Molecular basis of plant architecture

Analysis of the genetic basis of plant height-related traits in response to ethylene by QTL mapping in maize (Zea mays L.)

Ethylene (ET) is critical importance in the growth, development, and stress responses of plants. Plant hormonal stress responses have been extensively studied, however, the role of ET in plant growth, especially plant height (PH) remains unclear. Understanding the genetic control for PH in response to ET will provide insights into the regulation of maize development. To clarify the genetic basis of PH-related traits of maize in response to ET, we mapped QTLs for PH, ear height (EH), and internode length above the uppermost ear (ILAU) in two recombinant inbred line (RIL) populations of Zea mays after ET treatment and in an untreated control (CK) group. Sixty QTLs for the three traits were identified. Twenty-two QTLs were simultaneously detected under both ET treatment and untreated control, and five QTLs were detected at two geographic locations under ET treatment only. Individual QTL can be explained 3.87-17.71% of the phenotypic variance. One QTL (q2PH9-1, q1PH9, q1EH9/q1ILAU9-1, q2ILAU9, and q2EH9) for the measured traits (PH, EH, ILAU) was consistent across both populations. Two QTLs (q2PH2-5, q2ILAU2-2, q1PH2-2, and q1ILAU2-2; q1PH8-1, q1EH8-1, q2PH8-1) were identified for up to two traits in both locations and populations under both ET treatment and untreated control. These consistent and stable regions are important QTLs of potential hot spots for PH, ear height (EH), and internode length above the uppermost ear (ILAU) response to ET in maize; therefore, QTL fine-mapping and putative candidate genes validation should enable the cloning of PH, EH, and ILAU related genes to ET response. These results will be valuable for further fine-mapping and quantitative trait nucleotides (QTNs) determination, and elucidate the underlying molecular mechanisms of ET responses in maize.

Axillary meristem initiation-a way to branch out

Plants differ from most animals in their retained ability to initiate new cycles of growth and development, which relies on the establishment and activity of branch meristems. In seed plants, branching is achieved by axillary meristems, which are established in the axil of each leaf base and develop into lateral branches. Research into axillary meristem initiation has identified transcription factors and phytohormones as key regulators. Based on these findings, a mechanistic framework for understanding axillary meristem initiation has emerged. Taking recent research into account, we discuss mechanisms underlying stem cell fate regulation that enable axillary meristem formation.

A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus

Ranunculus trichophyllus is an amphibious plant that produces thin and cylindrical leaves if grown under water but thick and broad leaves if grown on land. We found that such heterophylly is widely controlled by two plant hormones, abscisic acid (ABA) and ethylene, which control terrestrial and aquatic leaf development respectively. Aquatic leaves produced higher levels of ethylene but lower levels of ABA than terrestrial leaves. In aquatic leaves, their distinct traits with narrow shape, lack of stomata, and reduced vessel development were caused by EIN3-mediated overactivation of abaxial genes, RtKANADIs, and accompanying with reductions of STOMAGEN and VASCULAR-RELATED NAC-DOMAIN7 (VDN7). In contrast, in terrestrial leaves, ABI3-mediated activation of the adaxial genes, RtHD-ZIPIIIs, and STOMAGEN and VDN7 established leaf polarity, and stomata and vessel developments. Heterophylly of R.trichophyllus could be also induced by external cues such as cold and hypoxia, which is accompanied with the changes in the expression of leaf polarity genes similar to aquatic response. A closely-related land plant R. sceleratus did not show such heterophyllic responses, suggesting that the changes in the ABA/ethylene signaling and leaf polarity are one of key evolutionary steps for aquatic adaptation.

Auxin and above-ground meristems

In contrast to animals, plants maintain life-long post-embryonic organogenesis from specialized tissues termed meristems. Shoot meristems give rise to all aerial tissues and are precisely regulated to balance stem cell renewal and differentiation. The phytohormone auxin has a dynamic and differential distribution within shoot meristems and during shoot meristem formation. Polar auxin transport and local auxin biosynthesis lead to auxin maxima and minima to direct cell fate specification, which are critical for meristem formation, lateral organ formation, and lateral organ patterning. In recent years, feedback regulatory loops of auxin transport and signaling have emerged as major determinants of the self-organizing properties of shoot meristems. Systems biology approaches, which involve molecular genetics, live imaging, and computational modeling, have become increasingly important to unravel the function of auxin signaling in shoot meristems.

Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (Arachis hypogaea L.)

The peanut (Arachis hypogaea L.) is an important grain legume extensively cultivated worldwide, supplying edible oil and protein for human consumption. As in many other crops, plant height is a crucial factor in determining peanut architecture traits and has a unique effect on resistance to lodging and efficiency of mechanized harvesting as well as yield. Currently, the genetic basis underlying plant height remains unclear in peanut, which have hampered marker-assisted selection in breeding. In this study, we conducted a quantitative trait locus (QTL) analysis for peanut plant height by using two recombinant inbred line (RIL) populations including "Yuanza 9102 × Xuzhou 68-4 (YX)" and "Xuhua 13 × Zhonghua 6 (XZ)". In the YX population, 38 QTLs including 10 major QTLs from 9 chromosomes were detected in 4 environments, and 8 consensus QTLs integrated by meta-analysis expressed stably across multiple environments. In the XZ population, 3 major QTLs and seven minor QTLs from 6 chromosomes were detected across 3 environments. Generally, most major QTLs from the two populations were located on pseudomolecule chromosome 9 of Arachis duranesis (A09), indicating there would be key genes on A09 controlling plant height. Further analysis revealed that qPHA09.1a from the XZ population and one consensus QTL, cqPHA09.d from the YX population were co-localized in a reliable 3.4 Mb physical interval on A09, which harbored 161 genes including transcription factors and enzymes related to signaling transduction and cell wall formation. The major and stable QTLs identified in this study may be useful for further gene cloning and identification of molecular markers applicable for breeding.

Enhanced Cold Tolerance and Tillering in Switchgrass (Panicum virgatum L.) by Heterologous Expression of Osa-miR393a

The microRNA393 (miR393) family is one of the conserved miRNA families in the plant kingdom. MiR393 was reported to regulate rice tillering and abiotic stress resistance positively through an auxin signaling pathway. However, little is known about the function of miR393 in switchgrass (Panicum virgatum L.), an important bioenergy C4 grass plant. We tested the expression level of miR393 and its four putative target genes (PvAFB1, PvAFB2, PvAFB3 and PvTIR1) in switchgrass, and found that these genes all responded to cold stress and exogenous 1-naphthaleneacetic acid (NAA) treatment. To investigate the function of miR393 in switchgrass, we enhanced miR393 expression by introducing an Osa-miR393a gene into switchgrass. The results showed that cold tolerance of the transgenic T0 and T1 generation plants was highly improved. Cold tolerance-related genes PvCOR47, PvICE1 and PvRAV1 were negatively regulated by exogenous NAA, and the expression of these genes was significantly higher in transgenic plants than in wild-type plants. The transgenic T1 seedlings were more tolerant to exogenous NAA treatment, accumulating less H2O2 after cold treatments. It was also observed that the miR393/target module regulates cold tolerance responses in Arabidopsis. In addition, transgenic plants overexpressing miR393 had significantly more tillers and higher biomass yield per plant in greenhouse and field tests. Forage quality analyses revealed that the soluble sugar contents of transgenic plants were increased markedly. Overall, the results suggested that overexpression of miR393 improved cold tolerance and tillering of switchgrass through regulation of auxin signaling transduction.

Comparative transcriptome analysis provides new insights into erect and prostrate growth in bermudagrass (Cynodon dactylon L.)

Bermudagrass (Cynodon dactylon L.) is a prominent warm-season turf and forage grass species with multiple applications. In most C. dactylon cultivars and accessions, erect-growing stems (shoot) and prostrate-growing stems (stolon) often coexist. These two types of stems are both formed through tillering but grow in two directions with different tiller angles. Elucidating the mechanism of tiller angle regulation in bermudagrass could provide important clues to breed cultivars with different plant architectural features for diverse usage. In this study, we compared the stem internode transcriptome of two bermudagrass wild accessions with extremely different tiller angles and stem growth directions. A total of 2088 and 12,141 unigenes were preferentially expressed in prostrate-growing wild accession C792 and erect-growing wild accession C793, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology-based Annotation System (KOBAS) analyses further indicated that light- and gravity-responsive genes were enriched in accession C792, whereas lignin synthesis-related genes were enriched in accession C793, which well explains the difference in lignification of vascular bundles and mechanical tissues in the two accessions. These results not only expand our understanding of the genetic control of tiller angle and stem growth direction in bermudagrass but also provide insight for future molecular breeding of C. dactylon and other turfgrass species with different plant architectures.

Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize

The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F_2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height. Ten QTL with an additive and dominant effect, 18 pairs of interacting QTL in the F_2:3 population and seventeen significant SNPs in the association population were detected for LA. Two major QTL, qLA3-4 and qLA7-1, were repeatedly detected and explained a large proportion of the phenotypic variation. The qLA3-4 was centered on lfy1, which is a dominant gene underlying extra leaves above the ear in leafy maize. Four LA QTL were found to overlap with flowering time and/or plant height, which suggested that these QTL might have a pleiotropic effect. The pleiotropy of the lfy1 locus on LA, flowering time and plant height were validated by near-isogenic line analysis. These results enhance our understanding of the genetic architecture affecting maize LA and the development of maize hybrids with increased LA.

RRM domain of Arabidopsis splicing factor SF1 is important for pre-mRNA splicing of a specific set of genes

The RNA recognition motif of Arabidopsis splicing factor SF1 affects the alternative splicing of FLOWERING LOCUS M pre-mRNA and a heat shock transcription factor HsfA2 pre-mRNA. Splicing factor 1 (SF1) plays a crucial role in 3' splice site recognition by binding directly to the intron branch point. Although plant SF1 proteins possess an RNA recognition motif (RRM) domain that is absent in its fungal and metazoan counterparts, the role of the RRM domain in SF1 function has not been characterized. Here, we show that the RRM domain differentially affects the full function of the Arabidopsis thaliana AtSF1 protein under different experimental conditions. For example, the deletion of RRM domain influences AtSF1-mediated control of flowering time, but not the abscisic acid sensitivity response during seed germination. The alternative splicing of FLOWERING LOCUS M (FLM) pre-mRNA is involved in flowering time control. We found that the RRM domain of AtSF1 protein alters the production of alternatively spliced FLM-β transcripts. We also found that the RRM domain affects the alternative splicing of a heat shock transcription factor HsfA2 pre-mRNA, thereby mediating the heat stress response. Taken together, our results suggest the importance of RRM domain for AtSF1-mediated alternative splicing of a subset of genes involved in the regulation of flowering and adaptation to heat stress.

Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators

In tomatoes, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF). Xu et al. show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB/POZ domain.

Plant productivity depends on inflorescences, flower-bearing shoots that originate from the stem cell populations of shoot meristems. Inflorescence architecture determines flower production, which can vary dramatically both between and within species. In tomato plants, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF), but the underlying mechanism is unknown. We show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB (Broad complex, Tramtrack, and Bric-a-brac)/POZ (POX virus and zinc finger) domain. TMF and three tomato BOPs (SlBOPs) interact with themselves and each other, and TMF recruits SlBOPs to the nucleus, suggesting formation of a transcriptional complex. Like TMF, SlBOP gene expression is highest during vegetative and transitional stages of meristem maturation, and CRISPR/Cas9 elimination of SlBOP function causes pleiotropic defects, most notably simplification of inflorescences into single flowers, resembling tmf mutants. Flowering defects are enhanced in higher-order slbop tmf mutants, suggesting that SlBOPs function with additional factors. In support of this, SlBOPs interact with TMF homologs, mutations in which cause phenotypes like slbop mutants. Our findings reveal a new flowering module defined by SlBOP–TMF family interactions that ensures a progressive meristem maturation to promote inflorescence complexity.

Genetic dissection of plant growth habit in chickpea

A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.

Characterization of a common wheat (Triticum aestivum L.) high-tillering dwarf mutant

A novel high-tillering dwarf mutant in common wheat Wangshuibai was characterized and mapped to facilitate breeding for plant height and tiller and the future cloning of the causal gene. Tiller number and plant height are two major agronomic traits in cereal crops affecting plant architecture and grain yield. NAUH167, a mutant of common wheat landrace Wangshuibai induced by ethylmethyl sulfide (EMS) treatment, exhibits higher tiller number and reduced plant height. Microscope observation showed that the dwarf phenotype was attributed to the decrease in the number of cells and their length. The same as the wild type, the mutant was sensitive to exogenous gibberellins. Genetic analysis showed that the high-tillering number and dwarf phenotype were related and controlled by a partial recessive gene. Using a RIL_2:6 population derived from the cross NAUH167/Sumai3, a molecular marker-based genetic map was constructed. The map consisted of 283 loci, spanning a total length of 1007.98 cM with an average markers interval of 3.56 cM. By composite interval mapping, a stable major QTL designated QHt.nau-2D controlling both traits, was mapped to the short arm of chromosome 2D flanked by markers Xcfd11 and Xgpw361. To further map the QHt.nau-2D loci, another population consisted of 180 F₂ progeny from a cross 2011I-78/NAUH167 was constructed. Finally, QHt.nau-2D was located within a genetic region of 0.8 cM between markers QHT239 and QHT187 covering a predicted physical distance of 6.77 Mb. This research laid the foundation for map-based cloning of QHt.nau-2D and would facilitate the characterization of plant height and tiller number in wheat.

Gibberellin in plant height control: old player, new story

Height relates to plant architecture, lodging resistance, and yield performance. Growth-promoting phytohormones gibberellins (GAs) play a pivotal role in plant height control. Mutations in GA biosynthesis, metabolism, and signaling cascades influence plant height. Moreover, GA interacts with other phytohormones in the modulation of plant height. Here, we first briefly describe the regulation of plant height by altered GA pathway. Then, we depict effects of the crosstalk between GA and other phytohormones on plant height. We also dissect the co-localization of GA pathway genes and established quantitative genetic loci for plant height. Finally, we suggest ways forward for the application of hormone GA knowledge in breeding of crops with plant height ideotypes.

The vascular plants: open system of growth

What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom. One of the foundations of their success relies on the plant-pollinator relationship, essentially unique to angiosperms that pushed large speciation in both plants and insects and on the presence of the carpel, the structure devoted to seed enclosure. A seed represents the main organ preserving the genetic information of a plant; during embryogenesis, the primary axis of development is established by two groups of pluripotent cells: the shoot apical meristem (SAM), responsible for gene rating all aboveground organs, and the root apical meristem (RAM), responsible for producing all underground organs. During postembryonic shoot development, axillary meristem (AM) initiation and outgrowth are responsible for producing all secondary axes of growth including inflorescence branches or flowers. The production of AMs is tightly linked to the production of leaves and their separation from SAM. As leaf primordia are formed on the flanks of the SAM, a region between the apex and the developing organ is established and referred to as boundary zone. Interaction between hormones and the gene network in the boundary zone is fundamental for AM initiation. AMs only develop at the adaxial base of the leaf; thus, AM initiation is also strictly associated with leaf polarity. AMs function as new SAMs: form axillary buds with a few leaves and then the buds can either stay dormant or develop into shoot branches to define a plant architecture, which in turn affects assimilate production and reproductive efficiency. Therefore, the radiation of angiosperms was accompanied by a huge diversification in growth forms that determine an enormous morphological plasticity helping plants to environmental changes. In this review, we focused on the developmental processes of AM initiation and outgrowth. In particular, we summarized the primary growth of SAM, the key role of positional signals for AM initiation, and the dissection of molecular players involved in AM initiation and outgrowth. Finally, the interaction between phytohormone signals and gene regulatory network controlling AM development was discussed.

Molecular cloning, phylogenetic analysis, and expression patterns of LATERAL SUPPRESSOR-LIKE and REGULATOR OF AXILLARY MERISTEM FORMATION-LIKE genes in sunflower (Helianthus annuus L.)

The wild sunflower (Helianthus annuus) plants develop a highly branched form with numerous small flowering heads. The origin of a no branched sunflower, producing a single large head, has been a key event in the domestication process of this species. The interaction between hormonal factors and several genes organizes the initiation and outgrowth of axillary meristems (AMs). From sunflower, we have isolated two genes putatively involved in this process, LATERAL SUPPRESSOR (LS)-LIKE (Ha-LSL) and REGULATOR OF AXILLARY MERISTEM FORMATION (ROX)-LIKE (Ha-ROXL), encoding for a GRAS and a bHLH transcription factor (TF), respectively. Typical amino acid residues and phylogenetic analyses suggest that Ha-LSL and Ha-ROXL are the orthologs of the branching regulator LS and ROX/LAX1, involved in the growth habit of both dicot and monocot species. qRT-PCR analyses revealed a high accumulation of Ha-LSL transcripts in roots, vegetative shoots, and inflorescence shoots. By contrast, in internodal stems and young leaves, a lower amount of Ha-LSL transcripts was observed. A comparison of transcription patterns between Ha-LSL and Ha-ROXL revealed some analogies but also remarkable differences; in fact, the gene Ha-ROXL displayed a low expression level in all organs analyzed. In situ hybridization (ISH) analysis showed that Ha-ROXL transcription was strongly restricted to a small domain within the boundary zone separating the shoot apical meristem (SAM) and the leaf primordia and in restricted regions of the inflorescence meristem, beforehand the separation of floral bracts from disc flower primordia. These results suggested that Ha-ROXL may be involved to establish a cell niche for the initiation of AMs as well as flower primordia. The accumulation of Ha-LSL transcripts was not restricted to the boundary zones in vegetative and inflorescence shoots, but the mRNA activity was expanded in other cellular domains of primary shoot apical meristem as well as AMs. In addition, Ha-LSL transcript accumulation was also detected in leaves and floral primordia at early stages of development. These results were corroborated by qRT-PCR analyses that evidenced high levels of Ha-LSL transcripts in very young leaves and disc flowers, suggesting a role of Ha-LSL for the early outgrowth of lateral primordia.

ERAMOSA controls lateral branching in snapdragon

Plant forms display a wide variety of architectures, depending on the number of lateral branches, internode elongation and phyllotaxy. These are in turn determined by the number, the position and the fate of the Axillary Meristems (AMs). Mutants that affect AM determination during the vegetative phase have been isolated in several model plants. Among these genes, the GRAS transcription factor LATERAL SUPPRESSOR (Ls) plays a pivotal role in AM determination during the vegetative phase. Hereby we characterize the phylogenetic orthologue of Ls in Antirrhinum, ERAMOSA (ERA). Our data supported ERA control of AM formation during both the vegetative and the reproductive phase in snapdragon. A phylogenetic analysis combined with an analysis of the synteny of Ls in several species strongly supported the hypothesis that ERA is a phylogenetic orthologue of Ls, although it plays a broader role. During the reproductive phase ERA promotes the establishment of the stem niche at the bract axis but, after the reproductive transition, it is antagonized by the MADS box transcription factor SQUAMOSA (SQUA). Surprisingly double mutant era squa plants display a squa phenotype developing axillary meristems, which can eventually turn into inflorescences or flowers.

Gibberellins Promote Brassinosteroids Action and Both Increase Heterosis for Plant Height in Maize (Zea mays L.)

Brassinosteroids (BRs) and Gibberellins (GAs) are two classes of plant hormones affecting plant height (PHT). Thus, manipulation of BR and GA levels or signaling enables optimization of crop grain and biomass yields. We established backcross (BC) families, selected for increased PHT, in two elite maize inbred backgrounds. Various exotic accessions used in the germplasm enhancement in maize project served as donors. BC1-derived doubled haploid lines in the same two elite maize inbred backgrounds established without selection for plant height were included for comparison. We conducted genome-wide association studies to explore the genetic control of PHT by BR and GA. In addition, we used BR and GA inhibitors to compare the relationship between PHT, BR, and GA in inbred lines and heterozygotes from a physiological and biological perspective. A total of 73 genomic loci were discovered to be associated with PHT, with seven co-localized with GA, and two co-localized with BR candidate genes. PHT determined in field trials was significantly correlated with seedling stage BR and GA inhibitor responses. However, this observation was only true for maize heterozygotes, not for inbred lines. Path analysis results suggest that heterozygosity increases GA levels, which in turn promote BR levels. Thus, at least part of heterosis for PHT in maize can be explained by increased GA and BR levels, and seedling stage hormone inhibitor response is promising to predict heterosis for PHT.

Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.)

In many plants, architecture and grain yield are affected by both the environment and genetics. In rice, the tiller is a vital factor impacting plant architecture and regulated by many genes. In this study, we cloned a novel DHHC-type zinc finger protein gene Os02g0819100 and its alternative splice variant OsDHHC1 from the cDNA of rice (Oryza sativa L.), which regulate plant architecture by altering the tiller in rice. The tillers increased by about 40% when this type of DHHC-type zinc finger protein gene was over-expressed in Zhong Hua 11 (ZH11) rice plants. Moreover, the grain yield of transgenic rice increased approximately by 10% compared with wild-type ZH11. These findings provide an important genetic engineering approach for increasing rice yields.

Genome-Wide Association Mapping Reveals the Genetic Control Underlying Branch Angle in Rapeseed (Brassica napus L.)

Plant architecture is vital not only for crop yield, but also for field management, such as mechanical harvesting. The branch angle is one of the key factors determining plant architecture. With the aim of revealing the genetic control underlying branch angle in rapeseed (Brassica napus L.), the positional variation of branch angles on individual plants was evaluated, and the branch angle increased with the elevation of branch position. Furthermore, three middle branches of individual plants were selected to measure the branch angle because they exhibited the most representative phenotypic values. An association panel with 472 diverse accessions was estimated for branch angle trait in six environments and genotyped with a 60K Brassica Infinium® SNP array. As a result of association mapping, 46 and 38 significantly-associated loci were detected using a mixed linear model (MLM) and a multi-locus random-SNP-effect mixed linear model (MRMLM), which explained up to 62.2 and 66.2% of the cumulative phenotypic variation, respectively. Numerous highly-promising candidate genes were identified by annotating against Arabidopsis thaliana homologous, including some first found in rapeseed, such as TAC1, SGR1, SGR3, and SGR5. These findings reveal the genetic control underlying branch angle and provide insight into genetic improvements that are possible in the plant architecture of rapeseed.

Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed (Brassica napus L.)

Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.

A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars

Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively. More QTLs were identified in indica than in japonica, and three major QTLs (qTA3, qTA1b/DWARF2 (D2) and qTA9c/TAC1) were fixed in japonica but segregating in indica, which explained the wider variation observed in indica compared with that in japonica. No common QTLs were identified between the indica and japonica subpopulations. Mutant analysis for the candidate gene of qTA3 on chromosome 3 indicated a novel gene, Tiller Angle Control 3 (TAC3), encoding a conserved hypothetical protein controlling tiller angle. TAC3 is preferentially expressed in the tiller base. The ebisu dwarf (d2) mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A nucleotide diversity analysis revealed that TAC3, D2 and TAC1 have been subjected to selection during japonica domestication. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1, which may be used for breeding plants with an ideal architecture. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3 together with TAC1, D2, and other newly identified genes in this study that controls tiller angle in rice cultivars.

Tiller angle is the key component of plant architecture that greatly affect grain yield. However, few tiller angle-related genes that can be used for improving rice plant architecture have been isolated based on natural variation. Here, we identified 7 common tiller angle-related QTLs by a genome-wide association study, including the previously reported major gene TAC1, in two environments in the 529 diverse rice accessions and dozens of QTLs specially identified in one environment. Two QTLs were validated by mutant analysis: A novel gene TAC3, encoding a conserved hypothetical protein and preferentially expressing in the tiller base, was the candidate gene of qTA3; d2 mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1 in indica, which may be used for breeding plants with an ideal architecture, while they were all subjected to selection and fixed in japonica. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3, together with TAC1 and D2 that greatly controls tiller angle in rice cultivars.

Change in Auxin and Cytokinin Levels Coincides with Altered Expression of Branching Genes during Axillary Bud Outgrowth in Chrysanthemum

In the production and breeding of Chrysanthemum sp., shoot branching is an important quality aspect as the outgrowth of axillary buds determines the final plant shape. Bud outgrowth is mainly controlled by apical dominance and the crosstalk between the plant hormones auxin, cytokinin and strigolactone. In this work the hormonal and genetic regulation of axillary bud outgrowth was studied in two differently branching cut flower Chrysanthemum morifolium (Ramat) genotypes. C17 is a split-type which forms an inflorescence meristem after a certain vegetative period, while C18 remains vegetative under long day conditions. Plant growth of both genotypes was monitored during 5 subsequent weeks starting one week before flower initiation occurred in C17. Axillary bud outgrowth was measured weekly and samples of shoot apex, stem and axillary buds were taken during the first two weeks. We combined auxin and cytokinin measurements by UPLC-MS/MS with RT-qPCR expression analysis of genes involved in shoot branching regulation pathways in chrysanthemum. These included bud development genes (CmBRC1, CmDRM1, CmSTM, CmLsL), auxin pathway genes (CmPIN1, CmTIR3, CmTIR1, CmAXR1, CmAXR6, CmAXR2, CmIAA16, CmIAA12), cytokinin pathway genes (CmIPT3, CmHK3, CmRR1) and strigolactone genes (CmMAX1 and CmMAX2). Genotype C17 showed a release from apical dominance after floral transition coinciding with decreased auxin and increased cytokinin levels in the subapical axillary buds. As opposed to C17, C18 maintained strong apical dominance with vegetative growth throughout the experiment. Here high auxin levels and decreasing cytokinin levels in axillary buds and stem were measured. A differential expression of several branching genes accompanied the different hormonal change and bud outgrowth in C17 and C18. This was clear for the strigolactone biosynthesis gene CmMAX1, the transcription factor CmBRC1 and the dormancy associated gene CmDRM1, that all showed a decreased expression in C17 at floral transition and an increased expression in C18 with continuous vegetative growth. These results offer a case study for Chrysanthemum, showing an altered cytokinin to auxin balance and differential gene expression between vegetative growth with apical dominance and transition to generative growth with loss of apical dominance and axillary bud outgrowth. This suggests a conservation of several aspects of the hormonal and genetical regulation of bud outgrowth in Chrysanthemum. Furthermore, 15 previously uncharacterised genes in chrysanthemum, were described in this study. Of those genes involved in axillary bud outgrowth we identified CmDRM1, CmBRC1 and CmMAX1 as having an altered expression preceding axillary bud outgrowth, which could be useful as markers for bud activity.

Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana

Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia

The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica 'Pocomoke' (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle.

Fertilization Independent Endosperm genes repress NbGH3.6 and regulate the auxin level during shoot development in Nicotiana benthamiana

The Fertilization Independent Endosperm (FIE) gene is required to restrict endosperm development without fertilization, and it represses flowering during embryo and seedling development in Arabidopsis thaliana However, the regulatory mechanism of the FIE gene in postembryonic shoot development is not well understood. Silencing of Nicotiana benthamiana homologues of the FIE gene, NbFIE1 and NbFIE2, resulted in the enhanced outgrowth of axillary buds and the impairment of secondary xylem differentiation. RNA sequencing analysis found that one of the auxin-responsive GRETCHEN HAGEN 3(GH3) family genes, NbGH3.6, was upregulated and maintained a high expression during the time course of silencing NbFIE genes. Chromatin immunoprecipiation (ChIP)-PCR results showed a lack of H3K27me3 marks on NbGH3.6 chromatin in NbFIE-silenced plants compared with negative control plants, indicating that NbGH3.6 was a direct target of NbFIE genes during postembryonic shoot development. Moreover, the free IAA content was reduced significantly in NbFIE-silenced plants, which might cause the enhanced outgrowth of axillary buds as well as impaired secondary xylem differentiation. These results clearly indicated that NbGH3.6 was a primary target of NbFIE genes during postembryonic shoot development, and NbFIE genes regulated axillary bud growth and secondary xylem formation through tuning endogenous auxin homeostasis, possibly by regulating the expression of the NbGH3.6 gene.

Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria

The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F7 recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C4 model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture.

To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages

The architecture of the cotton plant, including fruit branch formation and flowering pattern, is the most important characteristic that directly influences light exploitation, yield and cost of planting. Nulliplex branch is a useful phenotype to study cotton architecture. We used RNA sequencing to obtain mRNA and miRNA profiles from nulliplex- and normal-branch cotton at three developmental stages. The differentially expressed genes (DEGs) and miRNAs were identified that preferentially/specifically expressed in the pre-squaring stage, which is a key stage controlling the transition from vegetative to reproductive growth. The DEGs identified were primarily enriched in RNA, protein, and signalling categories in Gossypium barbadense and Gossypium hirsutum. Interestingly, during the pre-squaring stage, the DEGs were predominantly enriched in transcription factors in both G. barbadense and G. hirsutum, and these transcription factors were mainly involved in branching and flowering. Related miRNAs were also identified. The results showed that fruit branching in cotton is controlled by molecular pathways similar to those in Arabidopsis and that multiple regulated pathways may affect the development of floral buds. Our study showed that the development of fruit branches is closely related to flowering induction and provides insight into the molecular mechanisms of branch and flower development in cotton.

Genetic dissection of plant architecture and yield-related traits in Brassica napus

An optimized plant architecture (PA) is fundamental for high-yield breeding but the genetic control of the important trait is largely unknown in rapeseed. Here plant architecture factors (PAFs) were proposed to consist of main inflorescence length proportion (MILP), branch height proportion (BHP), and branch segment proportion (BSP). Comparison of different genotypes in a DH population grown in diverse environments showed that an optimized PAF performance with MILP and BHP between 0.3–0.4 was important for high yield potential. In total, 163 unique quantitative trait loci (QTLs) for PA- and plant yield (PY)-related traits were mapped onto a high-density genetic map. Furthermore, 190 PA-related candidate genes for 91 unique PA QTLs and 2350 PY epistatic interaction loci-pairs were identified, which explain 2.8–51.8% and 5.2–23.6% of phenotypic variation, respectively. Three gene categories, transcription factor, auxin/IAA, and gibberellin, comprise the largest proportions of candidate genes for PA-related QTLs. The effectiveness of QTL candidate genes prediction was demonstrated by cloning of three candidate genes, Bna.A02.CLV2, Bna.A09.SLY2, and Bna.C07.AHK4. The study thus outlines a gene network for control of PA-related traits and provides novel information for understanding the establishment of ideal PA and for developing effective breeding strategies for yield improvement in rapeseed and other crops.

Genetics-based dynamic systems model of canopy photosynthesis: the key to improve light and resource use efficiencies for crops

Improving canopy photosynthetic light use efficiency instead of leaf photosynthesis holds great potential to catalyze the next "green revolution". However, leaves in a canopy experience different biochemical limitations due to the heterogeneities of microclimates and also physiological parameters. Mechanistic dynamic systems models of canopy photosynthesis are now available which can be used to design the optimal canopy architectural and physiological parameters to maximize CO 2 uptake. Rapid development of modern crop genetics research now makes it possible to link such canopy models with genetic variations of crops to develop genetics-based dynamic systems models of canopy photosynthesis. Such models can guide marker-assisted breeding or genomic selection or engineering of crops to enhance light and nitrogen use efficiencies for different regions under future climate change scenarios.

Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map

Background

Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups.

Results

We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3–24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3–46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome.

Conclusions

This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2316-4) contains supplementary material, which is available to authorized users.

Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize

Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.

Reassessment of the Four Yield-related Genes Gn1a, DEP1, GS3, and IPA1 in Rice Using a CRISPR/Cas9 System

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) systems have been successfully used as efficient tools for genome editing in a variety of species. We used the CRISPR/Cas9 system to mutate the Gn1a (Os01g0197700), DEP1 (Os09g0441900), GS3 (Os03g0407400), and IPA1 (Os08g0509600) genes of rice cultivar Zhonghua 11, genes which have been reported to function as regulators of grain number, panicle architecture, grain size and plant architecture, respectively. Analysis of the phenotypes and frequencies of edited genes in the first generation of transformed plants (T0) showed that the CRISPR/Cas9 system was highly efficient in inducing targeted gene editing, with the desired genes being edited in 42.5% (Gn1a), 67.5% (DEP1), 57.5% (GS3), and 27.5% (IPA1) of the transformed plants. The T2 generation of the gn1a, dep1, and gs3 mutants featured enhanced grain number, dense erect panicles, and larger grain size, respectively. Furthermore, semi-dwarf, and grain with long awn, phenotypes were observed in dep1 and gs3 mutants, respectively. The ipa1 mutants showed two contrasting phenotypes, having either fewer tillers or more tillers, depending on the changes induced in the OsmiR156 target region. In addition, we found that mutants with deletions occurred more frequently than previous reports had indicated and that off-targeting had taken place in highly similar target sequences. These results proved that multiple regulators of important traits can be modified in a single cultivar by CRISPR/Cas9, and thus facilitate the dissection of complex gene regulatory networks in the same genomic background and the stacking of important traits in cultivated varieties.

Regulation of Axillary Meristem Initiation by Transcription Factors and Plant Hormones

One distinctive feature of plant post-embryonic development is that plants can undergo reiterative growth and continuous organogenesis throughout their lifetimes. Axillary meristems (AMs) in leaf axils play a central role in this growth and differences in meristem initiation and development produce the diversity of plant architecture. Studies in the past 15 years have shown that several transcription factors (TFs) and phytohormones affect AM initiation. In this review, we highlight recent research using systems biology approaches to examine the regulatory hierarchies underlying AM initiation and the role of auxins and cytokinins in AM initiation and development. This research revealed a developmental mechanism in which phytohormone signals act with a gene regulatory network containing multiple TFs to contribute to the initiation of AMs.

Breadfruit (Artocarpus altilis) gibberellin 2-oxidase genes in stem elongation and abiotic stress response

Breadfruit (Artocarpus altilis) is a traditional staple tree crop in the Oceania. Susceptibility to windstorm damage is a primary constraint on breadfruit cultivation. Significant tree loss due to intense tropical windstorm in the past decades has driven a widespread interest in developing breadfruit with dwarf stature. Gibberellin (GA) is one of the most important determinants of plant height. GA 2-oxidase is a key enzyme regulating the flux of GA through deactivating biologically active GAs in plants. As a first step toward understanding the molecular mechanism of growth regulation in the species, we isolated a cohort of four full-length GA2-oxidase cDNAs, AaGA2ox1- AaGA2ox4 from breadfruit. Sequence analysis indicated the deduced proteins encoded by these AaGA2oxs clustered together under the C19 GA2ox group. Transcripts of AaGA2ox1, AaGA2ox2 and AaGA2ox3 were detected in all plant organs, but exhibited highest level in source leaves and stems. In contrast, transcript of AaGA2ox4 was predominantly expressed in roots and flowers, and displayed very low expression in leaves and stems. AaGA2ox1, AaGA2ox2 and AaGA2ox3, but not AaGA2ox4 were subjected to GA feedback regulation where application of exogenous GA3 or gibberellin biosynthesis inhibitor, paclobutrazol was shown to manipulate the first internode elongation of breadfruit. Treatments of drought or high salinity increased the expression of AaGA2ox1, AaGA2ox2 and AaGA2ox4. But AaGA2ox3 was down-regulated under salt stress. The function of AaGA2oxs is discussed with particular reference to their role in stem elongation and involvement in abiotic stress response in breadfruit.

Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture

Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.)

Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.

A GRAS-like gene of sunflower (Helianthus annuus L.) alters the gibberellin content and axillary meristem outgrowth in transgenic Arabidopsis plants

The GRAS proteins belong to a plant transcriptional regulator family that function in the regulation of plant growth and development. Despite their important roles, in sunflower only one GRAS gene (HaDella1) with the DELLA domain has been reported. Here, we provide a functional characterisation of a GRAS-like gene from Helianthus annuus (Ha-GRASL) lacking the DELLA motif. The Ha-GRASL gene contains an intronless open reading frame of 1,743 bp encoding 580 amino acids. Conserved motifs in the GRAS domain are detected, including VHIID, PFYRE, SAW and two LHR motifs. Within the VHII motif, the P-H-N-D-Q-L residues are entirely maintained. Phylogenetic analysis reveals that Ha-GRASL belongs to the SCARECROW LIKE4/7 (SCL4/7) subfamily of the GRAS consensus tree. Accumulation of Ha-GRASL mRNA at the adaxial boundaries from P6/P7 leaf primordia suggests a role of Ha-GRASL in the initiation of median and basal axillary meristems (AMs) of sunflower. When Ha-GRASL is over-expressed in Arabidopsis wild-type plants, the number of lateral bolts increases differently from untransformed plants. However, Ha-GRASL slightly affects the lateral suppressor (las-4-) mutation. Therefore, we hypothesise that Ha-GRASL and LAS are not functionally equivalent. The over-expression of Ha-GRASL reduces metabolic flow of gibberellins (GAs) in Arabidopsis and this modification could be relevant in AM development. Phylogenetic analysis includes LAS and SCL4/7 in the same major clade, suggesting a more recent separation of these genes with respect to other GRAS members. We propose that some features of their ancestor, as well as AM initiation and outgrowth, are partially retained in both LAS and SCL4/7.

Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.)

To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively, and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R(2 )= 22.8% and 32.1%), were colocalised with opposite effects, and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.

Transcription Profiles Reveal Sugar and Hormone Signaling Pathways Mediating Flower Induction in Apple (Malus domestica Borkh.)

Flower induction in apple (Malus domestica Borkh.) is regulated by complex gene networks that involve multiple signal pathways to ensure flower bud formation in the next year, but the molecular determinants of apple flower induction are still unknown. In this research, transcriptomic profiles from differentiating buds allowed us to identify genes potentially involved in signaling pathways that mediate the regulatory mechanisms of flower induction. A hypothetical model for this regulatory mechanism was obtained by analysis of the available transcriptomic data, suggesting that sugar-, hormone- and flowering-related genes, as well as those involved in cell-cycle induction, participated in the apple flower induction process. Sugar levels and metabolism-related gene expression profiles revealed that sucrose is the initiation signal in flower induction. Complex hormone regulatory networks involved in cytokinin (CK), abscisic acid (ABA) and gibberellic acid pathways also induce apple flower formation. CK plays a key role in the regulation of cell formation and differentiation, and in affecting flowering-related gene expression levels during these processes. Meanwhile, ABA levels and ABA-related gene expression levels gradually increased, as did those of sugar metabolism-related genes, in developing buds, indicating that ABA signals regulate apple flower induction by participating in the sugar-mediated flowering pathway. Furthermore, changes in sugar and starch deposition levels in buds can be affected by ABA content and the expression of the genes involved in the ABA signaling pathway. Thus, multiple pathways, which are mainly mediated by crosstalk between sugar and hormone signals, regulate the molecular network involved in bud growth and flower induction in apple trees.

Combined Small RNA and Degradome Sequencing Reveals Novel MiRNAs and Their Targets in the High-Yield Mutant Wheat Strain Yunong 3114

Wheat is one of the main food sources worldwide; large amount studies have been conducted to improve wheat production. MicroRNAs (miRNAs) with about 20-30 nucleotide are a class of regulatory small RNAs (sRNAs), which could regulate gene expression through sequence-specific base pairing with target mRNAs, playing important roles in plant growth. An ideal plant architecture (IPA) is crucial to enhance yield in bread wheat. In this study, the high-yield wheat strain Yunong 3114 was EMS-mutagenesis from the wild-type strain Yunong 201, exhibiting a preferable plant structure compared with the wild-type strain. We constructed small RNA and degradome libraries from Yunong 201 and Yunong 3114, and performed small RNA sequencing of these libraries in order identify miRNAs and their targets related to IPA in wheat. Totally, we identified 488 known and 837 novel miRNAs from Yunong 3114 and 391 known and 533 novel miRNAs from Yunong 201. The number of miRNAs in the mutant increased. A total of 37 known and 432 putative novel miRNAs were specifically expressed in the mutant strain; furthermore, 23 known and 159 putative novel miRNAs were specifically expressed in the wild-type strain. A total of 150 known and 100 novel miRNAs were differentially expressed between mutant and wild-type strains. Among these differentially expressed novel miRNAs, 4 and 8 predict novel miRNAs were evidenced by degradome sequencing and showed up-regulated and down-regulated expressions in the mutant strain Yunong 3114, respectively. Targeted gene annotation and previous results indicated that this set of miRNAs is related to plant structure. Our results further suggested that miRNAs may be necessary to obtain an optimal wheat structure.

PAY1 improves plant architecture and enhances grain yield in rice

Plant architecture, a complex of the important agronomic traits that determine grain yield, is a primary target of artificial selection of rice domestication and improvement. Some important genes affecting plant architecture and grain yield have been isolated and characterized in recent decades; however, their underlying mechanism remains to be elucidated. Here, we report genetic identification and functional analysis of the PLANT ARCHITECTURE AND YIELD 1 (PAY1) gene in rice, which affects plant architecture and grain yield in rice. Transgenic plants over-expressing PAY1 had twice the number of grains per panicle and consequently produced nearly 38% more grain yield per plant than control plants. Mechanistically, PAY1 could improve plant architecture via affecting polar auxin transport activity and altering endogenous indole-3-acetic acid distribution. Furthermore, introgression of PAY1 into elite rice cultivars, using marker-assisted background selection, dramatically increased grain yield compared with the recipient parents. Overall, these results demonstrated that PAY1 could be a new beneficial genetic resource for shaping ideal plant architecture and breeding high-yielding rice varieties.

The effects of chromosome 6P on fertile tiller number of wheat as revealed in wheat-Agropyron cristatum chromosome 5A/6P translocation lines

This study explored the genetic constitutions of several wheat- A. cristatum translocation lines and determined the effects of A. cristatum 6P chromosome segments on fertile tiller number in wheat. Progress in wheat breeding is hampered by a relatively narrow range of genetic variation. To overcome this hurdle, wild relatives of common wheat with superior agronomic traits are often used as donors of desirable genes in wheat-breeding programs. One of the successfully utilized wheat wild relatives is Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genomes PPPP). We previously reported that WAT31-13 was a wheat-A. cristatum 5A-6P reciprocal translocation line with higher fertile tiller number and grain number per spike compared to common wheat. However, WAT31-13 was genetically unstable. In this study, we analyzed the 43 genetically stable progenies from WAT31-13 using genomic in situ hybridization, dual-color fluorescence in situ hybridization, and molecular markers. We classified them into three translocation types (TrS, TrL and TrA) and seven subtypes, and also pinpointed the translocation breakpoint. The genotypic data, combined with the phenotypes of each translocation type, enabled us to physically map agronomic traits to specific A. cristatum 6P chromosome arms or segments. Our results indicated that A. cristatum chromosome 6P played an important role in regulating fertile tiller number, and that positive and negative regulators of fertile tiller number existed on the A. cristatum chromosome arm 6PS and 6PL, respectively. By exploring the relationship between fertile tiller number and A. cristatum chromosome segment, this study presented a number of feasible approaches for creation, analysis, and utilization of wheat-alien chromosome translocation lines in genetic improvement of wheat.

Hd3a promotes lateral branching in rice

Accumulating evidence indicates that the FLOWERING LOCUS T (FT) protein is the mobile floral signal known as florigen. A rice FT homolog, Heading date 3a (Hd3a), is transported from the phloem to shoot apical cells, where it interacts with 14-3-3 proteins and transcription factor OsFD1 to form a florigen activation complex (FAC) that activates a rice homolog of the floral identity gene APETALA1. Recent studies showed that florigen has roles in plant development beyond flowering; however, the exact nature of these roles is not well understood. It is not clear whether FT is transported to organs outside the shoot apex, and whether FAC formation is required for processes other than flowering. We show here that the Hd3a protein accumulates in axillary meristems to promote branching, and that FAC formation is required. Analysis of transgenic plants revealed that Hd3a promotes branching through lateral bud outgrowth. Hd3a protein produced in the phloem reached the axillary meristem in the lateral bud, and its transport was required for promotion of branching. Moreover, mutant Hd3a proteins defective in FAC formation but competent with respect to transport did not promote branching. Finally, we show that Hd3a promotes branching independently from strigolactone and FC1, a transcription factor that inhibits branching in rice. Together, these results suggest that Hd3a functions as a mobile signal for branching in rice.

Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations

Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.

Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing

Using bulked segregant analysis based on next-generation sequencing, the recessive nulliplex-branch gene was mapped between two SNP markers ~600 kb apart. In a "nulliplex-branch" cotton mutant, most of the flowers arise directly from leaf axils on the main shoot, which usually does not have a fruiting branch. A nulliplex-branch is a useful trait by which to study cotton architecture; however, the genetic basis of this mutant has remained elusive. In this study, bulked segregant analysis combined with next-generation sequencing technology was used to finely map the underlying genes that result in a nulliplex-branch plant. The nulliplex-branch Pima cotton variety, Xinhai-18, was crossed with the normal branch upland cotton line, TM-1, resulting in an F2 population. The nulliplex-branch trait was found to be controlled by the recessive gene gb_nb1. Allelic single-nucleotide polymorphisms (SNPs) were discovered by reduced-representation sequencing between the parents, and their profiles were also characterized in the nulliplex-branch and normal branch bulks constructed using the F2 plants. A candidate ~9.0 Mb-long region comprising 42 SNP markers was found to be associated with gb_nb1, which helped localize it at the ~600-kb interval on Chr 16 by segregation analysis in the F2 population. The closely linked markers with gb_nb1 developed in this study will facilitate the marker-assisted selection of the nulliplex-branch trait, and the fine map constructed will accelerate map-based cloning of gb_nb1.

Semi-dwarfism and lodging tolerance in tef (Eragrostis tef) is linked to a mutation in the α-Tubulin 1 gene

Genetic improvement of native crops is a new and promising strategy to combat hunger in the developing world. Tef is the major staple food crop for approximately 50 million people in Ethiopia. As an indigenous cereal, it is well adapted to diverse climatic and soil conditions; however, its productivity is extremely low mainly due to susceptibility to lodging. Tef has a tall and weak stem, liable to lodge (or fall over), which is aggravated by wind, rain, or application of nitrogen fertilizer. To circumvent this problem, the first semi-dwarf lodging-tolerant tef line, called kegne, was developed from an ethyl methanesulphonate (EMS)-mutagenized population. The response of kegne to microtubule-depolymerizing and -stabilizing drugs, as well as subsequent gene sequencing and segregation analysis, suggests that a defect in the α-Tubulin gene is functionally and genetically tightly linked to the kegne phenotype. In diploid species such as rice, homozygous mutations in α-Tubulin genes result in extreme dwarfism and weak stems. In the allotetraploid tef, only one homeologue is mutated, and the presence of the second intact α-Tubulin gene copy confers the agriculturally beneficial semi-dwarf and lodging-tolerant phenotype. Introgression of kegne into locally adapted and popular tef cultivars in Ethiopia will increase the lodging tolerance in the tef germplasm and, as a result, will improve the productivity of this valuable crop.