breeding programs. Implications Combined information on phenotypic, genotypic and productivity value should benefit selection of promising parental lines associating good agronomic performance with sufficient variability, according to consumer preferences.

Uniformity test of the upland rice lines F8 from crosses of local Bangka rice and lodging resistance superior varieties in Belitung Regency

Lodging on plant rice can lead to reduces yields. Developing rice varieties with lodging resistance can do through the breeding activities. Crossing between local Bangka rice and lodging resistance superior varieties have been carried out and obtained F8 lines of upland rice. Before releasing the rice lines released into varieties, it must meet the high uniformity criteria. This research aims to determine the uniformity level of F8 upland rice lines. This research was conducted using an experimental method. The design used a randomized block design with 10 treatments (5 F8 lines and 5 comparison varieties). The F8 lines used 19I-06-09-23-03, 21B-57-21-21-23, 23F-04-10-18-18, 23A-56-20-07-20 and 23A-56-22-20-05. The comparison varieties used i.e. Danau Gaung, Inpago 8, Inpago 12, Rindang and PBM UBB 1. The research data were analyzed using qualitative descriptive, variability test, uniformity test, and Least Significant Increase (LSI) test. The result showed that F8 lines of upland rice had narrow genotypic and phenotypic variability values in all characters observed. The percentage of uniformity was obtained in the range between 83.3-100%. It shows that the F8 lines had a high uniformity. F8 lines of 19I-06-09-23-03, 21B-57-21-21-23, 23F-04-10-18-18, and 23A-56-20-07-20 showed 100% uniformity level in plant height, flag leaf length, panicle length, productive tillers number, and filled grains number. The result of LSI test obtained 23A-56-22-20-05 and 23A-56-20-07-20 lines are better than the comparison varieties.

Genetic progress evaluation of growth traits in Moghani sheep

For evaluation of growth traits' genetic progress, pedigree information of 39408 Moghani sheep, between 1986 to 2016, at the breeding station of Moghani sheep was used. Studied traits included birth weight, weaning weight, six months weight, nine months weight, and one yearling weight. Variance components and genetic parameters of traits were estimated by restricted likelihood and six animal models using Wombat software. Direct heritability of birth weight, weaning weight, six months weight, nine months weight, and one yearling weight was (0.07, 0.09, 0.15, 0.13, and 0.20 respectively). Breeding values for the calculation of genetic trends for each trait were estimated by using the univariate best animal model. Phenotypic, genetic, and environmental trends of traits were estimated via regression of phenotypic average, breeding value average, and difference of breeding value from phenotypic value divided by birth year. The calculated genetic trends of birth weight, weaning weight, six months weight, nine months weight, and yearling weight were 0.008, 0.012, 0.054, 0.74, and 0.145 kg/year respectively, except for birth weight, the others were significant (p&lt;0.01). The genetic gain of traits including birth weight, weaning weight, six months weight, nine months weight, and one yearling weight was estimated (0.213, 1.071, 1.171, 1.164, and 1.324 kg respectively). At evaluated years, many fluctuations were observed in the genetic trend of traits. In other words, it seems at the studied years, there wasn't a comprehensive plan for genetic breeding and improvement of body weight traits in Moghani sheep.

Towards mechanistic models of mutational effects: Deep learning on Alzheimer’s Aβ peptide

Deep Mutational Scanning (DMS) has enabled multiplexed measurement of mutational effects on protein properties, including kinematics and self-organization, with unprecedented resolution. However, potential bottlenecks of DMS characterization include experimental design, data quality, and depth of mutational coverage. Here, we apply deep learning to comprehensively model the mutational effect of the Alzheimer’s Disease associated peptide Aβ42 on aggregation-related biochemical traits from DMS measurements. Among tested neural network architectures, Convolutional Neural Networks and Recurrent Neural Networks are found to be the most cost-effective models with high performance even under insufficiently-sampled DMS studies. While sequence features are essential for satisfactory prediction from neural networks, geometric-structural features further enhance the prediction performance. Notably, we demonstrate how mechanistic insights into phenotype may be extracted from the neural networks themselves suitably designed. This methodological benefit is particularly relevant for biochemical systems displaying a strong coupling between structure and phenotype such as the conformation of Aβ42 aggregate and nucleation, as shown here using a Graph Convolutional Neural Network (GCN) developed from the protein atomic structure input. In addition to accurate imputation of missing values (which here ranged up to 55% of all phenotype values at key residues), the mutationally-defined nucleation phenotype generated from a GCN shows improved resolution for identifying known disease-causing mutations relative to the original DMS phenotype. Our study suggests that neural network derived sequence-phenotype mapping can be exploited not only to provide direct support for protein engineering or genome editing but also to facilitate therapeutic design with the gained perspectives from biological modeling.

Evaluation of genetic variability in fragrant rose (Rosa × hybrida L.) cultivars under open field cultivations

Twenty six rose (Rosa × hybrida L.) cultivars grown for open field conditions were characterized using 16 vegetative and floral traits to obtain information on the nature and magnitude of existing genetic variability. The cultivars, Night Time, Christian Dior and Pusa Abhishek were early in flowering and Local Collection 3, Local Collection 4, Kashmir Velvet and Edouard had longer flowering duration; Christian Dior and Bonne Nuit had bigger flowers; Pusa Bahadur had long flower stalk; Local Collection 3, Local Collection 4, Edouard and Kashmir Velvet were having more number of flowers per plant and Pusa Bahadur, Night Time and Christian Dior were found with higher flower weight and shall help in further selection and hybridisation. The higher genotypic and phenotypic coefficients of variation were recorded for plant height, plant spread (E-W), plant spread (N-S), stem girth, number of shoots/ plant, number of petals/ flower, flower stalk length, number of flowers/ plant and 100-flower weight, indicating that genotypic variation contributed markedly towards total variability for the above traits. There is a greater scope for selection in improving flower yield. The high heritability with high expected genetic advance over mean (GAM) was observed for plant height, plant spread (E-W), plant spread (N-S), stem girth, number of shoots/ plant, flower bud length, flower diameter and flower stalk length. This also revealed the lesser influence of environment on these traits. Therefore, simple selection based on phenotypic values for these traits could be useful in their improvement for achieving higher flower yield. The trait specification identified genotypes could ideally be used as donor parents in rose breeding programme to develop desired genotypes for open field cultivation.

Character Testing Of New Superior Rice Line Through Participatory Plant Breeding Method

Among the superior varieties can be obtained through breeding. The low level of farmer adoption of improved varieties resulting from breeding is partly due to the different preferences of farmers with breeding. The development of specific varieties will be successful through a participatory breeding program that involves breeders, farmers and rice industry players in the selection process for prospective new varieties. The research objective was to analyze and select the quantitative and qualitative characters of 12 new rice lines to produce new superior rice varieties that were more suitable to farmers' tastes. The research in the field was compiled using a Randomized Completely Block Design (RCBD), as a treatment consisting of 12 lines of F11 generation, each treatment was repeated three times. Observations were made on the like and dislike statements of respondents consisting of 20 farmers on the phenotypic character of each line, as well as an assessment of the phenotype acceptance of each line as assessed by the breeders (4 breeders) before harvest following the guidelines (IRRI, 2002) . The results showed that the F3 line had the highest preference value, namely the value of 0.9, meaning that the farmers liked the most. The line with the lowest preference value is the D2 line with a value of -1 (minus one), meaning that it is the least preferred. Based on the phenotype acceptance value of the breeders for each line, three lines had a phenotypic value of 1 or very good value, namely the B4, H1, and H4 lines, while those with a value of 3 or good were eight lines, namely the B2, B3, B7, D2, D3, F3, F4, and L2 lines. One line has a bad phenotype value, namely the K.

Evaluation of Epigenetic Age Acceleration Scores and Their Associations with CVD-Related Phenotypes in a Population Cohort.

We evaluated associations between nine epigenetic age acceleration (EAA) scores and 18 cardiometabolic phenotypes using an Eastern European ageing population cohort richly annotated for a diverse set of phenotypes (subsample, n = 306; aged 45-69 years). This was implemented by splitting the data into groups with positive and negative EAAs. We observed strong association between all EAA scores and sex, suggesting that any analysis of EAAs should be adjusted by sex. We found that some sex-adjusted EAA scores were significantly associated with several phenotypes such as blood levels of gamma-glutamyl transferase and low-density lipoprotein, smoking status, annual alcohol consumption, multiple carotid plaques, and incident coronary heart disease status (not necessarily the same phenotypes for different EAAs). We demonstrated that even after adjusting EAAs for sex, EAA-phenotype associations remain sex-specific, which should be taken into account in any downstream analysis involving EAAs. The obtained results suggest that in some EAA-phenotype associations, negative EAA scores (i.e., epigenetic age below chronological age) indicated more harmful phenotype values, which is counterintuitive. Among all considered epigenetic clocks, GrimAge was significantly associated with more phenotypes than any other EA scores in this Russian sample.

Genetic Variability and Path Analysis for Yield and Associated Traits in Linseed Genotypes

An experiment was conducted to study the nature and magnitude of genetic variability with yield and related traits and characters association in linseed. Twelve diverse linseed (Linum usitatissimum L.) genotypes were evaluated in randomized block design withthree replications duringrabiseason 2020-21 in the experiment field of AICRP on oilseeds in the college of agriculture Tikamgarh. The higher phenotypic coefficient values than corresponding genotypic coefficient values depicted influence of environment in the expression of traits. The data were recorded for days to flowering initiation, days to 50 % flowering, plant stand per hectare, plant height, primary branches per plant, capsules per plant, number of seeds per capsule, biological yield per plant, days to maturity,1000 seed weight, yield per plant, yield per ha., protein and oil content.High to moderate magnitude of PCV and GCV were observed for the traits viz., 1000 seed weight, yield per plant, plant height, biological yield per plant, days to flower initiation indicating the presence of significant variability in the existing collection and in path coefficient analysis revealed the positive direct effect at both genotypic and phenotypic levels for the characters for days to 50% flower, plant height, number of capsule per plant, 1000 seed weight and primary branches per plant respectively.

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice.

The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

Hyperphenylalaninemias genotyping: Results of over 60 years of history in Lombardy, Italy.

Hyperphenylalaninemias (HPA) are due to several gene mutations, of which the PAH gene is the most frequently involved. Prevalence and incidence of disease vary between populations, with genotype/phenotype correlations not always capable to correctly predict disease severity. The aim of this study was to give an overview of PAH mutations among one of the largest cohort of patients among Europe, born in Lombardy (Italy) starting from late 1970 s and including over a 60 years of activity; furthermore, to evaluate and discuss identified genotype/phenotype correlations and related reliability. Eight hundred and twenty-six HPA patients in current follow-up at the San Paolo Hospital in Milan (Italy) were retrospectively reviewed, including molecular results and allelic phenotype and genotype values (attributed on the basis of the APV/GPV system) to verify genotype-phenotype correlations. A total of 166 different PAH variants were reviewed; of those, seven variants were identified as not previously described in literature. Most frequently reported variant was p.Ala403Val, followed by p.Arg261Gln, p.Val245Ala, IVS10-11 g>a, p.Tyr414Cys and p.Leu48Ser. Phenotype prediction, based on APV/GPV, matched the actual phenotype in most cases, but not always. The cohort of patients included in this study constitute a representative sample of the HPA population worldwide. Studies on this sample may allow to improve clinical and genetic evaluation performances for affected patients, consequently to develop personalized medicine interventions and provide more precise indications on the correct treatment approach based on the accumulated evidence, also in light of a prognostically reliable but not always conclusive APV/GPV system.

Models of microglia depletion and replenishment elicit protective effects to alleviate vascular and neuronal damage in the diabetic murine retina

Microglia, the resident phagocytes of the retina, are believed to influence the development of retinopathy, but their exact contributions to vascular integrity and neuronal loss are unknown. Therefore, utilizing two models of microglia depletion, we aimed to deplete and repopulate microglia to clarify the contribution of microglia to neuronal loss and vascular damage in the diabetic retina in an STZ-induced model of hyperglycemia. Here, we report that 2 weeks exposure to diphtheria toxin (DTx) in diabetic CX3CR1CreER:R26iDTR transgenic mice induced a 62% increase in Iba1+ microglia associated with an increase in TUJ1+ axonal density and prevention of NeuN+RBPMS+ neuronal loss. Conversely, diabetic PBS controls exhibited robust TUJ1+ axonal and NeuN+RBPMS+ neuronal loss compared to non-diabetic controls. A 2-week recovery period from DTx was associated with a 40% reduction in angiogenesis and an 85% reduction in fibrinogen deposition into the diabetic retina in comparison to diabetic PBS-treated controls. Analysis of microglia morphology and marker expression revealed that following a 2-week recovery period microglia displayed a P2RY12+Ly6C– phenotype and high transformation index (TI) values complimented by a ramified-surveillant morphology closely resembling non-diabetic controls. In contrast, diabetic PBS-treated control mice displayed P2RY12+Ly6C+ microglia, with a 50% reduction in TI values with an amoeboid morphology. To validate these observations were due to microglia depletion, we used PLX-5622 to assess vascular and neuronal damage in the retinas of diabetic mice. Confocal microscopy revealed that PLX-5622 also induced an increase in TUJ1+ axonal density and prevented fibrinogen extravasation into the diabetic retina. mRNAseq gene expression analysis in retinal isolates revealed that PLX-5622-induced microglia depletion and repopulation induced a downregulation in genes associated with microglial activation and phagocytosis, B2m, Cx3cr1, and Trem2, and complement-associated synaptic pruning, C1qa, C1qb, and C1qc. Although the levels of microglia depletion induced with DTx in the CX3CR1CreER:R26iDTR model and those induced with the CSF-1R antagonists are distinct, our results suggest that microglia depletion and replenishment is neuroprotective by inducing the proliferation of a homeostatic microglia pool that supports neuronal and vascular integrity.