Making watercress (Nasturtium officinale) cropping sustainable: genomic insights into enhanced phosphorus use efficiency in an aquatic crop.

Watercress (Nasturtium officinale) is a nutrient-dense salad crop with high antioxidant capacity and glucosinolate concentration and with the potential to contribute to nutrient security as a locally grown outdoor aquatic crop in northern temperate climates. However, phosphate-based fertilizers used to support plant growth contribute to the eutrophication of aquatic habitats, often pristine chalk streams, downstream of farms, increasing pressure to minimize fertilizer use and develop a more phosphorus-use efficient (PUE) crop. Here, we grew genetically distinct watercress lines selected from a bi-parental mapping population on a commercial watercress farm either without additional phosphorus (P-) or under a commercial phosphate-based fertilizer regime (P+), to decipher effects on morphology, nutritional profile, and the transcriptome. Watercress plants sustained shoot yield in P- conditions, through enhanced root biomass, but with shorter stems and smaller leaves. Glucosinolate concentration was not affected by P- conditions, but both antioxidant capacity and the concentration of sugars and starch in shoot tissue were enhanced. We identified two watercress breeding lines, with contrasting strategies for enhanced PUE: line 60, with highly plastic root systems and increased root growth in P-, and line 102, maintaining high yield irrespective of P supply, but less plastic. RNA-seq analysis revealed a suite of genes involved in cell membrane remodeling, root development, suberization, and phosphate transport as potential future breeding targets for enhanced PUE. We identified watercress gene targets for enhanced PUE for future biotechnological and breeding approaches enabling less fertilizer inputs and reduced environmental damage from watercress cultivation.

The genetic basis of water-use efficiency and yield in lettuce.

BACKGROUND: Water supply limits agricultural productivity of many crops including lettuce. Identifying cultivars within crop species that can maintain productivity with reduced water supply is a significant challenge, but central to developing resilient crops for future water-limited climates. We investigated traits known to be related to water-use efficiency (WUE) and yield in lettuce, a globally important leafy salad crop, in a recombinant inbred line (RIL) lettuce mapping population, produced from a cross between the cultivated Lactuca sativa L. cv. Salinas and its wild progenitor L. serriola L. RESULTS: Wild and cultivated lettuce differed in their WUE and we observed transgressive segregation in yield and water-use traits in the RILs. Quantitative trait loci (QTL) analysis identified genomic regions controlling these traits under well-watered and droughted conditions. QTL were detected for carbon isotope discrimination, transpiration, stomatal conductance, leaf temperature and yield, controlling 4-23 % of the phenotypic variation. A QTL hotspot was identified on chromosome 8 that controlled carbon isotope discrimination, stomatal conductance and yield under drought. Several promising candidate genes in this region were associated with WUE, including aquaporins, late embryogenesis abundant proteins, an abscisic acid-responsive element binding protein and glutathione S-transferases involved in redox homeostasis following drought stress were also identified. CONCLUSIONS: For the first time, we have characterised the genetic basis of WUE of lettuce, a commercially important and water demanding crop. We have identified promising candidate genomic regions determining WUE and yield under well-watered and water-limiting conditions, providing important pre-breeding data for future lettuce selection and breeding where water productivity will be a key target.

Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra.

Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential. The three poplar genotypes differed in wood anatomy, lignin content and saccharification potential. Drought resulted in reduced cambial activity, decreased vessel and fiber lumina, and increased the saccharification potential. The saccharification potential was unrelated to lignin content as well as to most wood anatomical traits. RNA sequencing of the developing xylem revealed that 1.5% of the analyzed genes were differentially expressed in response to drought, while 67% differed among the genotypes. Weighted gene correlation network analysis identified modules of co-expressed genes correlated with saccharification potential. These modules were enriched in gene ontology terms related to cell wall polysaccharide biosynthesis and modification and vesicle transport, but not to lignin biosynthesis. Among the most strongly saccharification-correlated genes, those with regulatory functions, especially kinases, were prominent. We further identified transcription factors whose transcript abundances differed among genotypes, and which were co-regulated with genes for biosynthesis and modifications of hemicelluloses and pectin. Overall, our study suggests that the regulation of pectin and hemicellulose metabolism is a promising target for improving wood quality of second generation bioenergy crops. The causal relationship of the identified genes and pathways with saccharification potential needs to be validated in further experiments.

Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.).

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. 'North eastern' genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ(13)C. In contrast, 'southern' genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1-3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.

Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery.

Thermal imaging has been used in the past for remote detection of regions of canopy showing symptoms of stress, including water deficit stress. Stress indices derived from thermal images have been used as an indicator of canopy water status, but these depend on the choice of reference surfaces and environmental conditions and can be confounded by variations in complex canopy structure. Therefore, in this work, instead of using stress indices, information from thermal and visible light imagery was combined along with machine learning techniques to identify regions of canopy showing a response to soil water deficit. Thermal and visible light images of a spinach canopy with different levels of soil moisture were captured. Statistical measurements from these images were extracted and used to classify between canopies growing in well-watered soil or under soil moisture deficit using Support Vector Machines (SVM) and Gaussian Processes Classifier (GPC) and a combination of both the classifiers. The classification results show a high correlation with soil moisture. We demonstrate that regions of a spinach crop responding to soil water deficit can be identified by using machine learning techniques with a high accuracy of 97%. This method could, in principle, be applied to any crop at a range of scales.

Olig1 and Sox10 interact synergistically to drive myelin basic protein transcription in oligodendrocytes.

The oligodendrocyte lineage genes (Olig1/2), encoding basic helix-loop-helix transcription factors, were first identified in screens for master regulators of oligodendrocyte development. OLIG1 is important for differentiation of oligodendrocyte precursors into myelin-forming oligodendrocytes during development and is thought to play a crucial role in remyelination during multiple sclerosis. However, it is still unclear how OLIG1 interacts with its transcriptional cofactors and DNA targets. OLIG1 was reportedly restricted to mammals, but we demonstrate here that zebrafish and other teleosts also possess an OLIG1 homolog. In zebrafish, as in mammals, Olig1 is expressed in the oligodendrocyte lineage. Olig1 associates physically with another myelin-associated transcription factor, Sox10, and the Olig1/Sox10 complex activates mbp (myelin basic protein) transcription via conserved DNA sequence motifs in the mbp promoter region. In contrast, Olig2 does not bind to Sox10 in zebrafish, although both OLIG1 and OLIG2 bind SOX10 in mouse.

A regulatory network involving Foxn4, Mash1 and delta-like 4/Notch1 generates V2a and V2b spinal interneurons from a common progenitor pool.

In the developing central nervous system, cellular diversity depends in part on organising signals that establish regionally restricted progenitor domains, each of which produces distinct types of differentiated neurons. However, the mechanisms of neuronal subtype specification within each progenitor domain remain poorly understood. The p2 progenitor domain in the ventral spinal cord gives rise to two interneuron (IN) subtypes, V2a and V2b, which integrate into local neuronal networks that control motor activity and locomotion. Foxn4, a forkhead transcription factor, is expressed in the common progenitors of V2a and V2b INs and is required directly for V2b but not for V2a development. We show here in experiments conducted using mouse and chick that Foxn4 induces expression of delta-like 4 (Dll4) and Mash1 (Ascl1). Dll4 then signals through Notch1 to subdivide the p2 progenitor pool. Foxn4, Mash1 and activated Notch1 trigger the genetic cascade leading to V2b INs, whereas the complementary set of progenitors, without active Notch1, generates V2a INs. Thus, Foxn4 plays a dual role in V2 IN development: (1) by initiating Notch-Delta signalling, it introduces the asymmetry required for development of V2a and V2b INs from their common progenitors; (2) it simultaneously activates the V2b genetic programme.

A screen for mutations in zebrafish that affect myelin gene expression in Schwann cells and oligodendrocytes.

Myelin is the multi-layered glial sheath around axons in the vertebrate nervous system. Myelinating glia develop and function in intimate association with neurons and neuron-glial interactions control much of the life history of these cells. However, many of the factors that regulate key aspects of myelin development and maintenance remain unknown. To discover new molecules that are important for glial development and myelination, we undertook a screen of zebrafish mutants with previously characterized neural defects. We screened for myelin basic protein (mbp) mRNA by in situ hybridization and identified four mutants (neckless, motionless, iguana and doc) that lacked mbp expression in parts of the peripheral and central nervous systems (PNS or CNS), despite the presence of axons. In all four mutants electron microscopy revealed that myelin-forming glia were present and had formed loose wraps around axons but did not form compact myelin. We found that addition of exogenous retinoic acid (RA) rescued mbp expression in neckless mutant embryos, which lack endogenous RA synthesis. Timed application of the RA synthesis inhibitor DEAB to wild type embryos showed that RA signalling is required at least 48 h before the onset of myelin protein synthesis in both CNS and PNS.

Expression of defective proventriculus during head capsule development is conserved in Drosophila and stalk-eyed flies (Diopsidae).

Hypercephaly, in the form of lateral extensions of the head capsule, is observed in several families of Diptera. A particularly exaggerated form is found in Diopsid stalk-eyed flies, in which both eyes and antennae are laterally displaced at the end of stalks. The processes of early development and specification of the head capsule in stalk-eyed flies are similar to those in Drosophila melanogaster. In Drosophila the homeobox gene ocelliless (oc) shows a mediolateral gradient of expression across the region of the eye-antennal imaginal disc that gives rise to the head capsule and specifies the development of different head structures. The genes and developmental mechanisms that subsequently define head shape in Drosophila and produce hypercephaly in stalk-eyed flies remain unclear. To address this, we performed an enhancer trap screen for Drosophila genes expressed in the same region as oc and identified the homeobox gene defective proventriculus (dve). In the eye-antennal imaginal disc, dve is coexpressed with oc in the region that gives rise to the head capsule and is active along the medial edge of the antennal disc and in the first antennal segment. Analyses of dve expression in mutant eye-antennal discs are consistent with it acting downstream of oc in the development of the head capsule. We confirm that orthologues of dve are present in a diverse panel of five stalk-eyed fly species and analyse patterns of dve sequence variation within the clade. Our results indicate that dve expression and sequence are both highly conserved in stalk-eyed flies.

Delayed expression of the Crx gene and photoreceptor development in the Chx10-deficient retina.

PURPOSE: The Chx10 homeobox gene is expressed in neural progenitor cells during retinal development. The absence of Chx10 causes microphthalmia in humans and in the mouse mutant ocular retardation. The purpose of this study was to examine how neuronal development is affected by absence of the Chx10 transcription factor in the mouse retina. METHODS: Expression of transcription factor genes, Crx, Pou4f2, and Pax6, that mark specific cell types as they begin to differentiate was analyzed by RNA in situ hybridization of retina from wild-type and Chx10-null ocular retardation mice (Chx10(or-J/or-J)). RT-PCR analysis was used to compare expression of these genes and putative targets of Crx regulation. Photoreceptor development was analyzed by using peanut agglutinin (PNA)-rhodamine and blue cone opsin antibody to label cones and rhodopsin antibody to label rods. RESULTS: The photoreceptor gene Crx, normally expressed during embryonic retinal development, was not detected in the embryonic mutant retina, but was expressed after birth. Expression of the targets of Crx regulation, rhodopsin, peripherin, rod phosphodiesterase beta (Pdeb), and arrestin, with the exception of interphotoreceptor retinoid binding protein (Irbp), was delayed in the Chx10(or-J/or-J) retina. Rhodopsin localization in rod outer segments was also delayed. By contrast, temporal and spatial expression of Pou4f2 and Pax6 in developing ganglion and amacrine cells and PNA and blue opsin in developing cone cells was relatively normal in the mutant. CONCLUSIONS: Delay of the normal temporal expression of genes essential for photoreceptor disc morphogenesis leads to failure of correct rod and cone outer segment formation in the Chx10(or-J/or-J) mutant retina. In addition, the absence of Chx10 appears to affect the development of late-born cells more than that of early-born cells, in that a low number of rods develops, whereas formation of ganglion, amacrine, and cone cells is relatively unaffected.

The sex peptide of Drosophila melanogaster: female post-mating responses analyzed by using RNA interference.

Mating induces profound changes in female insect behavior and physiology. In Drosophila melanogaster, mating causes a reduction in sexual receptivity and an elevation in egg production for at least 5 days. Injection of the seminal fluid sex peptide (SP) induces both responses in virgin females, but only for 1-2 days. The role of SP in eliciting the responses to mating remains to be elucidated. Functional redundancy between seminal fluid components may occur. In addition, mating with spermless males results in brief (1- to 2-day) post-mating responses, indicating either that there is a "sperm effect" or that sperm act as carriers for SP or other seminal fluid components. Here we used RNA interference to suppress SP expression, to determine whether SP is required to elicit full post-mating responses, the magnitude of responses due to other seminal fluid components, and whether SP accounts for the "sperm effect." Receptivity was higher and egg production lower in females mated to SP knock-down males than in controls. Comparison with virgins showed that the responses were brief. SP is therefore required for normal magnitude and persistence of postmating responses. Sperm transfer and use were normal in mates of SP knock-down males, yet their post-mating responses were briefer than after normal matings, and similar to those reported in mates of spermless son-of-tudor males. The prolonged "sperm effect" on female receptivity and egg production is therefore entirely attributable to SP, but sperm are necessary for its occurrence.

Use of a cytoplasmically localised P-lacZ fusion to identify cell shapes by enhancer trapping inDrosophila.

The N-terminal 125 amino acids of theDrosophila P element transposase are necessary and sufficient for the nuclear localisation of a hybridlacZ gene product in most cell types of theDrosophila embryo. A P-lacZ enhancer-trap element lacking these residues is of use in visualizing the shapes of P-lacZ-expressing cells.