Sporogenesis and gametogenesis (later defined as “sporulation”) in Ulva species are important stages of their life cycle. However, the developmental and environmental factors controlling Ulva sporulation are poorly understood. In the present study we evaluated six protocols involving abiotic stresses, i.e. fragmentation, dehydration, chemical stress, nutrient starvation and cold shock, to induce the formation of reproductive tissues in strains from three Ulva species, Ulva lacinulata, Ulva compressa, and Ulva intestinalis. The most successful protocol combined fragmentation, cold shock (4 °C for 1 h) and nutrient depletion, achieving an overall success rate of 80%, across 32 Ulva strains, where U. compressa, U. intestinalis, and U. lacinulata exhibited success rates of 100%, 80% and 70%, respectively. The mean final reproductive tissue percentage (RT%), defined as the maximum percentage of cells within a thallus undergoing sporulation, did not differ significantly among the three species. However, U. compressa, gametophytes (n = 8) exhibited significantly higher mean RT% than sporophytes (n = 6), with values of 91.0 ± 8.1% and 66.2 ± 11.4%, respectively. Also, the gametophytes of U. compressa exhibited earlier sporulation onset (day 3) relative to sporophytes (day 6). The difference in duration of sporulation between U. lacinulata and U. compressa was statistically insignificant. Our findings provide new insights into the species and life stage specific responses of Ulva to abiotic stresses, and offer a reliable protocol for inducing reproduction in three Ulva species.

Abstract The sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and North-East Pacific but genetic improvement has been hindered by limited understanding of the genetic basis of economically important traits. We conducted the first genome-wide association study (GWAS) for this species using 202 self-fertilised pseudo-F1 individuals derived from 12 populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD-seq-derived SNP markers and phenotyped in a common garden experiment for four morphological traits (blade length, blade width, blade area, stipe length) and six metabolic traits related to nitrogen metabolism. We identified 26 significant marker-trait associations, with phenotypic variance explained (PVE) ranging from 0.65% to 52.44%. Major-effect loci were detected for blade width (52.44% PVE) and blade area (45.22% PVE) and a locus on chromosome 17 influenced both blade length and blade area. Marker-based heritability estimates ranged from 0.75 to 0.99 for morphological traits and from 0.00 to 0.99 for metabolic traits, though with large standard errors. Cross-validation of genomic selection models yielded predictive abilities of 0.21-0.59 across traits. Our findings reveal a mixed genetic architecture with major-effect loci suitable for marker-assisted selection and polygenic traits amenable to genomic selection, providing a foundation for genomics-assisted breeding programs in kelp aquaculture.

The rhodophyte Palmaria palmata (L.) Weber & Mohr is one of the target species of a growing European seaweed industry due to its high content of protein and essential amino acids which makes it suitable for human food, dietary supplements, and as salmon feed. However, the lack of a published nuclear genome limits phylogenetics analyses and gene function investigations which could help the development of a breeding programme. We present the first draft genome of P. palmata that was obtained with PacBio HiFi long read sequencing with average coverage of 10x, consisting of an assembly of 1.05 Gb, N50 = 2.75 Mb and BUSCO completeness of 72.1 %. This is the third largest genome in the Rhodophyta so far, characterized by the highest percentage of repeat elements, 91.3 %. The number of protein coding genes, 9641, two thirds of which are single-exon, is similar to that of other Florideophyceae. This number is far below land plants (ca 25-30,000), and lost protein-coding genes span all biological functions, with the exception of nucleotide metabolism. Reproduction and organogenesis were the most affected, with 98 and 97 % missing genes, respectively. Additionally, a population study on the whole genome of 33 P. palmata individuals from across the Northern East Atlantic area found three main clusters largely consistent with their geographic distribution. These results represent a fundamental step towards breeding and genetic studies to further explore the vastly unexploited economic potential of Palmaria palmata.

The transition from interbreeding populations to species continues to represent difficult terrain for phylogenetic investigations. Genotyping entire genomes holds promise for enhancing insights into the process of speciation and evolutionary relationships among recently speciated taxa. Northeast Pacific ribbon kelp was once recognized as four species before they were folded into Alaria marginata based on DNA barcodes, although several lineages continue to be recognized. We used whole genome sequencing to determine whether these lineages represente species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (United States) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of Alaria. Our analysis of >3.4 million single nucleotide polymorphisms reaffirmed that organellar and nuclear phylogenetic signals are incongruent in Alaria, producing different topologies among five organellar and six nuclear A. marginata lineages. Lineages appeared to be reproductively isolated, as evidenced by strong clustering and lack of recent admixture across nuclear genomes. Genetic divergence between A. marginata lineages also exceeded intra-lineage divergence, proxied by A. esculenta populations, but fell short of distances observed across other species of Alaria. Despite the genomic data supporting predictions of the biological and genetic species concepts, we encountered inherent limitations in declaring species status. While our work shifts taxonomic conversations toward a genome-scale framework that provides a more comprehensive picture of divergence and connectivity, our work also highlights that philosophical challenges inherent to defining species persist and that integrative approaches continue to be necessary in the genomic era.

Saccharina latissima is an important species for the emerging seaweed aquaculture industry in the northern Atlantic. In this study, genotype and phenotype data for a segregating F2 family was used to generate a high-density genetic map for S. latissima and to identify temperature-stress-related quantitative trait loci (QTLs). A temperature stress experiment detected distinct phenotypic classes with different stress responses within the F2 family and these phenotypic classes were shown to exhibit different transcriptomic responses to heat stress. The existence of heat tolerant, resilient and sensitive individuals within this segregating family indicates that it should be possible to breed temperature tolerant strains of S. latissima. This conclusion was supported by the identification of three QTLs that influenced recovery after temperature stress. The results of this study and the resources generated, in particular the high-density genetic map, represent an important foundation for future S. latissima breeding programs.

The uptake of sodium selenite (Se(IV)) and sodium selenate (Se(VI)) from aqueous medium by Lemna minor L. and the influence of different Se concentrations on its growth, morphological and ultrastructural characteristics were studied. L. minor was grown at different concentrations (1, 3, 5 and 10 mg L-1) of Se(IV) and Se(IV). The Se(IV) concentration in the plant tissue ranged between 77.7 (+/- 4.3) to 453 (+/- 0) mg kg(-1) DW. The Se(VI) concentration in plant tissues ranged between 117 (+/- 11) to 417 (+/- 2) mg kg(-1) DW. The highest bioconcentration factor for Se(VI) was 127 (+/- 7) at 3 mg/L, with a Se removal efficiency of 44%. For Se(IV), the highest bioconcentration factor was 77.7 (+/- 4.3) at 1 mg L-1, which had a Se removal efficiency of 23%. Growth of L. minor was suppressed at 10 mg L-1 Se in both forms. The addition of Se promoted the formation of starch granules in L. minor which occupied a chloroplast area of 74% for Se(IV) and 77% for Se(VI). The efficient uptake of both Se forms by L. minor indicates the potential application of this species for phytoremediation of Se laden wastewaters and its use as an alternative feedstock in biofuel production. [GRAPHICAL ABSTRACT]

Image analysis is widely used in plant biology to determine growth rates and other phenotypic characters, with segmentation into foreground and background being a primary challenge. Statistical clustering and learning approaches can reduce the need for user input into this process, though these are computationally demanding, can generalise poorly and are not intuitive to end users. As such, simple strategies that rely on the definition of a range of target colors are still frequently adopted. These are limited by the geometries in color space that are implicit to their definition; i.e. thresholds define cuboid volumes and selected colors with a radius define spheroid volumes. A more comprehensive specification of target color is a hull, in color space, enclosing the set of colors in the image foreground. We developed AlGrow, a software tool that allows users to easily define hulls by clicking on the source image or a three-dimensional projection of its colors. We implemented convex hulls and then alpha-hulls, i.e. a limit applied to hull edge length, to support concave surfaces and disjoint color volumes. AlGrow also provides automated annotation by detecting internal circular markers, such as pot margins, and applies relative indexes to support movement. Analysis of publicly available Arabidopsis image series and metadata demonstrated effective automated annotation and mean Dice coefficients of >0.95 following training on only the first and last images in each series. AlGrow provides both graphical and command line interfaces and is released free and open-source with compiled binaries for the major operating systems.

The sea lettuce Ulva spp is becoming an increasingly important macroalgae for aquaculture. Sea lettuce can be grown on- and off-shore, displays high growth rates, and its biomass possesses attractive nutritional benefits. Among those are their fatty acids (FA) and lipid profiles, rich in omega 3 Polyunsaturated Fatty Acids (PUFAs) as well as bioactive lipids. In order to tailor those properties for food applications, we explored the use of a short-term (seven days) low salinity treatment to modulate the lipid profile of two species of Ulva. We found large quantitative differences between species, and while a low-salinity treatment negatively affected growth, Ulva australis' lipid profile was positively impacted. Total FA particularly ɷ-3 PUFAs, increased three-fold, as well as most polar lipid species including known bioactive compounds. This study highlights profound differences between species and describes a simple method to increase the nutritional properties of Ulva biomass for food applications.

Sea lettuce (Ulva) is recognised for its potential in food, pharmaceutical, nutraceutical, biorefinery and bioremediation industries and is increasingly being cultivated. The requirements of those industries vary widely in terms of biomass composition. Ulva biomass composition and growth is known to be directly influenced by environmental factors, e.g., temperature, light, salinity, nutrient availability as well as by genetic factors and likely by microbiome composition. In order to select for the highest yielding strains in a given environment, we tested the suitability of common-garden experiments, i.e., the co-cultivation of different strains grown under shared conditions. Fifteen strains from six different foliose Ulva species were grown together under two different salinities, 35 ppt and 15 ppt. After 32 days, only U. australis strains remained at both salinities. If selection at low salinity was mostly based on survival, the selection process at seawater salinity was driven by competition, largely based on growth performance. Growth rates after a month were very similar at both salinities, suggesting the U. australis strains cope equally well in either condition. However, the composition of the biomass produced in both environments varied, with the content of all organic compounds being higher at low salinity, and the ash content being reduced in average by 66%. To summarize, this study provides an established bulk-selection protocol for efficiently screening large numbers of locally-sourced strains and highlights the potential of low salinity treatments for increased organic matter content, particularly in carbohydrates.

Light quality is a key factor affecting algal growth and biomass composition, particularly pigments such as carotenoids, known for their antioxidant properties. Light-emitting diodes (LEDs) are becoming a cost-effective solution for indoor seaweed production when compared to fluorescent bulbs, allowing full control of the light spectra. However, knowledge of its effects on Ulva biomass production is still scarce. In this study, we investigated the effects of LEDs on the phenotype of an Ulva lacinulata strain, collected on the Northern Portuguese coast. Effects of white (W), green (G), red (R), and blue (B) LEDs were evaluated for growth (fresh weight and area), photosynthetic activity, sporulation, and content of pigments and antioxidant compounds. The results showed that there were no significant differences in terms of fresh weight accumulation and reduced sporulation among the tested LEDs, while W light induced the highest expansion rate. Under G, U. lacinulata attained a quicker photoacclimation, and the highest content of pigments and total antioxidant activity; but with R and W, antioxidant compounds against the specific radicals O2•− and •NO were produced in a higher content when compared to other LEDs. Altogether, this study demonstrated that it is possible to modulate the bioactive properties of U. lacinulata by using W, R, and G light, opening the path to the production of biomass tailored for specific nutraceutical applications.

Sea lettuce (Ulva) is a genus of green macroalgae present along all the coasts of the world's oceans. It represents about 100 species with diverse habitats. Inter- and intra-species natural variation is very large, both in terms of growth characteristics and biomass biochemical composition. As a result, Ulva biomass has a wide range of applications and strain selection can achieve significant increases in yield(s). Establishing solid, long term and cost-effective methodologies for the conservation of Ulva genetic diversity is then required to safeguard and reuse selected strains. Here, we report a cryopreservation-based protocol for the long-term preservation of foliose Ulva strains. Strains from seven different Ulva species were cryopreserved for 15 and/or 120 days in liquid nitrogen, and of the 3 replicates cryopreserved, at least one survived, allowing us to successfully recover all strains. On average, among all specimen cryo-preserved, 82% of them survived and grew post cryo-preservation.

AbstractThe rhodophytePalmaria palmata(L.) Weber & Mohr is one of the target species of a growing European seaweed industry due to its high content of protein and essential amino acids which makes it suitable for human food, dietary supplements, and as salmon feed. However, the lack of a published nuclear genome limits phylogenetics analyses and gene function investigations which could help the development of a breeding programme.We present the first draft genome ofP. palmatathat was obtained with PacBio HiFi long read sequencing with average coverage of 10×, consisting of an assembly of 1.05 Gb, N50=2.75Mb and BUSCO completeness of 72.1%. Additionally, a population study on the whole genome of 33P. palmataindividuals from across the Northern East Atlantic area found three main clusters consistent with their geographic distribution: (1) Denmark and Norway, (2) France and western Ireland, (3) Faroe Islands. All individuals from Northern Ireland share ancestry with western Ireland and Denmark, and some individuals from the Faroe Islands show admixture from Faroe, western Ireland and Northern Ireland. These results represent a fundamental step towards breeding and genetic studies to further explore the vastly unexploited economic potential ofPalmaria palmata.Highlights- We report the first draft genome ofPalmaria palmata, from PacBio HiFi long reads.- The size of the genome, 1.05 Gb, is among the largest so far among the Rhodophyta.- Busco completeness of 72.1% and contig N50 of 2.75 Mb indicate good quality.- The genomes of 33 more individuals from North Atlantic Europe have been sequenced.- Phylogenetic analysis found three clusters consistent with geographic distribution.

Lettuce (Lactuca sativa L.) is one of the commercially important leafy vegetables worldwide. However, lettuce cultivars vary widely in their carotenoid concentrations at the time of harvest. While the carotenoid content of lettuce can depend on transcript levels of key biosynthetic enzymes, genes that can act as biomarkers for carotenoid accumulation at early stages of plant growth have not been identified. Transcriptomic and metabolomic analysis was performed on the inner and outer leaves of the six cultivars at different developmental stages to identify gene-to-metabolite networks affecting the accumulation of two key carotenoids, β-carotene and lutein. Statistical analysis, including principal component analysis, was used to better understand variations in carotenoid concentration between leaf age and cultivars. Our results demonstrate that key enzymes of carotenoid biosynthesis pathway can alter lutein and β-carotene biosynthesis across commercial cultivars. To ensure high carotenoids content in leaves, the metabolites sink from β-carotene and lutein to zeaxanthin, and subsequently, abscisic acid needs to be regulated. Based on 2–3-fold carotenoids increase at 40 days after sowing (DAS) as compared to the seedling stage, and 1.5–2-fold decline at commercial stage (60 DAS) compared to the 40 DAS stage, we conclude that the value of lettuce for human nutrition would be improved by use of less mature plants, as the widely-used commercial stage is already at plant senescence stage where carotenoids and other essential metabolites are undergoing degradation.

Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.

Fruit pungency is caused by the accumulation of capsaicinoids, secondary metabolites whose relation to primary metabolism remains unclear. We have selected ten geographically diverse accessions of Capsicum chinense Jacq with different pungency levels. A detailed metabolic profile was conducted in the fruit placenta and pericarp at 20, 45, and 60 days after anthesis aiming at increasing our understanding of the metabolic changes in these tissues across fruit development and their potential connection to capsaicin metabolism. Overall, despite the variation in fruit pungency among the ten accessions, the composition and metabolite levels in both placenta and pericarp were uniformly stable across accessions. Most of the metabolite variability occurred between the fruit developmental stages rather than among the accessions. Interestingly, different metabolite adjustments in the placenta were observed among pungent and non-pungent accessions, which seem to be related to differences in the genetic background. Furthermore, we observed high coordination between metabolites and capsaicin production in C. chinense fruits, suggesting that pungency in placenta is adjusted with primary metabolism.

Fructans are carbohydrates present in more than 15% of flowering plants. They represent the major pool of carbohydrates in some species, especially when facing cold or drought. However, the functions of fructans with high or low degrees of polymerization (DP), their diurnal use, and the regulation of their synthesis and degradation in response to stresses still remain unclear. Here we present an enzymatic protocol adapted to 96-well microplates that simultaneously allows the determination of fructans and glucose, fructose, and sucrose. Moreover, the protocol allows to estimate the average DP of the fructans in the samples. The protocol is based on the enzymatic degradation of fructans into glucose and fructose and their subsequent conversion into gluconate 6-phosphate concomitant with the formation of NADH in the presence of ATP.

SUMMARY Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species ( Solanum lycopersicum ). Several, including Solanum lycopersicoides , have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome‐scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein‐coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity‐associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides , which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β‐cyclase whose function we demonstrate.

The genus Ulva comprises a large number of species widespread in the world, several of which are of commercial value, mainly for their nutritional benefits. However, identifying Ulva species is notoriously difficult, which largely explains why very few studies have attempted to characterize physiological and nutritional differences within the genus. If environmental modulation of seaweed lipid biomass composition for a number of species is well-documented, much less is known about genetic-driven differences in lipid profiles within a species or a genus. In this study, we analyzed the lipid profile of strains belonging to three species of foliose Ulva grown in the same conditions. Fatty acid profiling revealed the presence of 25 different fatty acids, palmitic acid being the most abundant fatty acid (FA) present in all species (35.1–41.2%). Important differences between the three species studied (U. australis, U. lacinulata and U. rigida) were observed. U. lacinulata had a higher content of saturated FA and a lower content of n-3 FA, suggesting that U. australis and U. rigida have a higher nutritional value. In contrast, Ulva lacinulata exhibited the lowest n-6/n-3 ratio, an increasingly important nutritional parameter, at the expense of decreased contents in both n-6 and n-3 FAs. A comprehensive analysis of the polar lipidome showed differences in the composition of complex lipids. Major differences were found within the class of sulfolipids, which are specific to chloroplast membranes, and have been proposed as bioactive lipids. Ulva rigida contained high relative amounts of SQDG(32:2) and SQDG(36:5), although a low content of SQMG (16:0), which are sulfolipid species that have been described as having biological activity. Therefore, detailed lipid profiling highlighted inter-specific differences, contributing to a better understanding of the physiology of the species studied, while also highlighting their potential as sources of molecular lipid species with bioactivity and nutritional benefits.

Sea lettuce (Ulva spp.), with its worldwide distribution and remarkable ability to grow rapidly under various conditions, represents an important natural resource that is still under-exploited. Its biomass can be used for a wide range of applications in the food/feed, pharmaceutical, nutraceutical, biofuel, and bioremediation industries. However, knowledge of the factors affecting Ulva biomass yield and composition is far from complete. Indeed, the respective contributions of the microbiome, natural genetic variation in Ulva species, environmental conditions and importantly, the interactions between these three factors on the Ulva biomass, have been only partially elucidated. Further investigation is important for the implementation of large-scale Ulva aquaculture, which requires stable and controlled biomass composition and yields. In this review, we document Ulva biomass composition, describe the uses of Ulva biomass and we propose different strategies for developing a sustainable and profitable Ulva aquaculture industry.