Upland cotton gene GhFPF1 confers promotion of flowering time and shade-avoidance responses in Arabidopsis thaliana

A novel strategy to map a locus associated with flowering time in canola (Brassica napus L.)

Flowering time is an important agronomic trait for canola breeders, as it provides growers with options for minimizing exposure to heat stress during flowering and to more effectively utilize soil moisture. Plants have evolved various systems to control seasonal rhythms in reproductive phenology including an internal circadian clock that responds to environmental signals. In this study, we used canola cultivar 'Westar' as a recurrent parent and canola cultivar 'Surpass 400' as the donor parent to generate a chromosome segment substitution line (CSSL) and to map a flowering time locus on chromosome A10 using molecular marker-assisted selection. This CSSL contains an introgressed 4.6 mega-bases (Mb) segment (between 13 and 17.6 Mb) of Surpass 400, which substantially delayed flowering compared with Westar. To map flowering time gene(s) within this locus, eight introgression lines (ILs) were developed carrying a series of different lengths of introgressed chromosome A10 segments using five co-dominant polymorphic markers located at 13.5, 14.0, 14.5, 15.0, 15.5, and 16.0 Mb. Eight ILs were crossed with Westar reciprocally and flowering time of resultant 16 F1 hybrids and parents were evaluated in a greenhouse (2021 and 2022). Four ILs (IL005, IL017, IL035, and IL013) showed delayed flowering compared to Westar (P < 0.0001), and their reciprocal crosses displayed a phenotype intermediate in flowering time of both homozygote parents. These results indicated that flowering time is partial or incomplete dominance, and the flowering time locus mapped within a 1 Mb region between two co-dominant polymorphic markers at 14.5-15.5 Mb on chromosome A10. The flowering time locus was delineated to be between 14.60 and 15.5 Mb based on genotypic data at the crossover site, and candidate genes within this region are associated with flowering time in canola and/or Arabidopsis. The co-dominant markers identified on chromosome A10 should be useful for marker assisted selection in breeding programs but will need to be validated to other breeding populations or germplasm accessions of canola.

The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger

Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.

GhSWEET42 Regulates Flowering Time under Long-Day Conditions in Arabidopsis thaliana

Flowering in plants is pivotal for initiating and advancing reproductive processes, impacting regional adaptation and crop yield. Despite numerous cloned and identified flowering time genes, research in cotton remains sparse. This study identified GhSWEET42 as a key determinant of the flowering time in cotton, demonstrating that its heterologous expression in Arabidopsis accelerated flowering under LD conditions compared to WT. Transgenic plants exhibited upregulated expression of the flowering inducers AtFT, AtSOC1, AtGI, and AtFKF1, alongside downregulated expression of the repressors AtTSF, AtFLC, and AtRGL2, correlating with the earlier flowering phenotype. GhSWEET42 showed a constitutive expression pattern, with elevated levels in the leaves, petals, and flower buds, and was notably higher in early-maturing cotton varieties. Subcellular localization assays confirmed GhSWEET42's presence on the cell membrane. Transcriptome analysis between WT and GhSWEET42-overexpressing Arabidopsis plants revealed 2393 differentially expressed genes (DEGs), spanning 221 biological processes, 93 molecular functions, and 37 cellular components according to Gene Ontology (GO) enrichment analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis categorized the DEGs into metabolism and environmental information processing. These findings enhance the understanding of GhSWEET42's function and provide a foundation for elucidating the molecular mechanisms governing flowering time regulation in cotton.

Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton

Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), in Arabidopsis. FT is expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed with FT and whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, the FT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The master FT regulator, CONSTANS (CO), controls FLP1 expression, suggesting FLP1's involvement in the photoperiod pathway. FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA 3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions.

VERNALIZATION1 represses FLOWERING PROMOTING FACTOR1-LIKE1 in leaves for timely flowering in Brachypodium distachyon

FLOWERING PROMOTING FACTOR1 (FPF1), a small protein without any known domains, promotes flowering in several plants; however, its functional mechanism remains unknown. Here, we characterized 2 FPF1-like proteins, FPL1 and FPL7, which, in contrast, function as flowering repressors in Brachypodium distachyon. FPL1 and FPL7 interact with the components of the florigen activation complex (FAC) and inhibit FAC activity to restrict expression of its critical target, VERNALIZATION1 (VRN1), in leaves, thereby preventing overaccumulation of FLOWERING LOCUS T1 (FT1) at the juvenile stage. Further, VRN1 can directly bind to the FPL1 promoter and repress FPL1 expression; hence, as VRN1 gradually accumulates during the late vegetative stage, FAC is released. This accurate feedback regulation of FPL1 by VRN1 allows proper FT1 expression in leaves and ensures sufficient FAC formation in shoot apical meristems to trigger timely flowering. Overall, we define a sophisticated modulatory loop for flowering initiation in a temperate grass, providing insights toward resolving the molecular basis underlying fine-tuning flowering time in plants.

Recent advances and future perspectives in early-maturing cotton research

Cotton's fundamental requirements for long periods of growth and specific seasonal temperatures limit the global arable areas that can be utilized to cultivate cotton. This constraint can be alleviated by breeding for early-maturing varieties. By delaying the sowing dates without impacting the boll-opening time, early-maturing varieties not only mitigate the yield losses brought on by unfavorable weathers in early spring and late autumn but also help reducing the competition between cotton and other crops for arable land, thereby optimizing the cropping system. This review presents studies and breeding efforts for early-maturing cotton, which efficiently pyramid early maturity, high-quality, multiresistance traits, and suitable plant architecture by leveraging pleiotropic genes. Attempts are also made to summarize our current understanding of the molecular mechanisms underlying early maturation, which involves many pathways such as epigenetic, circadian clock, and hormone signaling pathways. Moreover, new avenues and effective measures are proposed for fine-scale breeding of early-maturing crops to ensure the healthy development of the agricultural industry.

Cotton proteomics: Dissecting the stress response mechanisms in cotton

The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton's response to stresses.

A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit

Reduced plant height due to shortened stems is beneficial for improving crop yield potential, better resilience to biotic/abiotic stresses, and rapid crop producer adoption of the agronomic and management practices. Breeding tomato plants with a reduced height, however, poses a particular challenge because this trait is often associated with a significant fruit size (weight) reduction. The tomato BRACHYTIC (BR) locus controls plant height. Genetic mapping and genome assembly revealed three flowering promoting factor 1 (FPF1) genes located within the BR mapping interval, and a complete coding sequence deletion of the telomere proximal FPF1 (Solyc01g066980) was found in the br allele but not in BR. The knock-out of Solyc01g066980 in BR large-fruited fresh-market tomato reduced the height and fruit yield, but the ability to produce large size fruits was retained. However, concurrent yield evaluation of a pair of sister lines with or without the br allele revealed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. A network analysis of gene-expression patterns across genotypes, tissues, and the gibberellic acid (GA) treatment revealed that member(s) of the FPF1 family may play a role in the suppression of the GA biosynthesis in roots and provided a framework for identifying the responsible molecular signaling pathways in br-mediated phenotypic changes. Lastly, mutations of br homologs also resulted in reduced height. These results shed light on the genetic and physiological mechanisms by which the br allele alters tomato architecture.

Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus

Flowering at the proper time is an important part of acclimation to the ambient environment and season and maximizes the plant yield. To reveal the genetic architecture and molecular regulation of flowering time in oilseed rape (Brassica napus), we performed an RNA-seq analysis of the two parents after vernalization at low temperature and combined this with quantitative trait loci (QTL) mapping in an F₂ population. A genetic linkage map that included 1,017 markers merged into 268 bins and covered 793.53 cM was constructed. Two QTLs associated with flowering time were detected in the F₂ population. qFTA06 was the major QTL in the 7.06 Mb interval on chromosome A06 and accounted for 19.3% of the phenotypic variation. qFTC08 was located on chromosome C06 and accounted for 8.6% of the phenotypic variation. RNA-seq analysis revealed 4,626 differentially expressed genes (DEGs) between two parents during vernalization. Integration between QTL mapping and RNA-seq analysis revealed six candidate genes involved in the regulation of flowering time through the circadian clock/photoperiod, auxin and ABA hormone signal, and cold signal transduction and vernalization pathways. These results provide insights into the molecular genetic architecture of flowering time in B. napus.

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

BACKGROUND

Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss.

RESULTS

To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting.

CONCLUSION

This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.

High-resolution temporal dynamic transcriptome landscape reveals a GhCAL-mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.)

The transition from vegetative to reproductive growth is very important for early maturity in cotton. However, the genetic control of this highly dynamic and complex developmental process remains unclear. A high-resolution tissue- and stage-specific transcriptome profile was generated from six developmental stages using 72 samples of two early-maturing and two late-maturing cotton varieties. The results of histological analysis of paraffin sections showed that flower bud differentiation occurred at the third true leaf stage (3TLS) in early-maturing varieties, but at the fifth true leaf stage (5TLS) in late-maturing varieties. Using pairwise comparison and weighted gene co-expression network analysis, 5312 differentially expressed genes were obtained, which were divided into 10 gene co-expression modules. In the MElightcyan module, 46 candidate genes regulating cotton flower bud differentiation were identified and expressed at the flower bud differentiation stage. A novel key regulatory gene related to flower bud differentiation, GhCAL, was identified in the MElightcyan module. Anti-GhCAL transgenic cotton plants exhibited late flower bud differentiation and flowering time. GhCAL formed heterodimers with GhAP1-A04/GhAGL6-D09 and regulated the expression of GhAP1-A04 and GhAGL6-D09. GhAP1-A04- and GhAGL6-D09-silenced plants also showed significant late flowering. Finally, we propose a new flowering regulatory pathway mediated by GhCAL. This study elucidated the molecular mechanism of cotton flowering regulation and provides good genetic resources for cotton early-maturing breeding.

OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa)

BACKGROUND

FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood.

RESULTS

As a homologue of AtFPF1, FPF1-like protein 4 of rice (OsFPFL4) is expressed in various tissues of plants. The functions of OsFPFL4 in rice were investigated by the reverse genetics approaches. Plants overexpressing OsFPFL4 have shorter primary root, more lateral roots and adventitious roots than wild type; however, RNA interference (RNAi) of OsFPFL4 significantly inhibits the growth of root system, and also delays the flowering time in rice. Interestingly, increased or repressed expression of OsFPFL4 leads to shrunken anthers and abnormal pollen grains. It is well recognized that auxin plays important roles in plant root and flower development, and the root elongation is also regulated by reactive oxygen species (ROS) homeostasis. Here, our results show that rice plants overexpressing OsFPFL4 accumulate more auxin in the shoot and root, whereas RNAi lines have less auxin than wild type. As expected, the transcript levels of genes responsible for auxin biosynthesis and polar transport are altered in these OsFPFL4 transgenic plants. As to ROS, slightly higher ROS levels were detected in overexpression root and inflorescence than the counterparts of wild type; however, the ROS levels were significantly increased in the RNAi lines, due to increased expression of ROS-producers and reduced expression of ROS-scavengers.

CONCLUSION

Our results reveal that OsFPFL4 is involved in modulating the root and flower development by affecting auxin and ROS homeostasis in rice plants. OsFPFL4 controls auxin accumulation via affecting auxin biosynthesis and transport, and also modulates ROS homeostasis by balancing ROS producing and scavenging. Thus, auxin-mediated ROS production might play a role in regulating redox status, which controls plant root and flower development.

Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome

When subject to vegetational shading, shade-avoiding plants detect neighbors by perceiving reduced light quantity and altered light quality. The former includes decreases in the ratio of red to far-red wavelengths (low R:FR) and low blue light ratio (LBL) predominantly detected by phytochromes and cryptochromes, respectively. By integrating multiple signals, plants generate a suite of responses, such as elongation of a variety of organs, accelerated flowering, and reduced branching, which are collectively termed the shade-avoidance syndrome (SAS). To trigger the SAS, interactions between photoreceptors and phytochrome-interacting factors are the general switch for activation of downstream signaling pathways. A number of transcription factor families and phytohormones, especially auxin, gibberellins, ethylene, and brassinosteroids, are involved in the SAS processes. In this review, shade signals, the major photoreceptors involved, and the phenotypic characteristics of the shade-intolerant plant Arabidopsis thaliana are described in detail. In addition, integration of the signaling mechanisms that link photoreceptors with multiple hormone signaling pathways is presented and future research directions are discussed.

Shade delays flowering in Medicago sativa

Shade-intolerant plants respond to the decrease in the red (R) to far-red (FR) light ratio (R:FR) occurring under shade by elongating stems and petioles and by re-positioning leaves, in a race to outcompete neighbors for the sunlight resource. In some annual species, the shade avoidance syndrome (SAS) is accompanied by the early induction of flowering. Anticipated flowering is viewed as a strategy to set seeds before the resources become severely limiting. Little is known about the molecular mechanisms of SAS in perennial forage crops like alfalfa (Medicago sativa). To study SAS in alfalfa, we exposed alfalfa plants to simulated shade by supplementing with FR light. Low R:FR light produced a classical SAS, with increased internode and petiole lengths, but unexpectedly also with delayed flowering. To understand the molecular mechanisms involved in uncoupling SAS from early flowering, we used a transcriptomic approach. The SAS is likely to be mediated by increased expression of msPIF3 and msHB2 in low R:FR light. Constitutive expression of these genes in Arabidopsis led to SAS, including early flowering, strongly suggesting that their roles are conserved. Delayed flowering was likely to be mediated by the downregulation of msSPL3, which promotes flowering in both Arabidopsis and alfalfa. Shade-delayed flowering in alfalfa may be important to extend the vegetative phase under suboptimal light conditions, and thus assure the accumulation of reserves necessary to resume growth after the next season.

A genome-wide association study of early-maturation traits in upland cotton based on the CottonSNP80K array

Genome-wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early-maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high-quality single-nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early-maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker-assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.

Auxin Contributes to the Intraorgan Regulation of Gene Expression in Response to Shade

Plants sense and respond to light via multiple photoreceptors including phytochrome. The decreased ratio of red to far-red light that occurs under a canopy triggers shade-avoidance responses, which allow plants to compete with neighboring plants. The leaf acts as a photoperceptive organ in this response. In this study, we investigated how the shade stimulus is spatially processed within the cotyledon. We performed transcriptome analysis on microtissue samples collected from vascular and nonvascular regions of Arabidopsis (Arabidopsis thaliana) cotyledons. In addition, we mechanically isolated and analyzed the vascular tissue. More genes were up-regulated by the shade stimulus in vascular tissues than in mesophyll and epidermal tissues. The genes up-regulated in the vasculature were functionally divergent and included many auxin-responsive genes, suggesting that various physiological/developmental processes might be controlled by shade stimulus in the vasculature. We then investigated the spatial regulation of these genes in the vascular tissues. A small vascular region within a cotyledon was irradiated with far-red light, and the response was compared with that when the whole seedling was irradiated with far-red light. Most of the auxin-responsive genes were not fully induced by the local irradiation, suggesting that perception of the shade stimulus requires that a wider area be exposed to far-red light or that a certain position in the mesophyll and epidermis of the cotyledon be irradiated. This result was consistent with a previous report that auxin synthesis genes are up-regulated in the periphery of the cotyledon. Hence, auxin acts as an important intraorgan signaling factor that controls the vascular shade response within the cotyledon.

Recent insights into cotton functional genomics: progress and future perspectives

Functional genomics has transformed from futuristic concept to well-established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re-sequencing broad diversity panels with the development of high-throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.

Characterization and Functional Analysis of PEBP Family Genes in Upland Cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is a naturally occurring photoperiod-sensitive perennial plant species. However, sensitivity to the day length was lost during domestication. The phosphatidylethanolamine-binding protein (PEBP) gene family, of which three subclades have been identified in angiosperms, functions to promote and suppress flowering in photoperiod pathway. Recent evidence indicates that PEBP family genes play an important role in generating mobile flowering signals. We isolated homologues of the PEBP gene family in upland cotton and examined their regulation and function. Nine PEBP-like genes were cloned and phylogenetic analysis indicated the genes belonged to four subclades (FT, MFT, TFL1 and PEBP). Cotton PEBP-like genes showed distinct expression patterns in relation to different cotton genotypes, photoperiod responsive and cultivar maturity. The GhFT gene expression of a semi-wild race of upland cotton were strongly induced under short day condition, whereas the GhPEBP2 gene expression was induced under long days. We also elucidated that GhFT but not GhPEBP2 interacted with FD-like bZIP transcription factor GhFD and promote flowering under both long- and short-day conditions. The present result indicated that GhPEBP-like genes may perform different functions. This work corroborates the involvement of PEBP-like genes in photoperiod response and regulation of flowering time in different cotton genotypes, and contributes to an improved understanding of the function of PEBP-like genes in cotton.

Functional characterization of GhSOC1 and GhMADS42 homologs from upland cotton (Gossypium hirsutum L.)

In Arabidopsis flowering pathway, MADS-box genes encode transcription factors, with their structures and functions highly conserved in many species. In our study, two MADS-box genes GhSOC1 and GhMADS42 (Gossypium hirsutum L.) were cloned from upland cotton CCRI36 and transformed into Arabidopsis. GhSOC1 was additionally transformed into upland cotton. Comparative analysis demonstrated sequence conservation between GhSOC1 and GhMADS42 and genes of other plant species. Tissue-specific expression analysis of GhSOC1 and GhMADS42 revealed spatiotemporal expression patterns involving high transcript levels in leaves, shoot apical buds, and flowers. In addition, overexpression of both GhSOC1 and GhMADS42 in Arabidopsis accelerated flowering, with GhMADS42 transgenic plants showing abnormal floral organ phenotypes. Overexpression of GhSOC1 in upland cotton also produced variations in floral organs. Furthermore, chromatin immunoprecipitation assay demonstrated that GhSOC1 could regulate GhMADS41 and GhMADS42, but not FLOWERING LOCUS T, by directly binding to the genes promoter. Finally, yeast two-hybrid and bimolecular fluorescence complementation approaches were undertaken to better understand the interaction of GhSOC1 and other MADS-box factors. These experiments showed that GhSOC1 can interact with APETALA1/FRUITFULL-like proteins in cotton.

Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus

BACKGROUND

Flowering time, plant height and seed yield are strongly influenced by climatic and day-length adaptation in crop plants. To investigate these traits under highly diverse field conditions in the important oilseed crop Brassica napus, we performed a genome-wide association study using data from diverse agroecological environments spanning three continents.

METHODS

A total of 158 European winter-type B.napus inbred lines were genotyped with 21,623 unique, single-locus single-nucleotide polymorphism (SNP) markers using the Brassica 60 K-SNP Illumina® Infinium consortium array. Phenotypic associations were calculated in the panel over the years 2010-2012 for flowering time, plant height and seed yield in 5 highly diverse locations in Germany, China and Chile, adding up to 11 diverse environments in total.

RESULTS

We identified 101 genome regions associating with the onset of flowering, 69 with plant height, 36 with seed yield and 68 cross-trait regions with potential adaptive value. Within these regions, B.napus orthologs for a number of candidate adaptation genes were detected, including central circadian clock components like CIRCADIAN CLOCK- ASSOCIATED 1 (Bna.CCA1) and the important flowering-time regulators FLOWERING LOCUS T (Bna.FT) and FRUITFUL (Bna.FUL).

DISCUSSION

Gene ontology (GO) enrichment analysis of candidate regions suggested that selection of genes involved in post-transcriptional and epigenetic regulation of flowering time may play a potential role in adaptation of B. napus to highly divergent environments. The classical flowering time regulators Bna.FLC and Bna.CO were not found among the candidate regions, although both show functional variation. Allelic effects were additive for plant height and yield, but not for flowering time. The scarcity of positive minor alleles for yield in this breeding pool points to a lack of diversity for adaptation that could restrict yield gain in the face of environmental change.

CONCLUSIONS

Our study provides a valuable framework to further improve the adaptability and yield stability of this recent allopolyploid crop under changing environments. The results suggest that flowering time regulation within an adapted B. napus breeding pool is driven by a high number of small modulating processes rather than major transcription factors like Bna.CO. In contrast, yield regulation appears highly parallel, therefore yield could be increased by pyramiding positively associated haplotypes.

Candidate Gene Identification of Flowering Time Genes in Cotton

Flowering time control is critically important to all sexually reproducing angiosperms in both natural ecological and agronomic settings. Accordingly, there is much interest in defining the genes involved in the complex flowering-time network and how these respond to natural and artificial selection, the latter often entailing transitions in day-length responses. Here we describe a candidate gene analysis in the cotton genus Gossypium, which uses homologs from the well-described Arabidopsis flowering network to bioinformatically and phylogenetically identify orthologs in the published genome sequence from G. raimondii Ulbr., one of the two model diploid progenitors of the commercially important allopolyploid cottons, G. hirsutum L. and G. barbadense L. Presence and patterns of expression were evaluated from 13 aboveground tissues related to flowering for each of the candidate genes using allopolyploid G. hirsutum as a model. Furthermore, we use a comparative context to determine copy number variability of each key gene family across 10 published angiosperm genomes. Data suggest a pattern of repeated loss of duplicates following ancient whole-genome doubling events in diverse lineages. The data presented here provide a foundation for understanding both the parallel evolution of day-length neutrality in domesticated cottons and the flowering-time network, in general, in this important crop plant.

Involvement of cotton gene GhFPF1 in the regulation of shade avoidance responses in Arabidopsis thaliana

Phytochrome system perceives the reduction in the ratio of red to far-red light when plants are grown under dense canopy. This signal, regarded as a warning of competition, will trigger a series of phenotypic changes to avoid shade. Progress has been made for several phytochrome signaling intermediates acting as positive regulators of accelerated elongation growth and promotion of flowering in shade-avoidance has been identified. Recently, a FPF1 homolog GhFPF1 was identified in upland cotton. Our data supported that transgenic Arabidopsis of over-expressing GhFPF1 displayed a constitutive shade-avoiding phenotype resembling phyB mutants in several respects such as accelerated elongation of hypocotyl and petioles, upward of leaf movement, and promoted flowering. In this addendum, by dissection of GhFPF1 acting as a component of shade-avoidance responses we suppose that GhFPF1 might influence the timing of the floral transition independently of shade-mediated early flowering. Furthermore, the opposite changes of IAA content in transgenic leaves and stems suggested that alteration of IAA storage and release took place during shade-avoidance responses.