Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis

Constitutive expression of CEN-like protein 2, a TFL1 ortholog of pigeon pea (Cajanus cajan [L.] Millspaugh) delays flowering in transgenic tobacco plants

CEN-like protein 2 of pigeon pea, a candidate anti-florigen gene and a close homolog of AtTFL1 (Arabidopsis Terminal Flower1) of the PEBP family has been characterized through constitutive expression in tobacco. In-silico analysis helped to demonstrate the absence of a nuclear binding domain and the conserveness of substrate binding sites of this protein across angiosperms. Transgenic tobacco lines with 2-eightfold higher expressions of CEN-like protein 2 showed delayed flowering (26-32 days) along with significant morphological changes, including vegetative vigour, number and size of flowers, fruit setting, etc. Together, these findings showed that CEN-like protein 2 not only delays floral transition through repression but also regulates a variety of developmental traits. Expression profiling of upstream and downstream interacting pathway genes explained that their expression modulation led to a prolonged vegetative phase of over-expressed lines. Floral inducer genes like APETALA1 and LEAFY were drastically down-regulated in transgenic lines, reconfirming the role of the CEN-like 2 gene in floral regulation. In conclusion, precisely controlling CcCEN-like 2 gene expression may prove useful for refining pigeon pea breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01572-8.

Characterization of pecan PEBP family genes and the potential regulation role of CiPEBP-like1 in fatty acid synthesis

Phosphatidyl ethanolamine-binding protein (PEBP) plays important roles in plant growth and development. However, few studies have investigated the PEBP gene family in pecan (Carya illinoinensis), particularly the function of the PEBP-like subfamily. In this study, we identified 12 PEBP genes from the pecan genome and classified them into four subfamilies: MFT-like, FT-like, TFL1-like and PEBP-like. Multiple sequence alignment, gene structure, and conserved motif analyses indicated that pecan PEBP subfamily genes were highly conserved. Cis-element analysis revealed that many light responsive elements and plant hormone-responsive elements are found in CiPEBPs promoters. Additionally, RNA-seq and RT-qPCR showed that CiPEBP-like1 was highly expressed during kernel filling stage. GO and KEGG enrichment analysis further indicated that CiPEBP-like1 was involved in fatty acid biosynthesis and metabolism progress. Overexpression of CiPEBP-like1 led to earlier flowering and altered fatty acid composition in Arabidopsis seeds. RT-qPCR confirmed that CiPEBP-like1 promoted fatty acid synthesis by regulating the expression of key genes. Overall, this study contributes to a comprehensive understanding of the potential functions of the PEBP family genes and lay a foundation to modifying fatty acid composition in pecan kernel.

Genome-wide identification of the Sec14 gene family and the response to salt and drought stress in soybean (Glycine max)

BACKGROUND

The Sec14 domain is an ancient lipid-binding domain that evolved from yeast Sec14p and performs complex lipid-mediated regulatory functions in subcellular organelles and intracellular traffic. The Sec14 family is characterized by a highly conserved Sec14 domain, and is ubiquitously expressed in all eukaryotic cells and has diverse functions. However, the number and characteristics of Sec14 homologous genes in soybean, as well as their potential roles, remain understudied.

RESULTS

In this study, we identified 77 Sec14 genes in the soybean genome that were unevenly distributed across 19 chromosomes. Based on the classification method used for Arabidopsis Sec14 members, GmSec14s can be categorized into three classes: GmPITP1 to GmPITP37, GmSFH1 to GmSFH25, and GmPATL1 to GmPATL15. Structural analysis of the GmSec14 genes revealed that the SFH subfamily contained more introns than the other subfamilies. A total of 10 conserved protein motifs were detected within GmSec14 proteins, with each subfamily possessing unique motifs. Two tandem duplications and 73 segmental duplications were identified among the GmSec14 genes. Additionally, a large number of cis-acting elements, particularly those related to plant hormones, were abundant in the promoter regions of the GmSec14 genes. Tissue expression analysis of the GmSec14 genes indicated that they exhibited distinct tissue-specific expression patterns. In response to salt stress, multiple genes were found to be either upregulated or downregulated. In contrast, the majority of genes were downregulated under drought stress conditions. Notably, 12 GmSec14 genes exhibited significant alterations in expression following salt or drought stress, suggesting a potential role for these genes in stress response mechanisms. Furthermore, the protein interaction network and miRNA regulation associated with GmSec14s were predicted to elucidate the potential functions of GmSec14 members.

CONCLUSIONS

This study provides a systematic and comprehensive examination of the Sec14 gene family in soybean, which will facilitate further functional research into their roles in response to salt and drought tolerance.

Evolution of FLOWERING LOCUS T-like genes in angiosperms: a core Lamiales-specific diversification

Plant life history is determined by two transitions, germination and flowering time, in which the phosphatidylethanolamine-binding proteins (PEBPs) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared with the highly conserved TFL1-like genes, FT-like genes vary significantly in copy numbers in gymnosperms, and monocots within the angiosperms, while sporadic duplications can be observed in eudicots. Here, via a systematic analysis of the PEBPs in angiosperms with a special focus on 12 representative species featuring high-quality genomes in the order Lamiales, we identified a successive lineage-specific but systematic expansion of FT-like genes in the families of core Lamiales. The first expansion event generated FT1-like genes mainly via a core Lamiales-specific whole-genome duplication (cL-WGD), while a likely random duplication produced the FT2-like genes in the lineages containing Scrophulariaceae and the rest of the core Lamiales. Both FT1- and FT2-like genes were further amplified tandemly in some families. These expanded FT-like genes featured highly diverged expression patterns and structural variation, indicating functional diversification. Intriguingly, some core Lamiales contained the relict MOTHER OF FT AND TFL1 like 2 (MFT2) that probably expanded in the common ancestor of angiosperms. Our data showcase the highly dynamic lineage-specific expansion of the FT-like genes, and thus provide important and fresh evolutionary insights into the gene regulatory network underpinning flowering time diversity in Lamiales and, more generally, in angiosperms.

CRISPR/Cas9-mediated mutagenesis of FT/TFL1 in petunia improves plant architecture and early flowering

Petunias are renowned ornamental species widely cultivated as pot plants for their aesthetic appeal both indoors and outdoors. The preference for pot plants depends on their compact growth habit and abundant flowering. While genome editing has gained significant popularity in many crop plants in addressing growth and development and abiotic and biotic stress factors, relatively less emphasis has been placed on its application in ornamental plant species. Genome editing in ornamental plants opens up possibilities for enhancing their aesthetic qualities, offering innovative opportunities for manipulating plant architecture and visual appeal through precise genetic modifications. In this study, we aimed to optimize the procedure for an efficient genome editing system in petunia plants using the highly efficient multiplexed CRISPR/Cas9 system. Specifically, we targeted a total of six genes in Petunia which are associated with plant architecture traits, two paralogous of FLOWERING LOCUS T (PhFT) and four TERMINAL FLOWER-LIKE1 (PhTFL1) paralogous genes separately in two constructs. We successfully induced homogeneous and heterogeneous indels in the targeted genes through precise genome editing, resulting in significant phenotypic alterations in petunia. Notably, the plants harboring edited PhTFL1 and PhFT exhibited a conspicuously early flowering time in comparison to the wild-type counterparts. Furthermore, mutants with alterations in the PhTFL1 demonstrated shorter internodes than wild-type, likely by downregulating the gibberellic acid pathway genes PhGAI, creating a more compact and aesthetically appealing phenotype. This study represents the first successful endeavor to produce compact petunia plants with increased flower abundance through genome editing. Our approach holds immense promise to improve economically important potting plants like petunia and serve as a potential foundation for further improvements in similar ornamental plant species.

Genome-wide identification, subcellular localization, and expression analysis of the phosphatidyl ethanolamine-binding protein family reveals the candidates involved in flowering and yield regulation of Tartary buckwheat (Fagopyrum tataricum)

Background

PEBP (phosphatidyl ethanolamine-binding protein) is widely found in eukaryotes including plants, animals and microorganisms. In plants, the PEBP family plays vital roles in regulating flowering time and morphogenesis and is highly associated to agronomic traits and yields of crops, which has been identified and characterized in many plant species but not well studied in Tartary buckwheat (Fagopyrum tataricum Gaertn.), an important coarse food grain with medicinal value.

Methods

Genome-wide analysis of FtPEBP gene family members in Tartary buckwheat was performed using bioinformatic tools. Subcellular localization analysis was performed by confocal microscopy. The expression levels of these genes in leaf and inflorescence samples were analyzed using qRT-PCR.

Results

Fourteen Fagopyrum tataricum PEBP (FtPEBP) genes were identified and divided into three sub-clades according to their phylogenetic relationships. Subcellular localization analysis of the FtPEBP proteins in tobacco leaves indicated that FT- and TFL-GFP fusion proteins were localized in both the nucleus and cytoplasm. Gene structure analysis showed that most FtPEBP genes contain four exons and three introns. FtPEBP genes are unevenly distributed in Tartary buckwheat chromosomes. Three tandem repeats were found among FtFT5/FtFT6, FtMFT1/FtMFT2 and FtTFL4/FtTFL5. Five orthologous gene pairs were detected between F. tataricum and F. esculentum. Seven light-responsive, nine hormone-related and four stress-responsive elements were detected in FtPEBPs promoters. We used real-time PCR to investigate the expression levels of FtPEBPs among two flowering-type cultivars at floral transition time. We found FtFT1/FtFT3 were highly expressed in leaf and young inflorescence of early-flowering type, whereas they were expressed at very low levels in late-flowering type cultivars. Thus, we deduced that FtFT1/FtFT3 may be positive regulators for flowering and yield of Tartary buckwheat. These results lay an important foundation for further studies on the functions of FtPEBP genes which may be utilized for yield improvement.

Functional Differentiation of the Duplicated Gene BrrCIPK9 in Turnip (Brassica rapa var. rapa)

Gene duplication is a key biological process in the evolutionary history of plants and an important driving force for the diversification of genomic and genetic systems. Interactions between the calcium sensor calcineurin B-like protein (CBL) and its target, CBL-interacting protein kinase (CIPK), play important roles in the plant's response to various environmental stresses. As a food crop with important economic and research value, turnip (Brassica rapa var. rapa) has been well adapted to the environment of the Tibetan Plateau and become a traditional crop in the region. The BrrCIPK9 gene in turnip has not been characterized. In this study, two duplicated genes, BrrCIPK9.1 and BrrCIPK9.2, were screened from the turnip genome. Based on the phylogenetic analysis, BrrCIPK9.1 and BrrCIPK9.2 were found located in different sub-branches on the phylogenetic tree. Real-time fluorescence quantitative PCR analyses revealed their differential expression levels between the leaves and roots and in response to various stress treatments. The differences in their interactions with BrrCBLs were also revealed by yeast two-hybrid analyses. The results indicate that BrrCIPK9.1 and BrrCIPK9.2 have undergone Asparagine-alanine-phenylalanine (NAF) site divergence during turnip evolution, which has resulted in functional differences between them. Furthermore, BrrCIPK9.1 responded to high-pH (pH 8.5) stress, while BrrCIPK9.2 retained its ancestral function (low K+), thus providing further evidence of their functional divergence. These functional divergence genes facilitate turnip's good adaptation to the extreme environment of the Tibetan Plateau. In summary, the results of this study reveal the characteristics of the duplicated BrrCIPK9 genes and provide a basis for further functional studies of BrrCBLs-BrrCIPKs in turnip.

The FLOWERING LOCUS T 5b positively regulates photoperiodic flowering and improves the geographical adaptation of soybean

Plants can sense the photoperiod to flower at the right time. As a sensitive short-day crop, soybean (Glycine max) flowering varies greatly depending on photoperiods, affecting yields. Adaptive changes in soybeans rely on variable genetic loci such as E1 and FLOWERING LOCUS T orthologs. However, the precise coordination and control of these molecular components remain largely unknown. In this study, we demonstrate that GmFT5b functions as a crucial factor for soybean flowering. Overexpressed or mutated GmFT5b resulted in significantly early or later flowering, altering expression profiles for several downstream flowering-related genes under a long-day photoperiod. GmFT5b interacts with the transcription factor GmFDL15, suggesting transcriptional tuning of flowering time regulatory genes via the GmFT5b/GmFDL15 complex. Notably, GmFT5a partially compensated for GmFT5b function, as ft5a ft5b double mutants exhibited an enhanced late-flowering phenotype. Association mapping revealed that GmFT5b was associated with flowering time, maturity, and geographical distribution of soybean accessions, all associated with the E1 locus. Therefore, GmFT5b is a valuable target for enhancing regional adaptability. Natural variants or multiple mutants in this region can be utilized to generate optimized soybean varieties with precise flowering times.

Synergistic optimization of crops by combining early maturation with other agronomic traits

Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.

Molecular breeding for improvement of photothermal adaptability in soybean

Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01406-z.

The genetic basis of shoot architecture in soybean

Shoot architecture refers to the three-dimensional body plan of the above ground organs of the plant. The patterning of this body plan results from the tight genetic control of the size and maintenance of meristems, the initiation of axillary growth, and the timing of developmental phase transition. Variation in shoot architecture can result in dramatic differences in plant productivity and/or grain yield due to their effects on light interception, photosynthetic efficiency, response to agronomic inputs, and environmental adaptation. The fine-tuning of shoot architecture has consequently been of great interest to plant breeders, driving the need for deeper understanding of the genes and molecular mechanisms governing these traits. In soybean, the world's most important oil and protein crop, major components of shoot architecture include stem growth habit, plant height, branch angle, branch number, leaf petiole angle, and the size and shape of leaves. Key genes underlying some of these traits have been identified to integrate hormonal, developmental, and environmental signals modulating the growth and orientation of shoot organs. Here we summarize the current knowledge and recent advances in the understanding of the genetic control of these important architectural traits in soybean.

Functional characterization of three TERMINAL FLOWER 1-like genes from Platanus acerifolia

KEY MESSAGE

TFL1-like genes of the basal eudicot Platanus acerifolia have conserved roles in maintaining vegetative growth and inhibiting flowering, but may act through distinct regulatory mechanism. Three TERMINAL FLOWER 1 (TFL1)-like genes were isolated and characterized from London plane tree (Platanus acerifolia). All genes have conserved genomic organization and characteristic of the phosphatidylethanolamine-binding protein (PEBP) family. Sequence alignment and phylogenetic analysis indicated that two genes belong to the TFL1 clade, designated as PlacTFL1a and PlacTFL1b, while another one was grouped in the BFT clade, named as PlacBFT. qRT-PCR analysis showed that all three genes primarily expressed in vegetative phase, but the expression of PlacTFL1a was much higher and wider than that of PlacTFL1b, with the latter only detected at relatively low expression levels in apical and lateral buds in April. PlacBFT was mainly expressed in young stems of adult trees followed by juvenile tissues. Ectopic expression of any TFL1-like gene in Arabidopsis showed phenotypes of delayed or repressed flowering. Furthermore, overexpression of PlacTFL1a gene in petunia also resulted in extremely delayed flowering. In non-flowering 35:PlacTFL1a transgenic petunia plants, the FT-like gene (PhFT) gene was significantly upregulated and AP1 homologues PFG, FBP26 and FBP29 were significantly down-regulated in leaves. Yeast two-hybrid analysis indicated that only weak interactions were detected between PlacTFL1a and PlacFDL, and PlacTFL1a showed no interaction with PhFDL1/2. These results indicated that the TFL1-like genes of Platanus have conserved roles in repressing flowering, but probably via a distinct regulatory mechanism.

An Improved Genome-Wide Association Procedure Explores Gene-Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population

In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene-allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADL_DSF and AAT_DSF, 130-141 genes with 384-406 alleles were explored, and for DFM and its related ADL_DFM and AAT_DFM, 124-135 genes with 362-384 alleles were explored, in a total of six gene-allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene-allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks.

Identification, evolution and expression analyses of the whole genome-wide PEBP gene family in Brassica napus L

BACKGROUND

With the release of genomic data for B.rapa, B.oleracea, and B.napus, research on the genetic and molecular functions of Brassica spp. has entered a new stage. PEBP genes in plants play an important role in the transition to flowering as well as seed development and germination. Molecular evolutionary and functional analyses of the PEBP gene family in B.napus based on molecular biology methods can provide a theoretical basis for subsequent investigations of related regulators.

RESULTS

In this paper, we identified a total of 29 PEBP genes from B.napus that were located on 14 chromosomes and 3 random locations. Most members contained 4 exons and 3 introns; motif 1 and motif 2 were the characteristic motifs of PEBP members. On the basis of intraspecific and interspecific collinearity analyses, it is speculated that fragment replication and genomic replication are the main drivers of for the amplification and evolution of the PEBP gene in the B.napus genome. The results of promoter cis-elements prediction suggest that BnPEBP family genes are inducible promoters, which may directly or indirectly participate in multiple regulatory pathways of plant growth cycle. Furthermore, the tissue-specific expression results show that the expression levels of BnPEBP family genes in different tissues were quite different, but the gene expression organization and patterns of the same subgroup were basically the same. qRT‒PCR revealed certain spatiotemporal patterns in the expression of the PEBP subgroups in roots, stems, leaves, buds, and siliques, was tissue-specific, and related to function.

CONCLUSIONS

A systematic comparative analysis of the B.napus PEBP gene family was carried out at here. The results of gene identification, phylogenetic tree construction, structural analysis, gene duplication analysis, prediction of promoter cis-elements and interacting proteins, and expression analysis provide a reference for exploring the molecular mechanisms of BnPEBP family genes in future research.

MOTHER-OF-FT-AND-TFL1 regulates the seed oil and protein content in soybean

Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed oil and protein are regulated by complex quantitative trait loci (QTLs) and have undergone intensive selections during the domestication of soybean. It is essential to identify the major genetic components and understand their mechanism behind seed oil and protein in soybean. We report that MOTHER-OF-FT-AND-TFL1 (GmMFT) is the gene of a classical QTL that has been reported to regulate seed oil and protein content in many studies. Mutation of MFT decreased seeds oil content and weight in both Arabidopsis and soybean, whereas increased expression of GmMFT enhanced seeds oil content and weight. Haplotype analysis showed that GmMFT has undergone selection, which resulted in the extended haplotype homozygosity in the cultivated soybean and the enriching of the oil-favorable allele in modern soybean cultivars. This work unraveled the GmMFT-mediated mechanism regulating seed oil and protein content and seed weight, and revealed a previously unknown function of MFT that provides new insights into targeted soybean improvement and breeding.

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

Genome-wide identification and expression analysis disclose the pivotal PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN members that may be utilized for yield improvement of Chenopodium quinoa

Quinoa (Chenopodium quinoa) is a prospective orphan crop that needs yield improvement. Previous studies indicate PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family genes are highly associated with the key agronomic traits of crops. Characterizing the pivotal PEBP genes will speed up the domestication and yield improvement of quinoa. Previous investigations on PEBP genes of Chenopodium species indicated that, the PEBP genes, despite in the same subclade, may have experienced functional diversification. Especially, the allotetraploidy (AABB) and numerous segmental duplications and chromosomal rearrangements in quinoa make it more difficult to understand the functions of PEBP genes. More recently, 6 quinoa FT subfamily genes were predicted to be related to flowering of quinoa. However, investigation on the whole PEBP family members is still lacking. In this study, we obtained 23 PEBP genes, including 5 MFT, 11 FTL and 7 TFL genes. We found 7 orthologous gene pairs, from sub-genome A and sub-genome B, respectively, showing collinearities with sugar beet. Evolution analysis on PEBP genes of two quinoa sub-genomes, sugar beet and relatives of diploid ancestors indicated that, the reasons for gene duplication events varied and 4 tandem duplications are the major reason for PEBP family expansion. Tissue-specific expression analysis suggested that expression patterns are mostly differing between orthologous gene pairs. Analysis on gene expressions at 6 stages suggested the possible positive roles of CqFTL1/CqFTL2, CqFTL5, CqFTL8, CqFTL6/CqFTL9 and CqTFL6/CqTFL7, and negative roles of CqTFL1/CqTFL2/CqTFL3, CqTFL4/CqTFL5 in inflorescence branching. Expression analysis in ABA-treated seed, in combination with the cis-acting element distribution analysis, indicated that CqMFT2, CqMFT3 and CqMFT4 may regulate seed germination via ABA signaling. Observations on responses to night break and photoperiod changes highlighted the roles of CqFTL5 and CqFTL8 under short day, and CqFTL6 under long day for quinoa flowering. Further, co-expression network analysis indicated that 64 transcription factors may act upstream of CqFTL5 and CqFTL8 to regulate flowering. Together, this study will help us identify the pivotal PEBP genes that may be utilized for quinoa breeding in future.

Large-scale analyses of angiosperm Flowering Locus T genes reveal duplication and functional divergence in monocots

FLOWERING LOCUS T (FT) are well-known key genes for initiating flowering in plants. Delineating the evolutionary history and functional diversity of FT genes is important for understanding the diversification of flowering time and how plants adapt to the changing surroundings. We performed a comprehensive phylogenetic analysis of FT genes in 47 sequenced flowering plants and the 1,000 Plant Transcriptomes (1KP) database with a focus on monocots, especially cereals. We revealed the evolutionary history of FT genes. The FT genes in monocots can be divided into three clades (I, II, and III), whereas only one monophyletic group was detected in early angiosperms, magnoliids, and eudicots. Multiple rounds of whole-genome duplications (WGD) events followed by gene retention contributed to the expansion and variation of FT genes in monocots. Amino acid sites in the clade II and III genes were preferentially under high positive selection, and some sites located in vital domain regions are known to change functions when mutated. Clade II and clade III genes exhibited high variability in important regions and functional divergence compared with clade I genes; thus, clade I is more conserved than clade II and III. Genes in clade I displayed higher expression levels in studied organs and tissues than the clade II and III genes. The co-expression modules showed that some of the FT genes might have experienced neofunctionalization and subfunctionalization, such as the acquisition of environmental resistance. Overall, FT genes in monocots might form three clades by the ancient gene duplication, and each clade was subsequently subjected to different selection pressures and amino acid substitutions, which eventually led to different expression patterns and functional diversification. Our study provides a global picture of FT genes' evolution in monocots, paving a road for investigating FT genes' function in future.

Natural allelic variation of GmST05 controlling seed size and quality in soybean

Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.

GmFT3a fine-tunes flowering time and improves adaptation of soybean to higher latitudes

Onset of flowering of plants is precisely controlled by extensive environmental factors and internal molecular networks, in which FLOWERING LOCUS T (FT) is a key flowering integrator. In soybean, a typical short-day plant, 11 FT homologues are found in its genome, of which several homologues are functionally diversified in flowering pathways and the others including GmFT3a are yet unknown. In the current study, we characterized GmFT3a, which is located on the same chromosome as the flowering promoters GmFT2a and GmFT5a. Overexpression of GmFT3a significantly promoted flowering of Arabidopsis under the inductive long-day (LD) photoperiod. GmFT3a over-expressed soybean also flowered earlier than the control under LD, but they were not significantly different under inductive short-day (SD) conditions, indicating that GmFT3a acts as a flowering promoter in the non-inductive photoperiod in soybean. Compared with other GmFT homologues, GmFT3a exhibited a slighter effect in flowering promotion than GmFT2a, GmFT5a and GmFT2b under LD conditions. GmFT3a promoted flowering by regulating the expression of downstream flowering-related genes and also affected the expression of other GmFTs. According to the re-sequencing data, the regional distributions of two major haplotypes in 176 soybean varieties were analyzed. The varieties with GmFT3a-Hap2 haplotype matured relatively early, and relative higher expression of GmFT3a was detected in early maturing varieties, implying that Hap2 variation may contribute to the adaptation of soybean to higher latitude regions by increasing expression level of genes in metabolism and signaling pathways. The early flowering germplasm generated by overexpression of GmFT3a has potential to be planted at higher latitudes where non-inductive long day is dominant in the growing season, and GmFT3a can be used to fine-tune soybean flowering and maturity time and improve the geographical adaptation.

Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation

Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.

Ferroptosis in plants: regulation of lipid peroxidation and redox status

Regulated cell death (RCD) is an essential process that plays key roles along the plant life cycle. Unlike accidental cell death, which is an uncontrolled biological process, RCD involves integrated signaling cascades and precise molecular-mediated mechanisms that are triggered in response to specific exogenous or endogenous stimuli. Ferroptosis is a cell death pathway characterized by the iron-dependent accumulation of lipid reactive oxygen species. Although first described in animals, ferroptosis in plants shares all the main core mechanisms observed for ferroptosis in other systems. In plants as in animals, oxidant and antioxidant systems outline the process of lipid peroxidation during ferroptosis. In plants, cellular compartments such as mitochondria, chloroplasts and cytosol act cooperatively and coordinately to respond to changing redox environments. This particular context makes plants a unique model to study redox status regulation and cell death. In this review, we focus on our most recent understanding of the regulation of redox state and lipid peroxidation in plants and their role during ferroptosis.

Genome-Wide Identification and Expression Profiling of CONSTANS-Like Genes in Pepper (Capsicum annuum): Gaining an Insight to Their Phylogenetic Evolution and Stress-Specific Roles

CONSTANS-like (COL) genes play important regulatory roles in multiple growth and development processes of plants but have rarely been studied in Capsicum annuum. This study explored the evolutionary relationship and expression patterns of COL genes from C. annuum. A total of 10 COL genes were identified in the genome of the cultivated pepper Zunla-1 and were named CaCOL01-10. These genes were unequally distributed among five chromosomes and could be divided into three groups based on differences in gene structure characteristics. During evolutionary history, duplications and retentions were divergent among different groups of COL genes. Tandem duplication caused amplification of group I genes. Genetic distance among COL genes was the largest in group III, suggesting that group III genes undergo more relaxed selection pressure compared with the other groups. Expression patterns of CaCOLs in tissues were significantly different, with CaCOL08 exhibiting the highest expression in stem and leaf. Some COL orthologous genes showed markedly different expression patterns in pepper compared with tomato, such as COL_1 orthologs, which may be involved in fruit development in pepper. In addition, CaCOLs participated in the regulation of abiotic stresses to varying degrees. Five CaCOL genes were induced by cold, and CaCOL02 and CaCOL03 were specifically upregulated by cold and downregulated by heat. This study provides a theoretical basis for the in-depth understanding of the functions of COL genes in pepper and their molecular mechanisms involved in growth and development and responses to abiotic stresses.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean

The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.

Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time

Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.

Tuber and Tuberous Root Development

Root and tuber crops have been an important part of human nutrition since the early days of humanity, providing us with essential carbohydrates, proteins, and vitamins. Today, they are especially important in tropical and subtropical regions of the world, where they help to feed an ever-growing population. Early induction and storage organ size are important agricultural traits, as they determine yield over time. During potato tuberization, environmental and metabolic status are sensed, ensuring proper timing of tuberization mediated by phloem-mobile signals. Coordinated cellular restructuring and expansion growth, as well as controlled storage metabolism in the tuber, are executed. This review summarizes our current understanding of potato tuber development and highlights similarities and differences to important tuberous root crop species like sweetpotato and cassava. Finally, we point out knowledge gaps that need to be filled before a complete picture of storage organ development can emerge.

Molecular mechanisms for the photoperiodic regulation of flowering in soybean

Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.

The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity

The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.

Diversification in Functions and Expressions of Soybean FLOWERING LOCUS T Genes Fine-Tunes Seasonal Flowering

The proper timing of flowering in response to environmental changes is critical for ensuring crop yields. FLOWERING LOCUS T (FT) homologs of the phosphatidylethanolamine-binding protein family play important roles as floral integrators in many crops. In soybean, we identified 17 genes of this family, and characterized biological functions in flowering for ten FT homologs. Overexpression of GmFT homologs in Arabidopsis revealed that a set of GmFT homologs, including GmFT2a/2b, GmFT3a/3b, and GmFT5a/5b, promoted flowering similar to FT; in contrast, GmFT1a/1b, GmFT4, and GmFT6 delayed flowering. Consistently, expressions of GmFT2a, GmFT2b, and GmFT5a were induced in soybean leaves in response to floral inductive short days, whereas expressions of GmFT1a and GmFT4 were induced in response to long days. Exon swapping analysis between floral activator GmFT2a and floral repressor GmFT4 revealed that the segment B region in the fourth exon is critical for their antagonistic functions. Finally, expression analysis of GmFT2a, GmFT5a, and GmFT4 in soybean accessions exhibiting various flowering times indicated that the mRNA levels of GmFT2a and GmFT5a were higher in early flowering accessions than in late-flowering accessions, while GmFT4 showed the opposite pattern. Moreover, the relative mRNA levels between GmFT2a/GmFT5a and GmFT4 was important in determining day length-dependent flowering in soybean accessions. Taken together, our results suggest that the functions of GmFT homologs have diversified into floral activators and floral repressors during soybean evolution, and the timing of flowering in response to changing day length is determined by modulating the activities of antagonistic GmFT homologs.

Ferroptosis in plants: triggers, proposed mechanisms, and the role of iron in modulating cell death

Regulated cell death plays key roles during essential processes throughout the plant life cycle. It takes part in specific developmental programs and maintains homeostasis of the organism in response to unfavorable environments. Ferroptosis is a recently discovered iron-dependent cell death pathway characterized by the accumulation of lipid reactive oxygen species. In plants, ferroptosis shares all the main hallmarks described in other systems. Those specific features include biochemical and morphological signatures that seem to be conserved among species. However, plant cells have specific metabolic pathways and a high degree of metabolic compartmentalization. Together with their particular morphology, these features add more complexity to the plant ferroptosis pathway. In this review, we summarize the most recent advances in elucidating the roles of ferroptosis in plants, focusing on specific triggers, the main players, and underlying pathways.

Circadian Clock Components Offer Targets for Crop Domestication and Improvement

During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

Cotton architecture: examining the roles of SINGLE FLOWER TRUSS and SELF-PRUNING in regulating growth habits of a woody perennial crop

By specifying patterns of determinate and indeterminate growth, FLOWERING LOCUS T/SINGLE FLOWER TRUSS (SFT) and TERMINAL FLOWER 1/SELF-PRUNING (SP) regulate plant architecture. Though well characterized in Arabidopsis, the impacts of these genes on the architectures of diverse crops cultivated in different environments, and their potential to enhance crop productivity and management, are less well addressed. Cotton (Gossypium spp.) is naturally a short-day photoperiodic perennial that is now grown primarily as a day-neutral, annual row crop. Different environments and cultivation practices favor specific growth habits to optimize yield, and in cotton, especially in regions that rely heavily on mechanized harvest, the trend has been to more determinate varieties. Identifying and functionally characterizing SFT and SP homologs in cotton uncovered new aspects of how ratios of indeterminate and determinate growth are balanced, and unraveling their genetic networks emphasized how broadly these gene products affect cotton growth habits.

GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light

Soybean is an important legume crop that displays the classic shade avoidance syndrome (SAS), including exaggerated stem elongation, which leads to lodging and yield reduction under density farming conditions. Here, we compared the effects of two shade signals, low red light to far-red light ratio (R:FR) and low blue light (LBL), on soybean status and revealed that LBL predominantly induces excessive stem elongation. We used CRISPR-Cas9-engineered Gmcry mutants to investigate the functions of seven cryptochromes (GmCRYs) in soybean and found that the four GmCRY1s overlap in mediating LBL-induced SAS. Light-activated GmCRY1s increase the abundance of the bZIP transcription factors STF1 and STF2, which directly upregulate the expression of genes encoding GA2 oxidases to deactivate GA1 and repress stem elongation. Notably, GmCRY1b overexpression lines displayed multiple agronomic advantages over the wild-type control under both dense planting and intercropping conditions. Our study demonstrates the integration of GmCRY1-mediated signals with the GA metabolic pathway in the regulation of LBL-induced SAS in soybean. It also provides a promising option for breeding lodging-resistant, high-yield soybean cultivars in the future.

Functional characterization of soybean (Glycine max) DIRIGENT genes reveals an important role of GmDIR27 in the regulation of pod dehiscence

DIRIGENT (DIR) genes play important roles in regulating plant growth and development and have been studied in many plant species. However, information on DIR genes in soybean is limited. Here, we identified and characterized 54 GmDIRs and studied the characteristics of GmDIRs. Most of the GmDIRs contained a classical gene structure, one exon; 26 conserved motifs were found among these GmDIRs. The GmDIRs were grouped into four subfamilies, DIR-a, DIR-b, DIR-e and DIR-f, based on a phylogenetic analysis, and 24 duplicated gene pairs were identified. Differences in the cis-acting elements in the GmDIR promoter regions might result in distinct expression patterns of GmDIRs in different tissues. In addition, GmDIR27 had a close relationship with the pod dehiscence gene GmPdh1, and overexpression of GmDIR27 increased pod dehiscence by affecting several pod dehiscence-related gene expressions. Generally, our results provide essential information that aids future efforts to functionally characterize soybean GmDIR genes.

Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis

CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.

Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

SINGLE FLOWER TRUSS and SELF-PRUNING signal developmental and metabolic networks to guide cotton architectures

Patterns of indeterminate and determinate growth specify plant architecture and influence crop productivity. In cotton (Gossypium hirsutum), SINGLE FLOWER TRUSS (SFT) stimulates the transition to flowering and determinate growth, while its closely related antagonist SELF-PRUNING (SP) maintains meristems in indeterminate states to favor vegetative growth. Overexpressing GhSFT while simultaneously silencing GhSP produces highly determinate cotton with reduced foliage and synchronous fruiting. These findings suggest that GhSFT, GhSP, and genes in these signaling networks hold promise for enhancing 'annualized' growth patterns and improving cotton productivity and management. To identify the molecular programs underlying cotton growth habits, we used comparative co-expression networks, differential gene expression, and phenotypic analyses in cotton varieties expressing altered levels of GhSFT or GhSP. Using multiple cotton and tomato datasets, we identified diverse genetic modules highly correlated with SFT or SP orthologs which shared related Gene Ontologies in different crop species. Notably, altering GhSFT or GhSP levels in cotton affected the expression of genes regulating meristem fate and metabolic pathways. Further phenotypic analyses of gene products involved in photosynthesis, secondary metabolism, and cell wall biosynthesis showed that early changes in GhSFT and GhSP levels profoundly impacted later development in distal tissues. Identifying the molecular underpinnings of GhSFT and GhSP activities emphasizes their broad actions in regulating cotton architecture.

Meta-analysis of QTL reveals the genetic control of yield-related traits and seed protein content in pea

Pea is one of the most important grain legume crops in temperate regions worldwide. Improving pea yield is a critical breeding target. Nine inter-connected pea recombinant inbred line populations were evaluated in nine environments at INRAE Dijon, France and genotyped using the GenoPea 13.2 K SNP array. Each population has been evaluated in two to four environments. A multi-population Quantitative Trait Loci (QTL) analysis for seed weight per plant (SW), seed number per plant (SN), thousand seed weight (TSW) and seed protein content (SPC) was done. QTL were then projected on the multi-population consensus map and a meta-analysis of QTL was performed. This analysis identified 17 QTL for SW, 16 QTL for SN, 35 QTL for TSW and 21 QTL for SPC, shedding light on trait relationships. These QTL were resolved into 27 metaQTL. Some of them showed small confidence intervals of less than 2 cM encompassing less than one hundred underlying candidate genes. The precision of metaQTL and the potential candidate genes reported in this study enable their use for marker-assisted selection and provide a foundation towards map-based identification of causal polymorphisms.

Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.

Genome-wide identification and characterization of nonspecific lipid transfer protein (nsLTP) genes in Arachis duranensis

Nonspecific lipid transfer proteins (nsLTPs) play vital roles in lipid metabolism, cell apoptosis and biotic and abiotic stresses in plants. However, the distribution of nsLTPs in Arachis duranensis has not been fully characterized. In this study, we identified 64 nsLTP genes in A. duranensis (designated AdLTPs), which were classified into six subfamilies and randomly distributed along nine chromosomes. Tandem and segmental duplication events were detected in the evolution of AdLTPs. The K_s and ω values differed significantly between Types 1 and D subfamilies, and eight AdLTPs were under positive selection. The expression levels of AdLTPs were changed after salinity, PEG, low-temperature and ABA treatments. Three AdLTPs were associated with resistance to nematode infection, and DOF and WRI1 transcription factors may regulate the AdLTP response to nematode infection. Our results may provide valuable genomic information for the breeding of peanut cultivars that are resistant to biotic and abiotic stresses.

Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

Background

Nitrogen is an indispensable nutrient for plant growth. It is used and transported in the form of amino acids in living organisms. Transporting amino acids to various parts of plants requires relevant transport proteins, such as amino acid permeases (AAPs), which were our focus in this study.

Results

We found that 5 AAP genes were present in Chlorophyte species and more AAP genes were predicted in Bryophyta and Lycophytes. Two main groups were defined and group I comprised 5 clades. Our phylogenetic analysis indicated that the origin of clades 2, 3, and 4 is Gymnospermae and that these clades are closely related. The members of clade 1 included Chlorophyta to Gymnospermae. Group II, as a new branch consisting of non-seed plants, is first proposed in our research. Our results also indicated that the AAP family was already present in Chlorophyta and then expanded accompanying the development of vasculature. Concurrently, the AAP family experienced multiple duplication events that promoted the generation of new functions and differentiation of sub-functions.

Conclusions

Our findings suggest that the AAP gene originated in Chlorophyta, and some non-seed AAP genes clustered in one group. A second group, which contained plants of all evolutionary stages, indicated the evolution of AAPs. These new findings can be used to guide future research.

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 Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.

TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem

The floral transition is a critical step in the life cycle of flowering plants, and several mechanisms control this finely orchestrated process. TERMINAL FLOWER1 (TFL1) is a floral repressor and close relative of the florigen, FLOWERING LOCUS T (FT). During the floral transition, TFL1 expression is up-regulated in the inflorescence apex to maintain the indeterminate growth of the shoot apical meristem (SAM). Both TFL1 and FT are mobile proteins, but they move in different ways. FT moves from the leaves to the SAM, while TFL1 appears to move within the SAM. The importance of TFL1 movement for its function in the regulation of flowering time and shoot indeterminacy and its molecular function are still largely unclear. Our results using Arabidopsis (Arabidopsis thaliana) indicate that TFL1 moves from its place of expression in the center of the SAM to the meristem layer L1 and that the movement in the SAM is required for the regulation of the floral transition. Chromatin immunoprecipitation sequencing and RNA sequencing demonstrated that TFL1 functions as a cotranscription factor that associates with and regulates the expression of hundreds of genes. These newly identified direct TFL1 targets provide the possibility to discover new roles for TFL1 in the regulation of floral transition and inflorescence development.

Soybean adaption to high-latitude regions is associated with natural variations of GmFT2b, an ortholog of FLOWERING LOCUS T

Day length has an important influence on flowering and growth habit in many plant species. In crops such as soybean, photoperiod sensitivity determines the geographical range over which a given cultivar can grow and flower. The soybean genome contains ~10 genes homologous to FT, a central regulator of flowering from Arabidopsis thaliana. However, the precise roles of these soybean FTs are not clearly. Here we show that one such gene, GmFT2b, promotes flowering under long-days (LDs). Overexpression of GmFT2b upregulates expression of flowering-related genes which are important in regulating flowering time. We propose a 'weight' model for soybean flowering under short-day (SD) and LD conditions. Furthermore, we examine GmFT2b sequences in 195 soybean cultivars, as well as flowering phenotypes, geographical distributions and maturity groups. We found that Hap3, a major GmFT2b haplotype, is associated with significantly earlier flowering at higher latitudes. We anticipate our assay to provide important resources for the genetic improvement of soybean, including new germplasm for soybean breeding, and also increase our understanding of functional diversity in the soybean FT gene family.

Evolution and Expression of Reproductive Transition Regulatory Genes FT/TFL1 With Emphasis in Selected Neotropical Orchids

Flowering is a rigorously timed and morphologically complex shift in plant development. This change depends on endogenous as well as environmental factors. FLOWERING LOCUS T (FT) integrates several cues from different pathways acting as a flowering promoter. Contrary to the role of FT, its paralog TERMINAL FLOWER 1 (TFL1) delays floral transition. Although FT/TFL1 homologs have been studied in model eudicots and monocots, scarce studies are available in non-model monocots like the Orchidaceae. Orchids are very diverse and their floral complexity is translated into a unique aesthetic display, which appeals the ornamental plant market. Nonetheless, orchid trade faces huge limitations due to their long vegetative phase and intractable indoor flowering seasons. Little is known about the genetic basis that control reproductive transition in orchids and, consequently, manipulating their flowering time remains a challenge. In order to contribute to the understanding of the genetic bases that control flowering in orchids we present here the first broad-scale analysis of FT/TFL1-like genes in monocots with an expanded sampling in Orchidaceae. We also compare expression patterns in three selected species and propose hypotheses on the putative role of these genes in their reproductive transition. Our findings show that FT-like genes are by far more diversified than TFL1-like genes in monocots with six subclades in the former and only one in the latter. Within MonFT1, the comparative protein sequences of MonFT1A and MonFT1B suggest that they could have recruited functional roles in delaying flowering, a role typically assigned to TFL1-like proteins. On the other hand, MonFT2 proteins have retained their canonical motifs and roles in promoting flowering transition. This is also shown by their increased expression levels from the shoot apical meristem (SAM) and leaves to inflorescence meristems (IM) and floral buds (FBs). Finally, TFL1-like genes are retained as single copy and often times are lost. Their loss could be linked to the parallel recruitment of MonFT1A and MonFT1B homologs in delaying flowering and maintaining indeterminacy of the inflorescence meristem. These hypotheses lay the foundation for future functional validation in emerging model orchid species and comparative analyses in orchids with high horticultural potential in the market.

B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis

B-box (BBX) proteins are important factors involved in plant growth and developmental regulation, and they have been identified in many species. However, information on the characteristics and transcription patterns of BBX genes in wild peanut are limited. In this study, we identified and characterized 24 BBX genes from a wild peanut, Arachis duranensis. Many characteristics were analyzed, including chromosomal locations, phylogenetic relationships, and gene structures. Arachis duranensis B-box (AdBBX) proteins were grouped into five classes based on the diversity of their conserved domains: I (3 genes), II (4 genes), III (4 genes), IV (9 genes), and V (4 genes). Fifteen distinct motifs were found in the 24 AdBBX proteins. Duplication analysis revealed the presence of two interchromosomal duplicated gene pairs, from group II and IV. In addition, 95 kinds of cis-acting elements were found in the genes’ promoter regions, 53 of which received putative functional predictions. The numbers and types of cis-acting elements varied among different AdBBX promoters, and, as a result, AdBBX genes exhibited distinct expression patterns in different tissues. Transcriptional profiling combined with synteny analysis suggests that AdBBX8 may be a key factor involved in flowering time regulation. Our study will provide essential information for further functional investigation of AdBBX genes.

Characterization and quantitative trait locus mapping of late-flowering from a Thai soybean cultivar introduced into a photoperiod-insensitive genetic background

The timing of both flowering and maturation determine crop adaptability and productivity. Soybean (Glycine max) is cultivated across a wide range of latitudes. The molecular-genetic mechanisms for flowering in soybean have been determined for photoperiodic responses to long days (LDs), but remain only partially determined for the delay of flowering under short-day conditions, an adaptive trait of cultivars grown in lower latitudes. Here, we characterized the late-flowering (LF) habit introduced from the Thai cultivar K3 into a photoperiod-insensitive genetic background under different photo-thermal conditions, and we analyzed the genetic basis using quantitative trait locus (QTL) mapping. The LF habit resulted from a basic difference in the floral induction activity and from the suppression of flowering, which was caused by red light-enriched LD lengths and higher temperatures, during which FLOWERING LOCUS T (FT) orthologs, FT2a and FT5a, were strongly down-regulated. QTL mapping using gene-specific markers for flowering genes E2, FT2a and FT5a and 829 single nucleotide polymorphisms obtained from restriction-site associated DNA sequencing detected three QTLs controlling the LF habit. Of these, a QTL harboring FT2a exhibited large and stable effects under all the conditions tested. A resequencing analysis detected a nonsynonymous substitution in exon 4 of FT2a from K3, which converted the glycine conserved in FT-like proteins to the aspartic acid conserved in TERMINAL FLOWER 1-like proteins (floral repressors), suggesting a functional depression in the FT2a protein from K3. The effects of the remaining two QTLs, likely corresponding to E2 and FT5a, were environment dependent. Thus, the LF habit from K3 may be caused by the functional depression of FT2a and the down-regulation of two FT genes by red light-enriched LD conditions and high temperatures.