The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E

Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate

Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. To investigate leaf shape variation in species with inconsistent shapes, we analyzed approximately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. Our results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.

DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.

SpykProps: an imaging pipeline to quantify architecture in unilateral grass inflorescences

BACKGROUND

Inflorescence properties such length, spikelet number, and their spatial distribution across the rachis, are fundamental indicators of seed productivity in grasses and have been a target of selection throughout domestication and crop improvement. However, quantifying such complex morphology is laborious, time-consuming, and commonly limited to human-perceived traits. These limitations can be exacerbated by unfavorable trait correlations between inflorescence architecture and seed yield that can be unconsciously selected for. Computer vision offers an alternative to conventional phenotyping, enabling higher throughput and reducing subjectivity. These approaches provide valuable insights into the determinants of seed yield, and thus, aid breeding decisions.

RESULTS

Here, we described SpykProps, an inexpensive Python-based imaging system to quantify morphological properties in unilateral inflorescences, that was developed and tested on images of perennial grass (Lolium perenne L.) spikes. SpykProps is able to rapidly and accurately identify spikes (RMSE < 1), estimate their length (R2 = 0.96), and number of spikelets (R2 = 0.61). It also quantifies color and shape from hundreds of interacting descriptors that are accurate predictors of architectural and agronomic traits such as seed yield potential (R2 = 0.94), rachis weight (R2 = 0.83), and seed shattering (R2 = 0.85).

CONCLUSIONS

SpykProps is an open-source platform to characterize inflorescence architecture in a wide range of grasses. This imaging tool generates conventional and latent traits that can be used to better characterize developmental and agronomic traits associated with inflorescence architecture, and has applications in fields that include breeding, physiology, evolution, and development biology.

Identification and expression analysis of the KNOX genes during organogenesis and stress responseness in Camellia sinensis (L.) O. Kuntze

Tea plant (Camellia sinensis L.), whose leaves are the major reproductive organs, has been cultivated and consumed widely for its economic and health benefits. The Knotted1-like Homeobox (KNOX) proteins play significant roles in leaf morphology formation and development. However, the functions of KNOX proteins in tea plants are still unknown. Here, 11 CsKNOX genes from the tea plants were cloned and divided into Class I, II, and KNATM clades based on their protein sequences. These 11 CsKNOX genes were mapped on 8 out of 15 tea plant chromosomes, all localized in the nucleus. Specific spatiotemporal expression patterns of CsKNOX genes were found in various tissues and different development periods of buds, flowers, and roots of tea plants. Meanwhile, transcript levels of CsKNOX in tea leaves were strongly correlated with the accumulation of flavan-3-ols and proanthocyanidins. It was found that most of the CsKNOX genes could respond to drought, salt, cold, and exogenous MeJA and GA3 by analysis of transcriptomics data and promoter elements. The protein interaction analysis showed that CsKNOX could cooperate with CsAS1 and other critical functional proteins. In conclusion, this research provided the basic information for the functions of the CsKNOX family during organogenesis and stress response in tea plants, which was necessary for further functional characterization verification.

Drought stress-induced the formation of heteromorphic leaves of Populus euphratica Oliv: evidence from gene transcriptome

Populus euphratica Oliv., a dominant species of arid desert community, grows heteromorphic leaves at different crown positions. Whether heteromorphic leaves are a strategy of plant adaptation to drought stress is rarely reported. This study sequenced the transcriptome of three typical heteromorphic leaves (lanceolate, ovate and broad-ovate leaves) of P. euphratica, and measured their drought stress. We wanted to reveal the molecular mechanisms underlying the formation of heteromorphic leaves. Drought stress was increased significantly from lanceolate to ovate to broad-ovate leaves. Gene ontology (GO) and KEGG enrichment analysis showed that the MADs-box gene regulated the expression of peroxidase (POD) in the phenylpropane biosynthetic pathway. The up-regulated expression of the chalcone synthase (CHS) gene in broad-ovate leaves significantly activated the flavonoid biosynthetic pathway. In the process of leaf shape change, the different expressions of homeodomain leucine zipper (HD-ZIP) among the three heteromorphic leaves had potential interactions on the AUX and ABA pathways. The expression of Sucrose phosphate synthase (SPS) and sucrose synthase (SUS) increased from lanceolate to broad-ovate leaves, resulting in a consistent change in starch and sucrose content. We concluded that these resistance-related pathways are expressed in parallel with leaf formation genes, thereby inducing the formation of heteromorphic leaves. Our work provided a new insights for desert plants to adapt to drought stress.

Marginal leaf galls on Pliocene leaves from India indicate mutualistic behavior between Ipomoea plants and Eriophyidae mites

We report a new type of fossil margin galls arranged in a linear series on dicot leaf impressions from the latest Neogene (Pliocene) sediments of the Chotanagpur Plateau, Jharkhand, eastern India. We collected ca. 1500 impression and compression leaf fossils, of which 1080 samples bear arthropod damage referable to 37 different damage types (DT) in the 'Guide to Insect (and Other) Damage Types in Compressed Plant Fossils'. A few leaf samples identified as Ipomoea L. (Convolvulaceae) have specific margin galls that do not match any galling DT previously described. This type of galling is characterized by small, linearly arranged, irregular, sessile, sub-globose, solitary, indehiscent, solid pouch-galls with irregular ostioles. The probable damage inducers of the present galling of the foliar margin might be members of Eriophyidae (Acari). The new type of gall suggests that marginal gall-inducing mites on leaves of Ipomoea did not change their host preference at the genus level since the Pliocene. The development of marginal leaf galling in Ipomoea is linked to extrafloral nectaries that do not offer protection against arthropod galling but indirectly protect the plant against herbivory from large mammals.

Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies

PREMISE

The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification.

METHODS AND RESULTS

MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold-based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner.

CONCLUSIONS

MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.

Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.

Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea

Purple leaf veins and leaf edge cracks comprise the typical leaf phenotype of Brassica juncea; however, the molecular mechanisms and metabolic pathways of the formation of purple leaf veins and leaf edge cracks remain unclear. In this study, transcriptome and metabolome analyses were conducted to explore the regulation pathway of purple leaf vein and leaf edge crack formation based on four mustard samples that showed different leaf colors and degrees of cracking. The results showed genes with higher expression in purple leaf veins were mainly enriched in the flavonoid biosynthesis pathway. Integrating related genes and metabolites showed that the highly expressed genes of ANS (BjuA004031, BjuB014115, BjuB044852, and BjuO009605) and the excessive accumulation of dihydrokaempferol and dihydroquercetin contributed to the purple leaf veins by activating the synthetic pathways of pelargonidin-based anthocyanins and delphinidin-based anthocyanins. Meanwhile, “alpha-farnesene synthase activity” and “glucan endo-1, 3-beta-D-glucosidase activity” related to the adversity were mainly enriched in the serrated and lobed leaves, indicating that the environmental pressure was the dominant factor controlling the change in leaf shape. Overall, these results provided new insights into the regulation pathways for formation of purple leaf veins and leaf edge cracks, which could better accelerate the theoretical research on purple leaf vein color and leaf edge cracks in mustard.

Pilot Cultivation of the Vulnerable Cretan Endemic Verbascum arcturus L. (Scrophulariaceae): Effect of Fertilization on Growth and Quality Features

The domestication of wild-growing plants, including cultivation and fertilization protocols, is able to alleviate the ecological risks posed by the uncontrolled harvesting of range-restricted local endemic plants. In this field study focused on Verbascum arcturus, a vulnerable local endemic of Crete (Greece), the effect of two kinds of fertilization applied by two methods (foliar/root) was investigated. The foliar application included conventional or integrated nutrient management (INM) fertilization. Root application included the application of conventional fertilizers, biostimulants, or INM with biostimulants. Several properties of plant growth, physiology and nutrition were determined. The results showed that fertilization treatment affected neither leaf color and shape nor plant growth, morphology, dry mass partitioning or nutrient content. However, both kinds of foliar-applied fertilization enhanced Zn and B in leaves and soil-applied biostimulant increased leaf Ca. Considering both chlorophyll and antioxidant compounds’ content, foliar application of the INM fertilizers, as well as soil application of the conventional fertilizers or biostimulants, could be considered as accepted options. This study reports for the first time an assessment of the total phenolic and flavonoids content evidenced in V. arcturus and encourages the use of fertilization in promoting the herbal antioxidant profile without compromising visual quality or yield. The findings of this study could be considered as a documented contribution toward the sustainable exploitation of V. arcturus.

Potential Effects of Sweet Potato (Ipomoea batatas) in Hyperglycemia and Dyslipidemia-A Systematic Review in Diabetic Retinopathy Context

Hyperglycemia is a condition with high glucose levels that may result in dyslipidemia. In severe cases, this alteration may lead to diabetic retinopathy. Numerous drugs have been approved by officials to treat these conditions, but usage of any synthetic drugs in the long term will result in unavoidable side effects such as kidney failure. Therefore, more emphasis is being placed on natural ingredients due to their bioavailability and absence of side effects. In regards to this claim, promising results have been witnessed in the usage of Ipomoea batatas (I. batatas) in treating the hyperglycemic and dyslipidemic condition. Thus, the aim of this paper is to conduct an overview of the reported effects of I. batatas focusing on in vitro and in vivo trials in reducing high glucose levels and regulating the dyslipidemic condition. A comprehensive literature search was performed using Scopus, Web of Science, Springer Nature, and PubMed databases to identify the potential articles on particular topics. The search query was accomplished based on the Boolean operators involving keywords such as (1) Beneficial effect OR healing OR intervention AND (2) sweet potato OR Ipomoea batatas OR traditional herb AND (3) blood glucose OR LDL OR lipid OR cholesterol OR dyslipidemia. Only articles published from 2011 onwards were selected for further analysis. This review includes the (1) method of intervention and the outcome (2) signaling mechanism involved (3) underlying mechanism of action, and the possible side effects observed based on the phytoconstiuents isolated. The comprehensive literature search retrieved a total of 2491 articles using the appropriate keywords. However, on the basis of the inclusion and exclusion criteria, only 23 articles were chosen for further review. The results from these articles indicate that I. batatas has proven to be effective in treating the hyperglycemic condition and is able to regulate dyslipidemia. Therefore, this systematic review summarizes the signaling mechanism, mechanism of action, and phytoconstituents responsible for those activities of I. batatas in treating hyperglycemic based on the in vitro and in vivo study.

Genomic Analyses of Phenotypic Differences Between Native and Invasive Populations of Diffuse Knapweed (Centaurea diffusa)

Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed [Centaurea diffusa Lam. (Asteraceae)]. To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7,058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.

Leaf shape in Populus tremula is a complex, omnigenic trait

Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.

Leaf shape is a predictor of fruit quality and cultivar performance in tomato

Commercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits. Here the role of leaf morphology was investigated for its impact on fruit quality. Heirloom cultivars were grown in field conditions, and BRIX by yield (BY) and other traits were measured over a 14-wk period. The complex relationships among these morphological and physiological traits were evaluated using partial least-squares path modeling, and a consensus model was developed. Photosynthesis contributed strongly to vegetative biomass and sugar content of fruits but had a negative impact on yield. Conversely leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield. Cultivars such as Stupice and Glacier, with very round leaves, had the highest performance in both fruit sugar and yield. Our model accurately predicted BY for two commercial cultivars using leaf shape data as input. This study revealed the importance of leaf shape to fruit quality in tomato, with rounder leaves having significantly improved fruit quality. This correlation was maintained across a range of diverse genetic backgrounds and shows the importance of leaf morphology in tomato crop improvement.