Phenotypic Classes Research Articles

Genetic variability assessment of indigenous and exotic saffron germplasm through morpho-agronomic characterization at Jammu and Kashmir, India

AbstractThe present study analysed a total of 272 saffron (Crocus sativus L.) genotypes using multivariate analysis. We carefully observed and recorded information about the floral, morphological and corm attributes. Significant variations were observed among the genotypes for all the traits, indicating a high level of variability and suggesting a great potential for saffron improvement. The phenotypic variances were found to be greater than the estimated genotypic variances. Descriptive data on various morphological traits revealed significant differences in the frequency of phenotype classes as well as a wide distribution range. The high heritability estimates were observed in average number of daughter corms per plant (ANDCPP), initial weight of corms (IWC g), no. of buds/corm (NBPC), – no. of leaves in main sprout, (NLMS), number of sprouted buds per corm (NSBpC) and total number of leaves (TNL), whereas average weight of daughter corms per plant (AWBCPP), corm diameter (CDcm), pistal length (PL) cm, style length (STYLcm), fresh weight of pistals per plant (FWOPPPmg) and stigma length (STML cm), revealed medium sense of heritability. The traits dry weight of pistals per plants (DWOPPP mg), inner tepal width (ITW cm), leaf length (LLcm), number of flowers per corm (NFpC), outer tepal length (OTLcm), parianth length with tube (PLWT cm) and weight of stigma (WSTG mg) exhibited low broad-sense heritability. Principal component analysis (PCA) divulged that the first eight component characters had an eigenvalue greater than one with a contributory cumulative variance of 66.15% to the total variance, while as rest of the 16 components contributed 33.85% of total variation in a set of 272 genotypes of saffron. The eigenvalues for yield attributing traits for significant PCs ranged from 5.48 (PC1) to 1.03(PC8). The current study has revealed that there was a sufficient variability in a set of saffron germplasm lines which forms the basis for performance-based clonal selection. Moreover, identified elite genotypes based on saffron yield and corm attributes could be used in the saffron breeding programme for the development of saffron varieties.

Exploring agro-morphological profiles of Phaseolus vulgaris germplasm shows manifest diversity and opportunities for genetic improvement

Common bean (Phaseolus vulgaris) is a seed crop with huge potential to contributing to food security in developing countries. In crop improvement, assessing genetic variability is a decisive step, requiring characterization of available crop germplasm. The present study aims at characterizing 39 common bean genotypes from various locations in Cameroon and five from Kenya using 19 qualitative and 36 quantitative traits of high descriptive values. Diversity among germplasm was assessed by determining diversity indices and carrying out multivariate analysis. Seventeen out of the nineteen qualitative traits (89.47%) were polymorphic, displaying each at least two phenotypic classes. High diversity was found. Average observed and expected number of phenotypic classes per trait were 3.74 and 2.53 respectively. Nei's genetic diversity value of 0.49 and Shannon-Weaver diversity index estimates of 0.74 were found. Significant differences were observed among genotypes for all measured quantitative traits. Yield traits showed significant correlation with other related quantitative traits. Cluster analysis separated the studied germplasm into three distinct groups, with the clustering pattern not showing any connection with location. The test of equality revealed significant difference between these clusters for most quantitative traits. Mahalanobis D2 statistics revealed germplasm of cluster I and III as potential parents for future breeding programs. This study identified genotypes with desirable agronomic traits such as higher number of seeds per pod, lower number of days to maturity, higher number of pods per plant, and higher yield. These and other important discriminatory traits are discussed and proposed for genetic improvement of common bean.

Наследование признака высокого содержания олеиновой кислоты в масле семян F2 и поколения BC1 рапса озимого (Brassica napus L.)

The aim of the work was to study the patterns of inheritance of the trait of high oleic content in the F2 and generation BC1 of winter rapeseed in order to obtain new knowledge about the genetic mechanisms of the high oleic acid contents in seed oil and scientifically based approaches to the development of the breeding germplasm with a high content of oleic acid. The studies were carried out in 2021– 2022 in the field. The material was reciprocal F1 hybrids from crossings of the high-oleic line VN-1848 (79.3%) and two lines from the cultivars Sarmat and Selegor of VNIIMK breeding with the traditional content of oleic acid in seed oil – 62.1 and 60.5%, respectively. Hybrids F1 were used to produce BC1 seeds. F2 and BC1 generations were obtained in 2022. In F2 hybrids, splitting into two phenotypic classes was observed in a ratio of 15 : 1. The first one included lines with oleic acid content in seed oil less than 79%, the second one – lines with high rates of this trait at the level or higher than the parental high-oleic component (18 : 1 > 79%). This proposes the control of a trait by two pairs of non-allelic genes with an additive effect. As a result of backcrosses using the high-oleic lines VN-1848 as the maternal component, 55 genotypes with a low content of oleic acid (18 : 1 < 79%) and 11 genotypes with high levels of this trait (18 : 1 > 79%) were obtained. This corresponded to a splitting ratio of 3 : 1. All χ2 values turned out to be less than 3.8, p > 0.05.The results of the studies confirm our assumption that the oleic acid content in seed oil is controlled by two pairs of non-allelic genes; the manifestation of this trait in plants is observed only when all alleles are in a homozygous recessive state.

Expression and inheritance of performance constituents and seed color in winter rye

Purpose. To establish peculiarities of inheritance of major breeding traits in lines - parents of winter rye hybrids; to assess the effectiveness of creating starting material for heterotic winter rye breeding based on lines - donors of purple seed color and a set of valuable economic characteristics. Material and methods. The experiments were conducted in the fields of Verkhniachka Experimental Breeding Station of the Institute of Bioenergy Crops and Sugar Beet (Verkhniachka EBS IBCSB) of NAAS of Ukraine (Umanskyi District of Cherkassy Region) in 2021-2022. The following F1 and F2 simple hybrids were studied: l.471 x l.44 and l.471 x l.4351H.4-1-22. F1 hybrids were sown manually in single-row sections of 1.5 m long by wide-row method (interrow distance = 25–30 cm) to a depth of 3–4 cm in 2020. The sowing design was as follows: female form – F1 – male form, using the female and male forms as references. All fully ripened plants were harvested with roots. For structural analysis, 25 plants of the hybrids, female and male forms were taken; they were evaluated for the following morphological features: plant height (PH), the productive shoot number (PSN), and spike length (SL). We analyzed such performance constituents as the flower number per spike (FMS), kernel number per spike (KNP), kernel weight per spike (KWS), kernel weight per plant (KWP), and thousand kernel weight (TKW). During the growing period, the phases of plant growth and development were monitored. Correspondence of the observed ratio of phenotypic classes to the theoretical one in F2 was assessed by the χ2 test. Results and discussion. Various forms from a genetic collection, carriers of dominant and recessive alleles of one or several marker traits were used as the starting material to explore expression and inheritance of morphological traits. Hybrid combination No. 16/17–743/18 (line 471) with purple seeds, which had been created by selection and self-pollination (inbreeding), was crossed with donors of the dominant ‘short stem’ trait with wild-type (light) color of seeds, l.44 and l.4351H.4-1-22. In F1 hybrids, the quantitative constituents of the plant performance, in particular the productive shoot number, flower number per spike, kernel number per spike, kernel weight per spike, and kernel weight per plant were higher than the parents’ mean values. High degree of dominance indicated that these traits were inherited by dominance and overdominance. In F2 hybrids, dihybrid segregation into genotypes with different colors was observed: purple due to pigments in the caryopsis coat, intermediate and wild-type color of the aleurone layer, with greater number of wild-type plants. The purple color of the caryopsis in the parental lines, l.44 and l.4351H.4-1-22, turned out to be recessive relative to the wild-type color, but at the same time it was dominant in l.471 / l.44 relative to intermediate color, and in l.4351H.4-1-22, on the contrary, it was recessive in relation to intermediate color. Epistasis in l.471 / l.44 was seen in the following sequence: wild-type ˃ purple ˃ intermediate, while in l.471 / l.4351H.4-1-22 the sequence differed: wild-type ˃ intermediate ˃ purple. Conclusions. Regardless of the genotypes of winter rye lines with colored and wild-type seeds included in crossings, the purple color of seeds showed a monogenic recessive inheritance.

A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans

Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue‐specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70–80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.

Long COVID Clinical Phenotypes up to 6 Months After Infection Identified by Latent Class Analysis of Self-Reported Symptoms.

The prevalence, incidence, and interrelationships of persistent symptoms after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection vary. There are limited data on specific phenotypes of persistent symptoms. Using latent class analysis (LCA) modeling, we sought to identify whether specific phenotypes of COVID-19 were present 3 months and 6 months post-infection. This was a multicenter study of symptomatic adults tested for SARS-CoV-2 with prospectively collected data on general symptoms and fatigue-related symptoms up to 6 months postdiagnosis. Using LCA, we identified symptomatically homogenous groups among COVID-positive and COVID-negative participants at each time period for both general and fatigue-related symptoms. Among 5963 baseline participants (4504 COVID-positive and 1459 COVID-negative), 4056 had 3-month and 2856 had 6-month data at the time of analysis. We identified 4 distinct phenotypes of post-COVID conditions (PCCs) at 3 and 6 months for both general and fatigue-related symptoms; minimal-symptom groups represented 70% of participants at 3 and 6 months. When compared with the COVID-negative cohort, COVID-positive participants had higher occurrence of loss of taste/smell and cognition problems. There was substantial class-switching over time; those in 1 symptom class at 3 months were equally likely to remain or enter a new phenotype at 6 months. We identified distinct classes of PCC phenotypes for general and fatigue-related symptoms. Most participants had minimal or no symptoms at 3 and 6 months of follow-up. Significant proportions of participants changed symptom groups over time, suggesting that symptoms present during the acute illness may differ from prolonged symptoms and that PCCs may have a more dynamic nature than previously recognized. Clinical Trials Registration. NCT04610515.

Elucidating the immunological landscape of acute myocardial infarction using an integrated single-cell enzyme and antibody quantification (iSEAQ) assay

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Research Foundation Background Characterizing enzyme secretion with surface antigen expression of circulating leukocytes provides deep immunological insights that may benefit diagnostics and therapeutics of acute myocardial infarction (AMI). Current methods are limited by laborious sample preparation, lengthy assay time and limited analytical throughput. Purpose We aimed to develop a point-of-care platform for real-time, granular immune profiling of AMI during index hospitalization. Methods We developed a system for a 40-min assay termed integrated single-cell enzyme and antigen quantification (iSEAQ), consisting of an integrated microfluidic device for a streamlined process to recover and isolate single leukocytes from whole blood, and a customized 5-channel high-speed droplet fluorescence cytometer for sensitive quantification of key protein activity resembling live leukocyte activity in-vivo (Figure 1). Using a panel of 2 secreted enzymes (granzyme B (GzB) and neutrophil elastase (NE)) and 3 surface antigens (cluster of differentiation (CD) 66b, CD3 and CD31), we tracked the longitudinal shift of immune functionality of 9 patients admitted for acute ST-segment elevation myocardial infarction (STEMI) patients (median age 52 years, 100% males) at 3 timepoints during the index hospitalization: 1) on admission prior to coronary revascularization, 2) within 24 hours of revascularization, and 3) pre-discharge. The 5-channel fluorescence data were imported using a python script and pre-processed, before piping into Numpy, Pandas, Scipy and UMAP library for data preparation and classification. Seaborn and Matplotlib were used for all data visualization and plots. Data was analyzed using student two-tailed t-tests, with a significance level of <5%. Results Leveraging on its ability to dissect enzyme secretion by phenotype class, iSEAQ unraveled distinct contributions of CD31, NE and GzB from peripheral granulocytes, T lymphocytes and other cells (Figure 2). The majority immune response is expressed in CD66b+ granulocytes showing increased NE+ secretion and CD31 surface antigen expression denoted in Class 0 in Figure 2. Compared to samples from healthy donors and STEMI patients on admission, the NE+ and CD31+ expressions were significantly lower in pre-discharge samples of STEMI patients (p<0.05). iSEAQ also distinguished anterior from inferior STEMI, as evident from a significantly elevated NE+CD31-secretion for CD66b+ granulocytes in anterior STEMI (365±70 vs 83±35 fg, p < 0.001), showing preliminary promise in the ability of iSEAQ to risk stratify. Conclusion iSEAQ provided a comprehensive granular immune atlas of the longitudinal immune responses to STEMI during hospital admission. With its open design for assay panel using commercial biosensors, iSEAQ is a potentially powerful tool for taking functionality snapshots of immune system in many diseases.

A Recombination Suppressed Region of Sunflower (<i>Helianthus annuus</i> L.) Linkage Group 13 Covers Restoration of Fertility (<i>Rf1</i>) and Downy Mildew Resistance (<i>Pl</i>) Gene Clusters

A number of genes that control valuable for breeding traits introgressed from wild relatives, i.e. pollen fertility restoration, resistance to fungal diseases (downy mildew and rust), are mapped on linkage group 13 of the cultivated sunflower Helianthus annuus L. genome. In sunflower and other plants, the recombination in the chromosome regions containing resistance genes can be suppressed that is favourable for marker assisted selection with applying molecular markers linked to these loci. The joint inheritance of the loci Rf1 (the phenotypic marker is fertility restoration trait) and Pl5/Pl8 conferring resistance to many races of Plasmopara halstedii (Farl) Berl. De Toni (the STS marker Ha-P1) was studied in the F2 generation of hybrids between a sterile line VIR 116A lines and pollen fertility restorers from sunflower VIR collection. In the crossing VIR 116А × VIR 740, the frequency of recombination between the loci Pl5Pl8 and Rf1 constituted 8.61 whereas in the crosses VIR 116А × VIR 195 and VIR 116А × VIR 80 turned out to be twice as high. In all examined F2 populations the absence of phenotypic class of sterile plants possessing paternal Нa-Р1 marker variant was mentioned. It has been shown by the cytological analysis that pollen fertility indices are most probably determined by the plant genotype rather than the male gametophyte allelic constitution. A deficiency of a recombinant F2 class was proposed to be associated with embryonic lethality, i.e. the collapse of zygotes carrying the recessive allele of fertility restoration gene and a specific allele of the resistance (susceptibility) gene obtained from the male parent.

Sa1249 SMOOTH MUSCLE PHENOTYPIC CLASS SWITCHING IN RESPONSE TO MECHANICAL STRESS: A STORY TOLD BY RNA SEQ

Sa1249 SMOOTH MUSCLE PHENOTYPIC CLASS SWITCHING IN RESPONSE TO MECHANICAL STRESS: A STORY TOLD BY RNA SEQ

The Cytokine, Chemokine, and Growth Factor Network of Prenatal Depression.

Neuro-immune pathways are engaged in antenatal and postpartum depression. To determine if immune profiles influence the severity of prenatal depression above and beyond the effects of adverse childhood experiences (ACE), premenstrual syndrome (PMS), and current psychological stressors. Using the Bio-Plex Pro human cytokine 27-plex test kit, we assayed M1 macrophage, T helper (Th)-1, Th-2, Th-17, growth factor, chemokine, and T cell growth immune profiles as well as indicators of the immune inflammatory response system (IRS) and compensatory immunoregulatory system (CIRS) in 120 pregnant females in the early (<16 weeks) and late (>24 weeks) pregnancy. The Edinburgh Postnatal Depression Scale (EPDS) was used to assess severity of antenatal depression. Cluster analyses showed that the combined effects of ACE, relationship dissatisfaction, unwanted pregnancy, PMS, and upregulated M1, Th-1, Th-2, and IRS immune profiles and the ensuing early depressive symptoms shape a stress-immune-depression phenotypic class. Elevated IL-4, IL-6, IL-8, IL-12p70, IL-15, IL-17, and GM-CSF are the cytokines associated with this phenotypic class. All immune profiles (except CIRS) were significantly associated with the early EPDS score, independent of the effects of psychological variables and PMS. There was a shift in immune profiles from early to late pregnancy, with an increase in the IRS/CIRS ratio. The late EPDS score was predicted by the early EPDS score, adverse experiences, and immune profiles, mainly the Th-2 and Th-17 phenotypes. Activated immune phenotypes contribute to early and late perinatal depressive symptoms above and beyond the effects of psychological stressors and PMS.

Optimisation Models for Pathway Activity Inference in Cancer.

With advances in high-throughput technologies, there has been an enormous increase in data related to profiling the activity of molecules in disease. While such data provide more comprehensive information on cellular actions, their large volume and complexity pose difficulty in accurate classification of disease phenotypes. Therefore, novel modelling methods that can improve accuracy while offering interpretable means of analysis are required. Biological pathways can be used to incorporate a priori knowledge of biological interactions to decrease data dimensionality and increase the biological interpretability of machine learning models. A mathematical optimisation model is proposed for pathway activity inference towards precise disease phenotype prediction and is applied to RNA-Seq datasets. The model is based on mixed-integer linear programming (MILP) mathematical optimisation principles and infers pathway activity as the linear combination of pathway member gene expression, multiplying expression values with model-determined gene weights that are optimised to maximise discrimination of phenotype classes and minimise incorrect sample allocation. The model is evaluated on the transcriptome of breast and colorectal cancer, and exhibits solution results of good optimality as well as good prediction performance on related cancer subtypes. Two baseline pathway activity inference methods and three advanced methods are used for comparison. Sample prediction accuracy, robustness against noise expression data, and survival analysis suggest competitive prediction performance of our model while providing interpretability and insight on key pathways and genes. Overall, our work demonstrates that the flexible nature of mathematical programming lends itself well to developing efficient computational strategies for pathway activity inference and disease subtype prediction.

Dual Functions of labial Resolve the Hox Logic of Chelicerate Head Segments.

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalp segment (lab-1) and in patterning the first walking leg identity (Dfd-1), respectively. However, extrapolations of these data across chelicerates are hindered by the existence of duplicated Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication (WGD) event. Here, we investigated the function of the single-copy ortholog of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject to this WGD. Embryonic RNA interference against lab resulted in two classes of phenotypes: homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalp and leg 1 segments. To test for combinatorial function, we performed a double knockdown of lab and Dfd, which resulted in a homeotic transformation of both pedipalps and the first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we performed expression surveys for lab and Dfd paralogs in scorpions and horseshoe crabs. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox genes lab and Dfd, irrespective of the number of gene copies.

Implications of qualitative trait diversity for future cowpea improvement and genetic resource conservation

• Collection and conservation for genetic enhancement and reducing genetic resource erosion. • Diversity was evident amongst genotypes based on the frequency distribution of phenotypic traits. • The estimate of H' ranged from 0.45 (intermediate pod curvature) to 1.00 (growth habit). • Clustering analysis followed the proximity-based trend and grouped the regions into five clusters. • Geographical distribution of diversity significantly affects genetic polymorphism of the cowpea. Understanding genetic diversity is indispensable for conserving and utilizing the genetic resources of orphan crops. Information on cowpea genetic resource collections, and its characterization and conservation in Ethiopia is limited. The objectives of this study were to determine the extent of genetic diversity within cowpea genotypes, assess the diversity patterns based on regions of origin, and identify regions for future cowpea collection and conservation. A total of 324 cowpea genotypes were evaluated using a 18 × 18 simple lattice design. Data on 22 qualitative traits were collected and subjected to the Shannon-Weaver diversity index (H') and multivariate analyses. A high level of diversity was evident amongst genotypes based on the frequency distribution of phenotypic traits. Individual phenotypic classes were not evenly distributed. The estimate of H' ranged from 0.45 (intermediate pod curvature) to 1.00 (growth habit). The highest (H'=0.77) and the lowest (H'=0.39) diversity values were obtained from the unknown category and the International Institute of Tropical Agriculture (IITA), respectively. Of the total variation, 82% was due to the populations within the regions of origin. Cluster analysis revealed five distinct groups. Seed colour and plant vigour contributed 84.9% of the variation in the first principal component between regions. In general, eye pattern, twining tendency, plant vigour, pod wall thickness, seed colour, testa texture, seed crowding, pod attachment to peduncle and immature pod pigmentation were the most effective traits for distinguishing amongst cowpea genotypes and could be used as selection criteria for improvement. This genetic diversity should be exploited by comprehensive cowpea variety development programs.

Phenotypic diversity of rosemary (Salvia rosmarinus Schleid.) accessions for qualitative characters

Rosemary is one of the industrially significant crops traded over the world. Its cultivation in many countries depends on locally adapted populations rather than on the use of improved varieties. Collection and characterization of the local populations could contribute to their conservation and selection of desirable traits. Therefore, this study was undertaken to estimate the diversity of 45 rosemary accessions collected from different parts of Ethiopia using qualitative morphological traits. The frequency distribution of characters reflected the polymorphism of the studied characters, and a total of 39 phenotypic classes were observed. Shannon-weaver diversity indices estimated across accessions ranged from 0.43 to 0.99 with a mean value of 0.79, demonstrating the existence of adequate phenotypic diversity among the accessions. Estimates of diversity indices within and among growing regions revealed that intra-region diversity (0.57) exceeds inter-region diversity (0.43). Cluster analysis classified the accessions into six major clusters regardless of the accessions' geographical origin. This was consistent with the estimated within and among growing regions diversity indices. The results clearly showed the presence of considerable levels of phenotypic diversity that could be exploited as a source of a valuable gene pool for future breeding programs.

Наследование устойчивости к расе G Orobanche cumana Wallr. в F2 и ВС1 у линии подсолнечника RGM

One of the most harmful biotic factors influencing the stability of sunflower yields is a parasite weed – broomrape (Orobanche Cumana Wallr.). Among the different measures of this parasite control, the usage of genetic resistance is the most ecologic. Lines of the different origin resistant to a race G were developed in V.S. Pustovoit All-Russian Research Institute of Oil Crops. However, inheritance of a trait of resistance was not studied in all lines. Thus, the purpose of this work was studying the genetic control of resistance to a broomrape race G in a line RGM in F2 and BC1. To analyze inheritance, we used the line RGM resistant to the broomrape race G and susceptible to this race the sterile and fertile forms of a line VK 680 of VNIIMK breeding. Resistance of plants in F2 and BC1 was tested in protected ground infected with seeds of a broomrape race G using a method of earlier diagnosis by A.Ya. Panchenko. Reciprocal crosses of the line RGM and susceptible sunflower lines resulted that all obtained hybrids F1 had low middle level of broom-rape infestation. When crossing heterozygous plants F1 and a susceptible parental form of sunflower in BC1 two phenotypes were obtained: susceptible and incomplete resistant (intermediate) in the ratio of 1 : 1. This is typical for monogenic inheritance of a trait. A value x2 was equal 1.38 that certifies the hypothesis the only gen controls resistance of this line with a probability from 0.20 to 0.30. In F2 population splitting for three phenotypical classes was observed: resistant, intermediate, and susceptible in the ratio of 1 : 2 : 1. A value x2 was equal 0.58 that certifies the hypothesis the only gen controls resistance of the studied line with an incomplete dominance with a probability from 0.20 to 0.30.

Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length.

Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.

Multispecies transcriptomes reveal core fruit development genes.

During angiosperm evolution there have been repeated transitions from an ancestral dry fruit to a derived fleshy fruit, often with dramatic ecological and economic consequences. Following the transition to fleshy fruits, domestication may also dramatically alter the fruit phenotype via artificial selection. Although the morphologies of these fruits are well documented, relatively less is known about the molecular basis of these developmental and evolutionary shifts. We generated RNA-seq libraries from pericarp tissue of desert tobacco and both cultivated and wild tomato species at common developmental time points and combined this with corresponding, publicly available data from Arabidopsis and melon. With this broadly sampled dataset consisting of dry/fleshy fruits and wild/domesticated species, we applied novel bioinformatic methods to investigate conserved and divergent patterns of gene expression during fruit development and evolution. A small set of 121 orthologous "core" fruit development genes show a common pattern of expression across all five species. These include key players in developmental patterning such as orthologs of KNOLLE, PERIANTHIA, and ARGONAUTE7. GO term enrichment suggests that these genes function in basic cell division processes, cell wall biosynthesis, and developmental patterning. We furthermore uncovered a number of "accessory" genes with conserved expression patterns within but not among fruit types, and whose functional enrichment highlights the conspicuous differences between these phenotypic classes. We observe striking conservation of gene expression patterns despite large evolutionary distances, and dramatic phenotypic shifts, suggesting a conserved function for a small subset of core fruit development genes.

Regulation of Archease by the mTOR-vATPase axis.

Larval terminal cells of the Drosophila tracheal system generate extensive branched tubes, requiring a huge increase in apical membrane. We discovered that terminal cells compromised for apical membrane expansion - mTOR-vATPase axis and apical polarity mutants - were invaded by the neighboring stalk cell. The invading cell grows and branches, replacing the original single intercellular junction between stalk and terminal cell with multiple intercellular junctions. Here, we characterize disjointed, a mutation in the same phenotypic class. We find that disjointed encodes Drosophila Archease, which is required for the RNA ligase (RtcB) function that is essential for tRNA maturation and for endoplasmic reticulum stress-regulated nonconventional splicing of Xbp1 mRNA. We show that the steady-state subcellular localization of Archease is principally nuclear and dependent upon TOR-vATPase activity. In tracheal cells mutant for Rheb or vATPase loci, Archease localization shifted dramatically from nucleus to cytoplasm. Further, we found that blocking tRNA maturation by knockdown of tRNAseZ also induced compensatory branching. Taken together, these data suggest that the TOR-vATPase axis promotes apical membrane growth in part through nuclear localization of Archease, where Archease is required for tRNA maturation.

A Tomato EMS-Mutagenized Population Provides New Valuable Resources for Gene Discovery and Breeding of Developmental Traits.

Tomato (Solanum lycopersicum L.) is a major horticultural crop and a model species among eudicots, especially for traits related to reproductive development. Although considerable progress has been made since the tomato genome sequence project was completed, most of the genes identified remain predictions with an unknown or hypothetical function. This lack of functional characterization hampers the use of the huge amount of genomic information available to improve the quality and productivity of this crop. Reverse genetics strategies such as artificial mutagenesis and next-generation sequencing approaches build the perfect tandem for increasing knowledge on functional annotation of tomato genes. This work reports the phenotypic characterization of a tomato mutant collection generated from an EMS chemical mutagenesis program aimed to identify interesting agronomic mutants and novel gene functions. Tomato mutants were grouped into fourteen phenotypic classes, including vegetative and reproductive development traits, and the inheritance pattern of the identified mutations was studied. In addition, causal mutation of a selected mutant line was isolated through a mapping-by-sequencing approach as a proof of concept of this strategy’s successful implementation. Results support tomato mutagenesis as an essential tool for functional genomics in this fleshy-fruited model species and a highly valuable resource for future breeding programs of this crop species aimed at the development of more productive and resilient new varieties under challenging climatic and production scenarios.

Induced variations of ethyl methane sulfonate mutagenized cowpea (Vigna unguiculata L. walp) plants.

Unique variants are desired in the development of genetically improved crops to meet farmer and market needs hence ethyl methane sulfonate (EMS) was used to induce genetic variability in cowpea (Vigna unguiculata cv. Asontem). The main objective of this research was to characterize induced variations in EMS chemically mutagenized population of cowpea (Vigna unguiculata L. Walp Var. Asontem) in the M1 and M2 generations. The optimum concentration (LD50) of EMS for generating the mutagenized population was determined by treating seeds with different concentrations of EMS (0.0, 0.2, 0.4, 0.6, and 0.8% v/v) and observing the germination count after 5 days of planting the seeds in Petri dishes. Three thousand cowpea seeds were treated with the 0.4% EMS to generate the M1 and M2 populations that were evaluated for agronomic and morphological traits with untreated seeds serving as control. Data analysis involved distribution of qualitative and quantitative traits. Germination was significantly reduced in the mutagenized population (17.8%) and compared with that of the wild type (61.6%). Percentage survival was significantly higher in wild type (98.38%) as compared with the M1 population (78.46%). Percentage germination in the M2 population (74.03%) was lower than the wild type (80%). A wide spectrum of agro-morphological abnormalities was observed in the M2 population. Wide variations and uniquely different phenotypic classes were observed in leaf color, leaf shape, growth habit, plant pigmentation, twining tendency, pod curvature, seed shape, and seed coat color. M2 individuals were widely distributed for days to flowering, number of pods per plant, number of seeds per pod, number of locules per pods, percentage seed set, pod length and number of seeds per plant. In conclusion, the EMS mutagenesis was effective in inducing the unique variations that will be useful for breeding and development of new farmer preferred varieties.