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Graphical abstract Highlights • Overexpression of the VcSOC1K increases blueberry productivity by promoting early and more flower bud formation. • Overexpression of the VcSOC1K increases blueberry's tolerance to high soil pH. • Overexpression of the VcSOC1K effectively modulates plant reproductive processes. • Comparative transcriptome reveals differentially expressed (DE) MADS-box genes in responding to the overexpression of the VcSOC1K. Abstract MADS-box genes play a significant role for plant flowering. Keratin-like (K) domains are involved in protein-to-protein interactions in the formation of the MIKC-type MADS-box domain proteins. In this study, the potential of utilizing the K domain of a Vaccinium corymbosum SOC1 -like gene (VcSOC1K) was investigated to modulate expression of other blueberry MADS-box genes for increasing blueberry productivity. Chilled transgenic blueberry plants overexpressing the VcSOC1K showed a significant increase in the number of canes, floral buds, and flower and fruit clusters compared to chilled non-transgenic plants. Additionally, nonchilled transgenic plants flowered whereas nonchilled non-transgenic plants did not. Transgenic plants showed an increase in tolerance to high soil pH. Comparative transcriptome analysis of transgenic and non-transgenic leaves showed differential expression of 17% of the MADS-box genes identified in blueberry. These differentially expressed (DE) MADS-box genes were associated with genes related to plant flowering, phytohormones, and response to various biotic and abiotic stimuli. The phenotypic changes and the DE MADS-box genes caused by the overexpression of VcSOC1K not only reveal that the MADS-box genes are involved in chilling/vernalization-mediated flowering in blueberry but also demonstrated that the overexpression of the K domain can effectively modulate plant reproductive processes. [ABSTRACT FROM AUTHOR]

The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid ( Gossypium raimondii and Gossypium arboreum ) and tetraploid ( Gossypium hirsutum ) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum . The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species. [ABSTRACT FROM AUTHOR]

• A total of 104 MADS-box genes were obtained from the genome of carrot. • 48 and 56 members belonged to Type Ⅰ and Type Ⅱ, respectively. • Yeast two-hybrid assay showed that some DcMDAS-box proteins had interactions. • The expression profiles of DcMADS-box genes had varietal and stage specificity. MADS-box is the important transcription factor involved in the process of nutritional and reproductive growth of plants. To explore the information of MADS-box transcription factors in carrots (Daucus carota L.), we conducted a genome-wide identification and characteristic analysis of MADS-box in carrot. A total of 104 MADS-box factors were identified, and 48 Type Ⅰ MADS-box factors were classified into three subfamilies, Mα, Mβ, and Mγ. Among the 56 type Ⅱ MADS-box factors, 51 MADS-box factors belonged to MIKCC and 5 factors belonged to MIKC*. Subcellular localization prediction indicated that most DcMADS-box proteins were localized in the nuclear. A total of 90 DcMADS-box genes were distributed on all 9 chromosomes, and 19 tandem duplication gene pairs and 20 segmental duplication gene pairs were identified. The DcMADS-box promoter contained a variety of cis -acting regulatory elements, such as light responsiveness elements, low-temperature responsiveness elements, and hormone responsiveness elements. The results of protein interaction prediction and yeast two-hybrid assay indicated that DcMDAS-box proteins related to flowering, such as DcMADS004 and DcMADS079 can interact with DcMADS012. In addition, we found that the expression profiles of floral organ-related genes showed varietal differences and stage specificity in the three stages (early flower bud stage, middle flower bud stage, and full bloom stage) of 'Kurodagosun' (KRD) and 'Deep purple' (DPP). These results provide a potential theoretical basis for exploring the molecular mechanisms of carrot flower organ development. [ABSTRACT FROM AUTHOR]

Sweet cherry (Prunus avium L.) is sensitive to high temperature during pistil development, but the spatial and temporal variability of high temperature and the molecular mechanism of its impact on the formation of double pistils are little known. An analysis of historical and projected climate data was conducted to characterize the spatial and temporal variability of high temperature from June to September at 5 stations in main sweet cherry growing regions of China and a warmer reference site. Several high temperature indices were developed to quantify heat frequency, intensity and duration during pistil development based on observed and projected maximum temperatures. The risk of high temperature was projected to increase under two Representative Concentration Pathways for 2035–2065 and 2070–2100, and the increasing rate was higher in the south station than the north except for Yantai city. Furthermore, to explore the mechanism of double fruit formation at high temperature, we investigated the regulation of FRUITFULL (FUL) during the growth of floral buds in sweet cherry. We identified a AP1/ FUL family gene FUL from sweet cherry, which was grouped with PpCAL, PpMADS6 from Prunus persica , ParFUL from Prunus armeniaca , PyeCAL from Prunus yedoensis , and PdCAL, PdAGL8 from Prunus dulcis by phylogenetic tree analysis. The seasonal expression level of PavFUL was higher in the high multi-pistil rate cultivar during summer stage and enhanced by high temperature. Moreover, overexpression of PavFUL led to multi-silique formation and early flowering in Arabidopsis. In addition, Y2H and BiFC assays revealed that PavFUL interacted with other MADS-box proteins, including PavLFY, PavSOC1, PavAP1, and PavSEP, to co-regulate the flowering and multi-silique formation. Our findings will help decipher the possible mechanism of high temperature-mediated double fruit via affecting FUL and other MADS-box genes in molecular level for tree fruit species. • The frequency, intensity and duration of high temperature during pistil development will be increased in the future. • A multi-silique phenotype was observed in transgenic Arabidopsis of the high-temperature-responsive gene PavFUL. • PavFUL was involved in double fruit formation and flowering by interacting with PavSOC1, PavAP1, PavSEP, and PavLFY. [ABSTRACT FROM AUTHOR]

For ornamental plants, in particular orchids, the flower is central to their beauty and commercial value. The ability to manipulate the floral transition from the vegetative to the reproductive phase and floral traits requires an understanding of the underlying molecular genetic mechanisms and robust transgenic protocols. Using Dendrobium species and hybrids, this review explores the advances that have been made in the genetics of flower development, color and senescence. Although the homologs of several MADS-box genes are still to be found, those that have already been cloned and analyzed bring promise to what has yet to be unraveled about the control of flower color and development. Recent advances in orchid transformation and the introduction of Dendrobium homologs into Arabidopsis thaliana have shed new light on the complexities of flower color and the ABCDE model of flower development in orchids, or the 'orchid code'. [ABSTRACT FROM AUTHOR]

Abstract: We cloned 10 Japanese pear (Pyrus pyrifolia) MIKC-type II MADS-box genes, and analyzed their expression during fruit development and ripening. PpMADS2-1 was APETALA (AP)1-like; PpMADS3-1 was FRUITFULL (FUL)/SQUAMOSA (SQUA)-like; PpMADS4-1 was AGAMOUS-like (AGL)6; PpMADS5-1 and PpMADS8-1 were SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC)-like; PpMADS9-1, PpMADS12-1, PpMADS14-1 and PpMADS16-1 were SEPALLATA (SEP)-like; while PpMADS15-1 was AGL/SHATTERPROOF (SHP)-like. Phylogenetic analysis showed their grouping into five major clades (and 10 sub-clades) that was consistent with their diverse functional types. Expression analysis in flower tissue revealed their distinct putative homeotic functional classes: A-class (PpMADS2-1, PpMADS3-1, PpMADS4-1, and PpMADS14-1), C-class (PpMADS15-1), E-class (PpMADS9-1, PpMADS12-1, and PpMADS16-1) and E (F)-class (PpMADS5-1 and PpMADS8-1). Differential gene expression was observed in different fruit tissues (skin, cortex and core) as well as in the cortex during the course of fruit development and ripening. Collectively, our results suggest their involvement in the diverse aspects of plant development including flower development and the course of fruit development and ripening. [Copyright &y& Elsevier]

Abstract: To further understand flowering and flower organ formation in the monocot crop saffron crocus (Crocus sativus L.), we cloned four MIKCc type II MADS-box cDNA sequences of the E-class SEPALLATA3 (SEP3) subfamily designated CsatSEP3a/b/c/c_as as well as the three respective genomic sequences. Sequence analysis showed that cDNA sequences of CsatSEP3 c and c_as are the products of alternative splicing of the CsatSEP3c gene. Bioinformatics analysis with putative orthologous sequences from various plant species suggested that all four cDNA sequences encode for SEP3-like proteins with characteristic motifs and amino acids, and highlighted intriguing sequence features. Phylogenetically, the isolated sequences were closest to the SEP3-like genes from monocots such as Asparagus virgatus, Oryza sativa, Zea mays, and the dicot Arabidopsis SEP3 gene. All four isolated C. sativus sequences were strongly expressed in flowers and in all flower organs: whorl1 tepals, whorl2 tepals, stamens and carpels, but not in leaves. Expression of CsatSEP3a/b/c/c_as cDNAs was compared in wild-type and mutant flowers. Expression of the isolatedCsatSEP3-like genes in whorl1 tepals together with E-class CsatAP1/FUL subfamily and B-class CsatAP3 and CsatPI subfamilies of genes, fits the ABCE “quartet model,” an extended form of the original ABC model proposed to explain the homeotic transformation of whorl1 sepals into whorl1 tepals in Liliales and Asparagales plants such as C. sativus. This conclusion was also supported by the interaction of the CsatSEP3b protein with CsatAP1/FUL and CsatAP3 proteins. In contrast, expression of both B-class CsatAP3 and CsatPI genes and the C-class CsatAGAMOUS genes together with E-class CsatSEP3-like genes in carpels, without any phenotypic effects on carpels, raises questions about the role of these gene classes in carpel formation in this non-grass monocot and requires further experimentation. Finally, taking advantage of the size and sequence differences in amplified genomic sequences of the triploid C. sativus and comparing them with the respective sequences from C. tomasii, C. hadriaticus and C. cartwrightianus, three putative wild-type diploid progenitor species, we examined the origin of CsatSEP3a sequence. [Copyright &y& Elsevier]

Abstract: Positive selection and relaxation of purifying constraints after duplication events have driven the functional diversification of gene families involved in development. One example of this occurred within the plant MADS-box genes. The evolution of the orchid flower was driven by duplication events followed by sub- and neo-functionalization of class B DEF-like MADS-box genes, which are present at three to four copies in the orchid genome. In contrast, the orchid PI/GLO-like class B MADS-box genes have been reported thus far as single-copy loci, with the only exception of Habenaria radiata. We isolated a novel PI/GLO-like gene (OrcPI2) in Orchis italica, which is different than the previously characterized OrcPI locus. The presence of two functional paralogs of PI/GLO-like genes in orchids is detectable only within the tribe Orchidinae. Evolutionary analyses revealed an apparent relaxation of purifying selection acting on the two PI/GLO-like paralogs of the Orchidinae when compared to the single-copy PI/GLO-like genes found in other orchid species. Furthermore, by measuring dN/dS (ω) ratios, we show that a high percentage of sites between the two PI/GLO-like paralogs have different evolutionary pressures. Interestingly, the apparent relaxation of selective constraints on the two PI/GLO-like paralogs is due to strong purifying selection at synonymous sites rather than to a high value of nonsynonymous substitution rate. This peculiar evolutionary pattern might be related to molecular processes such as mRNA folding and/or translational efficiency control. These processes could potentially be involved in or predate the functional diversification of the two PI/GLO-like paralogs within Orchidinae. [Copyright &y& Elsevier]

Abstract: MADS-box genes encode transcriptional regulators that are critical for flowering, flower organogenesis and plant development. Although there are extensive reports on genes involved in flower organogenesis in model and economically important plant species, there are few reports on MADS-box genes in woody plants. In this study, we have cloned and characterized AGAMOUS (AG), SEEDSTICK (STK) and SEPALLATA (SEP) homologs from peach tree (Prunus persica L. Batsch) and studied their expression patterns in different tissues as well as in fruit pericarp during pit hardening. AG- STK- and SEP-like homologs, representative of the C-, D-, E-like MADS-box gene lineages, respectively, play key roles in stamen, carpel, ovule and fruit development in Arabidopsis thaliana. Sequence similarities, phylogenetic analysis and structural characteristics were used to provide classification of the isolated genes in type C (PPERAG), type D (PPERSTK) and type E (PPERSEP1, PPERSEP3, PPERFB9) organ identity genes. Expression patterns were determined and in combination with phylogenetic data provided useful indications on the function of these genes. These data suggest the involvement of MADS-box genes in peach flower and fruit development and provide further evidence for the role of these genes in woody perennial trees that is compatible with their function in model plant species. [Copyright &y& Elsevier]

Abstract: OrcPI is a class B MADS-box gene of Orchis italica (Orchidaceae), homologous of the PISTILLATA/GLOBOSA gene isolated in Arabidopsis and Antirrhinum. Its role in determining petals and stamens is conserved in orchids, where it seems to be involved also in other functions, such as flower longevity and ovary development. The present study reports the genomic characterization of the OrcPI locus in O. italica including coding and noncoding regions (introns, 5′- and 3′ untranslated regions, and putative promoter). Nucleotide polymorphism distribution confirmed that this gene is subjected to different evolutionary forces, phylogenetic and distance analyses demonstrated that OrcPI is a useful nuclear marker at low taxonomic level in orchids. The expression pattern analysis showed that OrcPI transcripts are present in all the floral structures, undetected in the vegetative tissues, and decreased in the natural senescent flower. Finally, micro-RNAs putative target sites were identified within the OrcPI gene, conserved among orchids. [Copyright &y& Elsevier]

Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKCC subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF :: GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10 , AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton. [ABSTRACT FROM AUTHOR]

Abstract: The evolutionary analysis of OrcPI, the orchid homologue to the PISTILLATA/GLOBOSA gene, was conducted on some Mediterranean orchid species, measuring mean pairwise K a/K s ratios and nucleotide variability. Evidence for positive selection was tested using a maximum likelihood approach implemented in PAML, and neutrality tests were conducted to assess deviation from neutral evolution. Data were also examined partitioning the coding region into four regions, corresponding to different functional domains of the protein. The results show that OrcPI is subjected to different evolutionary forces: diffuse purifying selection, localized positive selection or selective sweep, and different partitions of selective constraints. [Copyright &y& Elsevier]

Abstract: Studies have shown that several plant species posses AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium thyrsiflorum, named DthyrAG1 and DthyrAG2, respectively, and analyzed their expression patterns. Quantification by real-time RT-PCR analysis shows that both are transcribed in the mature flowers and during ovule development. Localization of the transcripts by in situ hybridization analysis in flowers reveals that both genes are transcribed in the rostellum, stigma, and stylar canal. Expression analysis during ovule development shows that DthyrAG1 is expressed only in the initial periods of placenta- and ovule development, whereas the DthyrAG2 is transcribed throughout ovule development. These results suggest that both C- and D lineage orthologs are involved in various aspects of flower development and that DthyrAG2 have a more prominent role than DthyrAG1 in late ovule development in D. thyrsiflorum. [Copyright &y& Elsevier]

Abstract: We have cloned and characterized the expression of two flower specific B-class APETALA3 -like (AP3-like) MADS-box sequences of cultivated crocus (Crocus sativus L). Based on sequencing data two sequences designated CsatAP3a and CsatAP3b could be distinguished. These were different in the 5′and 3′ untranslated regions and had five single nucleotide differences in the coding region that led to a single amino acid difference in the coded protein. The deduced amino acid sequences of the genes indicated high similarity with members of the MADS-box family of transcription factors, and particularly with other members of the paleo-AP3 lineage of B-class MADS-box proteins that control floral organ identity. Phylogenetic analysis at the amino acid level confirmed that the isolated sequences belong to the monocot-specific paleoAP3 clade. In the sequence the typical domain structure of plant MADS box proteins was observed. The conserved N-terminal MADS-box, the I domain, the central K domain and a C terminal domain harboring a paleoAP3 motif were identified. Expression analysis indicated that transcripts of CsatAP3 and also an isolated PISTILLATA-like CsatPIc sequence are not restricted to organs of the second and third whorls of the flowers but are present also in the tepals of the first whorl and stigmata of the mature crocus flower of the fourth whorl. Extension of CsatAP3 and CsatPIc expression in organs of the first whorl could be a supportive evidence to explain the homeotic transformation of sepals into tepals in crocus. [Copyright &y& Elsevier]

Summary: Orchids serve as useful model plants for the discovery and study of genes involved in novel processes in floral development because of their highly modified flowers. In this study three different FRUITFULL (FUL)-like MADS-box genes, DthyrFL1, -2, and -3 have been isolated from the orchid Dendrobium thyrsiflorum. Sequence alignment indicates that the entire sequence of exon 6 is missing in DthyrFL3 and that a frame shift could explain the missing FUL-like motif found in the sequence of both DthyrFL1 and -2. Phylogenetic analysis of the APETALA1/FRUITFULL lineage shows that FUL-like sequences from monocots all fall within one major clade and that subsequent gene duplication within this group is specific to monocots. At least two major duplication events have occurred: one before the split of the Poaceae and another within the Poaceae. Quantitative real-time RT-PCR analysis of the DthyrFL genes shows that they are expressed at different levels during inflorescence development but also transcribed in ovules and at very low levels in roots and leaves. These results suggest that the three FUL-like members are involved in floral development in D. thyrsiflorum. [Copyright &y& Elsevier]

In search of maize MADS-box genes expressed during kernel development we identified two cDNA’s corresponding to the AGL2 MADS-box gene subfamily members ZMM6 and ZMM27. Expression analyses show that expression is restricted to developing infloresences and developing kernels. In kernels the accumulation of both transcripts increase after pollination, indicating that they play a role during kernel development. In situ hybridization revealed that ZMM27 is expressed in both maternal and zygotic kernel tissues, whereas ZMM6 expression becomes restricted to the endosperm transfer cell region and the embryo as the grain develops. In an attempt to elucidate the role of MADS-box genes expressed during maize kernel development, we identified Mutator-insertion loss-of-function alleles for both ZMM6 and ZMM27 using reverse genetics. Analyses of plants homozygous for the mutant allele of ZMM6 or ZMM27, as well as double homozygous mutants showed no obvious developmental defects in the kernel, suggesting the presence of additional members of the AGL2 clade in maize with functional redundancy with of ZMM6 or ZMM27. [Copyright &y& Elsevier]

We have cloned and characterized the expression of three homologous Apetala1-like (AP1-like) genes from a crocus variety (Crocus sativus L) cultivated exclusively in Kozani, at northern Greece. The three different homologous genes were designated CsAP1 (C. sativus APETALA1) and each one was named CsAP1a, CsAP1b, and CsAP1c. They are the first reported MADS-box genes isolated from this important monocot species cultivated for its flowers.The deduced amino acid sequence of the three genes indicated high homology with members of the MADS-box family of transcription factors, and particularly with other members of the AP1-like family of MADS-box proteins that control floral-meristem and floral-organ identity. All the isolated sequences lack the typical CaaX-motif that is present in dicot AP1 functional proteins but absent in the monocot homologues thus far examined. CsAP1a and CsAP1b are more similar having 88.2% identical amino acids while CsAP1c is more divergent having 70.9% similarity with CsAP1a, and 64.5% similarity with CsAP1b. Phylogenetic analysis of the isolated genes at the amino acid level indicated that they form a clade with other monocot AP1-like genes from maize (ZmM28), barley (BM3), and rice (OsMADS18). Southern experiments indicated the presence of additional AP1-like homologues in crocus.Expression analysis indicated the presence of different amount of steady-state mRNAs for all the three homologous genes in leaves, as well as, in the three mature flower parts, namely: tepals, stamen and carpels. Similar expression pattern display many monocot AP1-like MADS-box genes, which comprise a distinct phylogenetic clade of monocot class A MADS-box genes and may reflect a novel, yet unidentified role of their corresponding proteins in these species. [Copyright &y& Elsevier]

• Forty-three secreted proteins identified in jujube witches' broom phytoplasma genome. • Eight candidate effectors highly expressed in JWB phytoplasma-infected flower buds. • SJP3 overexpression in Arabidopsis altered floral organs into leaf-like structures. • Phyllody was associated with misexpression of floral organ identity genes. Jujube witches' broom (JWB), associated with ' Candidatus Phytoplasma ziziphi', is a devastating disease in Chinese jujube (Ziziphus jujuba Mill.). One of the symptoms in plants infected with phytoplasmas is the change of floral organs into leaf-like structures, known as phyllody. Effector proteins secreted by phytoplasmas are key to inducing this and other witches' broom symptoms. However, the phytoplasma effector proteins that induce phyllody in jujube remain unknown. We identified 43 candidate secreted JWB phytoplasma proteins (SJPs) in the JWB phytoplasma genome. Eight of the predicted candidate effector genes exhibited high transcript levels in infected flower buds. Among the eight candidate effectors, SJP3 experimentally showed the potential to induce phyllody. SJP3 expression in infected jujube was at a high level in young leaves and flowers. Ectopic expression of SJP3 in Arabidopsis induced leaf-like flowers and extra secondary flowers and significantly changed the transcript levels of PISTILLATA (PI), SHORT VEGETATIVE PHASE (SVP), AGAMOUS-LIKE 24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). The expression levels of these MADS-box homologous genes were also changed in infected jujube flower buds and all four whorls of the floral organs. The data showed that the effector SJP3 disrupts expression of several MADS-box genes associated with floral organ identity and flowering time and is likely key to inducing phyllody in phytoplasma-infected jujube. This study provides new insight into understanding the pathogenesis of JWB disease induced by phytoplasma. [ABSTRACT FROM AUTHOR]

• Global gene expression profiles at different developmental stages of female flowers in pecan by RNA-sequencing, combined with morphological characteristics. • Hormone signaling pathway genes, carbon and nitrogen metabolism and MADS-box transcription factors showed significant differential expression during the floral developmental process. The LHY , PHYA , ELF3 and DELLA genes function as key roles in floral pathways. • 299 floral-related genes to construct gene co-expression network, many modules of co-expressed genes and hub genes were identified. Pecan [ Carya illinoinensis (Wangenh.) K. Koch] is a famous high grade dry fruit, oil tree species and excellent tree species for both timber and fruit. Pecan is a monoecious plant, and the formation and number of female flowers directly determine the pecan yield. In this work, to illuminate the molecular mechanism of floral formation in pecan, scanning electron microscopy was employed to distinguish the developmental stages of female flower. Three flower buds and two flowering stages were collected for high throughput RNA sequencing. 65,680 unigenes were generated with 41, 806 differentially expressed genes annotated. Genes involved in hormone signaling, carbon and nitrogen metabolism showed significant differential expression during the floral developmental process. The MADS-box gene family was analyzed in depth, the six type-I genes were not expressed in the FL2 stage, while most type-II genes were highly expressed in the late flower stages. In order to explore the regulation mechanism of pecan flowering, we selected 299 floral-related genes to construct gene co-expression network. The photoperiod pathway genes LHY , PHYA , ELF3 and the gibberellin metabolic pathway gene DELLA proteins function as key roles in floral pathways. We also identified four hormone metabolic pathway genes correlated (SAUR15 , IPT1 , IAA29 , and ARF2) with CiMADS5 , CiMADS8 , CiMADS9 , CiMADS20 , and CiMADS39. Furthermore, the expression patterns of 16 unigenes involved in flower development were validated using quantitative real time PCR. These findings are of great significance for further understanding of the molecular basis for reproductive development in Carya Nutt species. [ABSTRACT FROM AUTHOR]