The strigolactone receptor SlDWARF14 plays a role in photosynthetic pigment accumulation and photosynthesis in tomato

Tomato DWARF14 regulates the development of roots, shoot branches and leaves, and also plays a role in photosynthetic pigment accumulation and photosynthetic capacity. Strigolactones (SLs) are a novel class of plant hormones. DWARF14 (D14) is the only SL receptor identified to date, but it is not functionally analyzed in tomato (Solanum lycopersicum). In the present study, we identified the potential SL receptor in tomato by bioinformatic analysis, which was designated as SlD14. SlD14 was expressed in roots, stems, flowers and developing fruits, with the highest expression level in leaves. sld14 mutant plants produced by the CRISPR/Cas9 system displayed reduced plant height and root biomass, increased shoot branching and altered leaf shape comparing with WT plants. The cytokinin biosynthetic gene ISOPENTENYLTRANSFERASE 3 (SlIPT3), auxin biosynthetic genes FLOOZY (SlFZY) and TRYPTOPHAN AMINOTRANSFERASE RELATED 1 (SlTAR1) and several auxin transport genes SlPINs, which are involved in branch formation, showed higher expression levels in the sld14 plant stem. In addition, sld14 plants exhibited light-green leaves, reduced chlorophyll and carotenoid contents, abnormal chloroplast structure and reduced photosynthetic capacity. Transcriptomic analysis showed that the transcript levels of six chlorophyll biosynthetic genes, three carotenoid biosynthetic genes and numerous chlorophyll a/b-binding protein genes were decreased in sld14 plants. These results suggest that tomato SL receptor gene SlD14 not only regulates the development of roots, shoot branches and leaves, but also plays a role in regulating photosynthetic pigment accumulation and photosynthetic capacity.

A SNP mutation in the CsCLAVATA1 leads to pleiotropic variation in plant architecture and fruit morphogenesis in cucumber (Cucumis sativus L.)

Plant architectures is predominantly determined by branching pattern, internode elongation, phyllotaxis, shoot determinacy and reproductive organs. Domestication or improvement of this critical agronomic trait played an important role in the breakthrough of crop yield. Here, we identified a mutant with fasciated plant architecture, named fas, from an ethyl methanesulfonate (EMS) induced mutant population in cucumber. The mutant exhibited abnormal phyllotaxy, flattened main stem, increased number of floral organs, and significantly shorter and thicker fruits. However, the molecular mechanism conferring this pleiotropic effect remains unknown. Using a map-based cloning strategy, we isolated the gene CsaV3_3G045960, encoding a leucine-rich repeat receptor-like kinase, a putative direct homolog of the Arabidopsis CLAVATA1 protein referred to as CsCLV1. Endogenous hormone assays showed that IAA and GA₃ levels in fas stems and ovaries were significantly reduced. Conformably, RNA-seq analysis showed that CsCLV1 regulates cucumber stem and ovary development by coordinating hormones and transcription factors. Our results contribute to the understanding of the function of CsCLV1 throughout the growth cycle, provide new evidence that the CLV signaling system is functionally conserved in Cucurbitaceae.

Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds

Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian-early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural model is comparable to modern tree ferns or cycads and adapted to have grown in light-deficient lower-storey (sub-) tropical forests, usually not exceeding 15 m in height. Apical meristematic growth dominated, whereas only minor secondary growth occurred during ontogenesis. The densely attached frond bases followed a 3/8 phyllotaxis and were most likely abscised shortly after becoming photosynthetically inactive. A high water-conducting potential is assumed due to the tree's cauline, petiolar and leaf vascular anatomies. Concerning the extensive leaf surface of the densely foliated fronds, considerable transpiration is hypothesised. Alethopteris schneideri foliage is stratigraphically significant for lower Permian (Asselian-Sakmarian) continental strata of central Europe, preferring habitats of wet clastic soils in sub-humid, seasonal palaeoclimate. The new insights provide a substantial step towards the first whole-plant concept of intramontane medullosaleans.

GhAPC8 regulates leaf blade angle by modulating multiple hormones in cotton (Gossypium hirsutum L.)

Leaf angle, including leaf petiole angle (LPA) and leaf blade angle (LBA), is an important trait affecting plant architecture. Anaphase-promoting complex/cyclosome (APC/C) genes play a vital role in plant growth and development, including regulation of leaf angle. Here, we identified and characterized the APC genes in Upland cotton (G. hirsutum L.) with a focus on GhAPC8, a homolog of soybean GmILPA1 involved in regulation of LPA. We showed that independently silencing the At or Dt sub-genome homoeolog of GhAPC8 using virus-induced gene silencing reduced plant height and LBA, and that reduction of LBA could be caused by uneven growth of cortex parenchyma cells on the adaxial and abaxial sides of the junction between leaf blade and leaf petiole. The junction between leaf blade and leaf petiole of the GhAPC8-silenced plants had an elevated level of brassinosteroid (BR) and a decreased levels of auxin and gibberellin. Consistently, comparative transcriptome analysis found that silencing GhAPC8 activated genes of the BR biosynthesis and signaling pathways as well as genes related to ubiquitin-mediated proteolysis. Weighted gene co-expression network analysis (WGCNA) identified gene modules significantly associated with plant height and LBA, and candidate genes bridging GhAPC8, the pathways of BR biosynthesis and signaling and ubiquitin-mediated proteolysis. These results demonstrated a role of GhAPC8 in regulating LBA, likely achieved by modulating the accumulation and signaling of multiple phytohormones.

Design Considerations for In-Field Measurement of Plant Architecture Traits Using Ground-Based Platforms

This work provides a high-level overview of system design considerations for measuring plant architecture traits in row crops using ground-based, mobile platforms. High-throughput phenotyping technologies are commonly deployed in isolated growth chambers or greenhouses; however, there is a need for field-based systems to measure large quantities of plants exposed to natural climates throughout a growing season. High-throughput methods using ground-based mobile systems collect valuable phenotypic information at higher temporal resolutions compared to manual methods (e.g., handheld calipers and measuring sticks). Additionally, the close proximity to plants when using ground-based systems compared to aerial platforms enables plant phenotyping at the organ level. While there is no single best platform for obtaining ground-based plant measurements across crop varieties with different planting configurations, there are a wide range of off-the-shelf systems and sensors that can be integrated to accommodate varying row widths, plant spacing, plant heights, and plot sizes, in addition to emerging commercially available platforms. This chapter will provide an overview of sensor types suitable for phenotyping plant size and shape, as well as provide guidance for deployment with ground-based systems, including push carts or buggies, modified tractors, and robotic platforms.

miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia

miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.

Modification of cereal plant architecture by genome editing to improve yields

We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.

Overexpression of MtRAV3 enhances osmotic and salt tolerance and inhibits growth of Medicago truncatula

Related to ABI3/VP1 (RAV) transcription factors play important roles in regulating plant growth and stress tolerance, which have been studied in many plant species, but have remained largely unidentified in legumes. To functionally characterize RAV in legumes, MtRAV3 from legume model plant Medicago truncatula was isolated and its function was investigated by overexpressing MtRAV3 in M. truncatula. Expression analysis demonstrated that MtRAV3 was markedly induced by NaCl and polyethylene glycol (PEG). MtRAV3 overexpression enhanced tolerance of transgenic M. truncatula to mannitol, drought and salt stresses, and induced the expression of adversity-related genes, including MtWRKY76, MtMYB61, cold-acclimation specific protein 31 (MtCAS31), alternative oxidase 1 (MtAOX1) and ethylene response factor 1 (MtERF1). There were lower relative electrolyte leakage and higher chlorophyll content of leaves in the MtRAV3 overexpression plants than in wild type plants under both salt and drought stress. MtRAV3 overexpression M. truncatula were featured by some phenotypes of dwarfing, late flowering, more branches, smaller flower and leaf organs. Further investigations showed that the expression levels of DWARF14 (MtD14), CAROTENOID CLEAVAGE DIOXYGENASES 7 (MtCCD7) and GA3-oxidase1 (MtGA3ox1), which related to dwarf and branch phenotype, were obviously reduced, as well as MtGA3ox1' (MTR_1g011580), GA20-oxidase1 (MtGA20ox1), MtGA20ox1' (MTR_1g102070) and GA20-oxidase2 (MtGA20ox2) involved in gibberellins (GAs) pathway. Overall, our results revealed that MtRAV3 exerted an important role in adversity response and plant growth, was a multifunctional gene in M. truncatula, which provided reference for genetic improvement of alfalfa (Medicago sativa).

Plant design gets its details: Modulating plant architecture by phase transitions

Plants evolved different strategies to better adapt to the environmental conditions in which they live: the control of their body architecture and the timing of phase change are two important processes that can improve their fitness. As they age, plants undergo two major phase changes (juvenile to adult and adult to reproductive) that are a response to environmental and endogenous signals. These phase transitions are accompanied by alterations in plant morphology and also by changes in physiology and the behavior of gene regulatory networks. Six main pathways involving environmental and endogenous cues that crosstalk with each other have been described as responsible for the control of plant phase transitions: the photoperiod pathway, the autonomous pathway, the vernalization pathway, the temperature pathway, the GA pathway, and the age pathway. However, studies have revealed that sugar is also involved in phase change and the control of branching behavior. In this review, we discuss recent advances in plant biology concerning the genetic and molecular mechanisms that allow plants to regulate phase transitions in response to the environment. We also propose connections between phase transition and plant architecture control.

Ecosystem engineering in the arboreal realm: heterogeneity of wood-boring beetle cavities and their use by cavity-nesting ants

Wood-boring beetle larvae act as ecosystem engineers by creating stem cavities that are used secondarily as nests by many arboreal ant species. Understanding the heterogeneity and distribution of available cavities and their use by ants is therefore key to understanding arboreal ant community assembly and diversity. Our goals were to quantify the abundance and diversity of beetle-produced cavity resources in a tropical canopy, reveal how ants use these resources, and determine which characteristics of the cavity resource contribute to ant use. We dissected branches from six common tree species in the Brazilian Cerrado savanna, measuring cavity characteristics and identifying the occupants. We sampled 2310 individual cavities, 576 of which were used as nests by 25 arboreal ant species. We found significant differences among tree species in the proportion of stem length bored by beetles, the number of cavities per stem length, average entrance-hole size, and the distribution of cavity volumes. The likelihood that a cavity was occupied was greater for cavities with larger entrance-hole sizes and larger volumes. In particular, there was a strong positive correlation between mean head diameters of ant species and the mean entrance-hole diameter of the cavities occupied by those ant species. Wood-boring beetles contribute to the structuring of the Cerrado ant community by differentially attacking the available tree species. In so doing, the beetles provide a wide range of entrance-hole sizes which ant species partition based on their body size, and large volume cavities that ants appear to prefer.

Heterotrimeric Gα subunit regulates plant architecture, organ size and seed weight in the oilseed Brassica juncea

Two BjuGα proteins exhibit conserved GTP-binding and GTP-hydrolysis activities, and function in maintaining overall plant architecture and controlling multiple yield-related traits in the oilseed Brassica juncea. Heterotrimeric G-protein (Gα, Gβ and Gγ) are key signal transducers, well characterized in model plants Arabidopsis and rice. However, our knowledge about the roles played by G-proteins in regulating various growth and developmental traits in polyploid crops, having a complex G-protein signalling network, is quite sparse. In the present study, two Gα encoding genes (BjuA.Gα1 and BjuB.Gα1) were isolated from the allotetraploid Brassica juncea, a globally cultivated oilseed crop of the Brassicaceae family. BjuGα1 genes share a close evolutionary relationship, and the encoded proteins exhibit highly conserved G-protein activities while showing expression differentiation, wherein BjuA.Gα1 was the highly abundant transcript during plant growth and developmental stages. RNAi based suppression of BjuGα1 displayed compromised effects on most of the tested vegetative and reproductive parameters, particularly plant height (32-58%), flower and siliques dimensions, and seed weight (11-13%). Further, over-expression of a constitutively active Gα, lacking the GTPase activity, produced plants with increased height, organ size and seed weight (7-25%), without altering seed quality traits like fatty acid composition, glucosinolates, oil and protein contents. Our study demonstrates that BjuGα1 proteins control overall plant architecture and multiple yield-related traits in the oilseed B. juncea, suggesting that BjuGα1 could be a promising target for crop improvement.

Knock-out of TERMINAL FLOWER 1 genes altered flowering time and plant architecture in Brassica napus

Background

TERMINAL FLOWER 1 (TFL1) is a member of phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in the determination of floral meristem identity and regulates flowering time in higher plants.

Results

Five BnaTFL1 gene copies were identified in the genome of Brassica napus. The phylogenetic analysis indicated that all five BnaTFL1 gene copies were clustered with their corresponding homologous copies in the ancestral species, B. rapa and B. oleracea. The expression of the BnaTFL1s were confined to flower buds, flowers, seeds, siliques and stem tissues and displayed distinct expression profiles. Knockout mutants of BnaC03.TFL1 generated by CRISPR/Cas9 exhibited early flowering phenotype, while the knockout mutants of the other gene copies had similar flowering time as the wild type. Furthermore, knock-out mutants of individual BnaTFL1 gene copy displayed altered plant architecture. The plant height, branch initiation height, branch number, silique number, number of seeds per silique and number of siliques on the main inflorescence were significantly reduced in the BnaTFL1 mutants.

Conclusions

Our results indicated that BnaC03.TFL1 negatively regulates flowering time in B. napus. BnaC03.TFL1 together with the other BnaTFL1 paralogues are essential for controlling the plant architecture.

A Mechanistic Model to Predict Distribution of Carbon Among Multiple Sinks

Modeling is a fundamental part of quantitative science used to bring together several quantitative components, often developed though detailed reductionist approach on component parts, e.g., sucrose transport through a membrane osmotic relation. It is now generally accepted that phloem transport is the result of bulk solution flow generated by the difference in osmotic pressure between source and sink tissues. However, there is still little agreement on how different sink tissues compete for available carbohydrate. Furthermore, the impact of phloem pathway leakage (unloading) and reloading on source-to-sink carbon transport remains unclear. Moreover, it is debated to what degree the interactions between phloem and xylem flows influence carbohydrate source-sink relations. These aspects are extremely difficult to research by a reductionist approach, with modeling being an important tool to examine the consequences of proposed mechanisms, which can then be tested on whole plants.Phloem/xylem modeling has been at the limits of quantitative modeling, especially when dynamic models are needed to explain tracer studies. Advances in computing now enable more realistic modeling, which are utilized by the PiafMunch approach described here. This model enables a high level of mechanistic detail to be incorporated and the observable effect of it to be tested. In the most recent version of the software with the introduction of tracer dynamics, it can now predict the effects of specific phloem mechanisms upon the shape of evolving tracer profiles.

Functional mutation allele mining of plant architecture and yield-related agronomic traits and characterization of their effects in wheat

BACKGROUND

Wheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. Plant architecture and yield-related features are important agronomic traits for wheat breeders and mining favorable alleles of these traits will improve wheat characteristics.

RESULTS

Here we used 190 wheat phenotypic mutants as material and by analyzing their SNP variation and phenotypic data, mutation alleles for plant architecture and yield-related traits were identified, and the genetic effects of these alleles were evaluated. In total, 32 mutation alleles, including three pleiotropic alleles, significantly associated with agronomic traits were identified from the 190 wheat mutant lines. The SNPs were distributed on 12 chromosomes and were associated with plant height (PH), tiller number, flag leaf angle (FLA), thousand grain weight (TGW), and other yield-related traits. Further phenotypic analysis of multiple lines carrying the same mutant allele was performed to determine the effect of the allele on the traits of interest. PH-associated SNPs on chromosomes 2BL, 3BS, 3DL, and 5DL might show additive effects, reducing PH by 10.0 cm to 31.3 cm compared with wild type, which means that these alleles may be favorable for wheat improvement. Only unfavorable mutation alleles that reduced TGW and tiller number were identified. A region on chromosome 5DL with mutation alleles for PH and TGW contained several long ncRNAs, and their sequences shared more than 90% identity with cytokinin oxidase/dehydrogenase genes. Some of the mutation alleles we mined were colocalized with previously reported QTLs or genes while others were novel; these novel alleles could also result in phenotypic variation.

CONCLUSION

Our results demonstrate that favorable mutation alleles are present in mutant resources, and the region between 409.5 to 419.8 Mb on chromosome 5DL affects wheat plant height and thousand grain weight.

Downregulation of SlGRAS15 manipulates plant architecture in tomato (Solanum lycopersicum)

GRAS family transcription factors (TF) are involved in multiple biological processes in plants. In recent years among the 54 identified GRAS proteins, only few have been studied functionally in tomato (Solanum lycopersicum). In the present study, a novel and previously uncharacterized member of tomato GRAS transcription factors family SlGRAS15 was isolated and functionally characterized. It was observed that SlGRAS15 preferably expressed in roots, followed by young leaves, stem, and comparatively low transcripts levels were noticed in all other tissues. To explore the SlGRAS15 function in detail, an RNA interference (RNAi) vector targeting SlGRAS15 was constructed and transformed into tomato plants. The transgenic plants carrying SlGRAS15-RNAi displayed pleiotropic phenotypes associated with multiple agronomical traits including reduced plant height and small leaf size with pointed margins, increased node number, lateral shoots, and petiolules length. In addition, transcriptional analysis revealed that silencing SlGRAS15 altered vegetative growth by downregulating gibberellin (GA) biosynthesis genes and stimulating the GA deactivating genes, thus lowering the endogenous GA content in tomato transgenic lines. Moreover, the GA signaling downstream gene (SlGAST1) was downregulated but the negative regulator of GA signaling (SlDELLA) was upregulated by SlGRAS15 silencing. The root and hypocotyl length in SlGRAS15-RNAi lines showed reduced growth under normal conditions (Mock) as compared with the wild type (WT) control plants. Taken together, these findings enhanced our understanding that suppression of SlGRAS15 lead to a series of developmental processes by modulating gibberellin signaling and demonstrate an association between the SlGRAS15 and GA signaling pathway during vegetative growth in tomato.

Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

BACKGROUND

The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production.

RESULTS

Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes.

CONCLUSIONS

We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

BACKGROUND

Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in the regulation of plant architecture and flowering time. The functions of PEBP genes have been studied in many plant species. However, little is known about the characteristics and expression profiles of PEBP genes in wild peanut species, Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanuts.

RESULTS

In this study, genome-wide identification methods were used to identify and characterize a total of 32 peanut PEBP genes, 16 from each of the two wild peanut species, A. duranensis and A. ipaensis. These PEBP genes were classified into 3 groups (TERMINAL FLOWER1-like, FLOWERING LOCUS T-like, and MOTHER OF FT AND TFL1-like) based on their phylogenetic relationships. The gene structures, motifs, and chromosomal locations for each of these PEBPs were analyzed. In addition, 4 interchromosomal duplications and 1 tandem duplication were identified in A. duranensis, and 2 interchromosomal paralogs and 1 tandem paralog were identified in A. ipaensis. Ninety-five different cis-acting elements were identified in the PEBP gene promoter regions and most genes had different numbers and types of cis-elements. As a result, the transcription patterns of these PEBP genes varied in different tissues and under long day and short day conditions during different growth phases, indicating the functional diversities of PEBPs in different tissues and their potential functions in plant photoperiod dependent developmental pathways. Moreover, our analysis revealed that AraduF950M/AraduWY2NX in A. duranensis, and Araip344D4/Araip4V81G in A. ipaensis are good candidates for regulating plant architecture, and that Aradu80YRY, AraduYY72S, and AraduEHZ9Y in A. duranensis and AraipVEP8T in A. ipaensis may be key factors regulating flowering time.

CONCLUSION

Sixteen PEBP genes were identified and characterized from each of the two diploid wild peanut genomes, A. duranensis and A. ipaensis. Genetic characterization and spatio-temporal expression analysis support their importance in plant growth and development. These findings further our understanding of PEBP gene functions in plant species.

Manipulating osa-MIR156f Expression by D18 Promoter to Regulate Plant Architecture and Yield Traits both in Seasonal and Ratooning Rice

Background

Rice (Oryza sativa L.) feeds more than half of the world's population. Ratooning rice is an economical alternative to the second seasonal rice, thus increasing the yield of ratooning rice is highly important.

Results

Here we report an applicable transgenic line constructed through the manipulation of osa-MIR156f expression in rice shoot using the OsGA3ox2 (D18) promoter. In seasonal rice, the D18-11 transgenic line showed moderate height and more effective tillers with normal panicle. In ratooning rice, axillary buds outgrew from the basal node of the D18-11 transgenic line before the harvest of seasonal rice. More effective tillers produced by the outgrowth of axillary buds contributed to the plant architecture improvement and yield increase. Additionally, it was found that osa-miR156f down-regulated the expression of tillering regulators, such as TEOSINTE BRANCHED1 (TB1) and LAX PANICLE 1 (LAX1). The expression of DWARF10, DWARF27 and DWARF53, three genes being involved in the biosynthesis and signaling of strigolactone (SL), decreased in the stem of the D18-11 transgenic line.

Conclusion

Our results indicated that the manipulation of osa-MIR156f expression may have application significance in rice genetic breeding. This study developed a novel strategy to regulate plant architecture and grain yield potential both in the seasonal and ratooning rice.

Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in upland cotton

BACKGROUND

Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important.

RESULTS

In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of the GH3 gene family, which are involved in auxin signal transduction, and CKX enzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS), EIN2/3 and ERF in the ethylene signal transduction pathway and genes related to JAR1, COI1 and MYC2 in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. The WRKY, ERF and bHLH TF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77.

CONCLUSIONS

Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, the WRKY, ERF and bHLH TFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches.

Genome-Wide Identification of the Aux/IAA Family Genes (MdIAA) and Functional Analysis of MdIAA18 for Apple Tree Ideotype

The Aux/IAA (auxin/indole-3-acetic acid) gene family is one of the early auxin-responsive gene families, which play a central role in auxin response. Few reports are involved in Aux/IAA genes in fruit trees, especially in apple (Malus × domestica Borkh.). A total of 33 MdIAA members were identified, of which 27 members contained four conserved domains, whereas the others lost one or two conserved domains. Several cis-elements in promoters of MdIAAs were predicted responsive to hormones and abiotic stress. Tissue-specific expression patterns of MdIAAs in different apple tree ideotypes were investigated by quantitative real-time PCR. A large number of MdIAAs were highly expressed in leaf buds and reproductive organs, and MdIAAs clustered in same group showed similar expression profiles. Overexpression of MdIAA18 in Arabidopsis resulted in compact phenotype. These results indicated that MdIAA genes may be involved in vegetative and reproductive growth of apple. Taken together, the results provide useful clues to reveal the function of MdIAAs in apple and control apple tree architecture by manipulation of MdIAAs.

CRISPR/Cas9-mediated targeted mutagenesis of GmSPL9 genes alters plant architecture in soybean

BACKGROUND

The plant architecture has significant effects on grain yield of various crops, including soybean (Glycine max), but the knowledge on optimization of plant architecture in order to increase yield potential is still limited. Recently, CRISPR/Cas9 system has revolutionized genome editing, and has been widely utilized to edit the genomes of a diverse range of crop plants.

RESULTS

In the present study, we employed the CRISPR/Cas9 system to mutate four genes encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors of the SPL9 family in soybean. These four GmSPL9 genes are negatively regulated by GmmiR156b, a target for the improvement of soybean plant architecture and yields. The soybean Williams 82 was transformed with the binary CRISPR/Cas9 plasmid, assembled with four sgRNA expression cassettes driven by the Arabidopsis thaliana U3 or U6 promoter, targeting different sites of these four SPL9 genes via Agrobacterium tumefaciens-mediated transformation. A 1-bp deletion was detected in one target site of the GmSPL9a and one target site of the GmSPL9b, respectively, by DNA sequencing analysis of two T0-generation plants. T2-generation spl9a and spl9b homozygous single mutants exhibited no obvious phenotype changes; but the T2 double homozygous mutant spl9a/spl9b possessed shorter plastochron length. In T4 generation, higher-order mutant plants carrying various combinations of mutations showed increased node number on the main stem and branch number, consequently increased total node number per plants at different levels. In addition, the expression levels of the examined GmSPL9 genes were higher in the spl9b-1 single mutant than wild-type plants, which might suggest a feedback regulation on the expression of the investigated GmSPL9 genes in soybean.

CONCLUSIONS

Our results showed that CRISPR/Cas9-mediated targeted mutagenesis of four GmSPL9 genes in different combinations altered plant architecture in soybean. The findings demonstrated that GmSPL9a, GmSPL9b, GmSPL9c and GmSPL9 function as redundant transcription factors in regulating plant architecture in soybean.

Genome-wide association study of maize plant architecture using F1 populations

Genome-wide association study of maize plant architecture using F₁ populations can better dissect various genetic effects that can provide precise guidance for genetic improvement in maize breeding. Maize grain yield has increased at least eightfold during the past decades. Plant architecture, including plant height, leaf angle, leaf length, and leaf width, has been changed significantly to adapt to higher planting density. Although the genetic architecture of these traits has been dissected using different populations, the genetic basis remains unclear in the F₁ population. In this work, we perform a genome-wide association study of the four traits using 573 F₁ hybrids with a mixed linear model approach and QTXNetwork mapping software. A total of 36 highly significant associated quantitative trait SNPs were identified for these traits, which explained 51.86-79.92% of the phenotypic variation and were contributed mainly by additive, dominance, and environment-specific effects. Heritability as a result of environmental interaction was more important for leaf angle and leaf length, while major effects (a, aa, and d) were more important for leaf width and plant height. The potential breeding values of the superior lines and superior hybrids were also predicted, and these values can be applied in maize breeding by direct selection of superior genotypes for the associated quantitative trait SNPs. A total of 108 candidate genes were identified for the four traits, and further analysis was performed to screen the potential genes involved in the development of maize plant architecture. Our results provide new insights into the genetic architecture of the four traits, and will be helpful in marker-assisted breeding for maize plant architecture.

Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton

BACKGROUND

Plant architecture and the vegetative-reproductive transition have major impacts on the agronomic success of crop plants, but genetic mechanisms underlying these traits in cotton (Gossypium spp.) have not been identified.

RESULTS

We identify four natural mutations in GoCEN-D_t associated with cluster fruiting (cl) and early maturity. The situ hybridization shows that GhCEN is preferentially expressed in cotton shoot apical meristems (SAM) of the main stem and axillary buds. Constitutive GhCEN-Dt overexpression suppresses the transition of the cotton vegetative apex to a reproductive shoot. Silencing GoCEN leads to early flowering and determinate growth, and in tetraploids causes the main stem to terminate in a floral bud, a novel phenotype that exemplifies co-adaptation of polyploid subgenomes and suggests new research and/or crop improvement approaches. Natural cl variations are enriched in cottons adapted to high latitudes with short frost-free periods, indicating that mutants of GoCEN have been strongly selected for early maturity.

CONCLUSION

We show that the cotton gene GoCEN-Dt, a homolog of Antirrhinum CENTRORADIALIS, is responsible for determinate growth habit and cluster fruiting. Insight into the genetic control of branch and flower differentiation offers new approaches to develop early maturing cultivars of cotton and other crops with plant architecture appropriate for mechanical harvesting.

Evolution of ALOG gene family suggests various roles in establishing plant architecture of Torenia fournieri

BACKGROUND

ALOG (Arabidopsis LSH1 and Oryza G1) family with a conserved domain widely exists in plants. A handful of ALOG members have been functionally characterized, suggesting their roles as key developmental regulators. However, the evolutionary scenario of this gene family during the diversification of plant species remains largely unclear.

METHODS

Here, we isolated seven ALOG genes from Torenia fournieri and phylogenetically analyzed them with different ALOG members from representative plants in major taxonomic clades. We further examined their gene expression patterns by RT-PCR, and regarding the protein subcellular localization, we co-expressed the candidates with a nuclear marker. Finally, we explored the functional diversification of two ALOG members, TfALOG1 in euALOG1 and TfALOG2 in euALOG4 sub-clades by obtaining the transgenic T. fournieri plants.

RESULTS

The ALOG gene family can be divided into different lineages, indicating that extensive duplication events occurred within eudicots, grasses and bryophytes, respectively. In T. fournieri, seven TfALOG genes from four sub-clades exhibit distinct expression patterns. TfALOG1-6 YFP-fused proteins were accumulated in the nuclear region, while TfALOG7-YFP was localized both in nuclear and cytoplasm, suggesting potentially functional diversification. In the 35S:TfALOG1 transgenic lines, normal development of petal epidermal cells was disrupted, accompanied with changes in the expression of MIXTA-like genes. In 35S:TfALOG2 transgenic lines, the leaf mesophyll cells development was abnormal, favoring functional differences between the two homologous proteins. Unfortunately, we failed to observe any phenotypical changes in the TfALOG1 knock-out mutants, which might be due to functional redundancy as the case in Arabidopsis.

CONCLUSION

Our results unraveled the evolutionary history of ALOG gene family, supporting the idea that changes occurred in the cis regulatory and/or nonconserved coding regions of ALOG genes may result in new functions during the establishment of plant architecture.

Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis

BACKGROUND

Precision plant genome engineering holds much promise for targeted improvement of crop traits via unprecedented single-base level control over the genetic material. Strigolactones (SLs) are a key determinant of plant architecture, known for their role in inhibiting shoot branching (tillering).

RESULTS

We used CRISPR/Cas9 in rice (Oryza sativa) for targeted disruption of CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), which controls a key step in SL biosynthesis. The ccd7 mutants exhibited a striking increase in tillering, combined with a reduced height, which could be rescued by application of the synthetic SL analog GR24. Striga germination assays and liquid chromatography-mass spectrometry analysis showed that root exudates of ccd7 mutants were also SL deficient.

CONCLUSIONS

Taken together, our results show the potential and feasibility of the use of the CRISPR/Cas9 system for targeted engineering of plant architecture and for elucidating the molecular underpinnings of architecture-related traits.