Special Issue: Translational Plant Biology   

November 2015, Volume 57 Issue 11, Pages 874每991.


Cover Caption: Translational Plant Biology
Multicellular trichomes in cucumber provides a model for elucidating cell differentiation. In this issue, Zhao et al. (pp. 925-935) studied a spontaneous micro-trichome (mict) mutant with dense and poorly developed trichomes, and performed map-based cloning of the Mict gene. Mict encodes a class I homeodomain-leucine zipper protein and is expressed specifically in trichome cells.

 

          Editorial
Translational plant biology  
Author: Dabing Zhang
Journal of Integrative Plant Biology 2015 57(11): 874每875
Published Online: November 10, 2015
DOI: 10.1111/jipb.12431
Abstract (Browse 410)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Invited Expert Reviews
Anther and pollen development: A conserved developmental pathway  
Author: José Fernández Gómez, Behzad Talle and Zoe A Wilson
Journal of Integrative Plant Biology 2015 57(11): 876每891
Published Online: August 27, 2015
DOI: 10.1111/jipb.12425
      
    

Pollen development is a critical step in plant development that is needed for successful breeding and seed formation. Manipulation of male fertility has proved a useful trait for hybrid breeding and increased crop yield. However, although there is a good understanding developing of the molecular mechanisms of anther and pollen anther development in model species, such as Arabidopsis and rice, little is known about the equivalent processes in important crops. Nevertheless the onset of increased genomic information and genetic tools is facilitating translation of information from the models to crops, such as barley and wheat; this will enable increased understanding and manipulation of these pathways for agricultural improvement.

 

Fernández Gómez J, Talle B, Wilson ZA (2015) Anther and pollen development: A conserved developmental pathway. J Integr Plant Biol 57: 876–891 doi: 10.1111/jipb.12425

Abstract (Browse 635)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Pollen development is a highly conserved trait in higher plants. Detailed understanding of pollen regulatory networks in models is enabling identification of homologous genes for plant fertility in crops; however, functional conservation has to be proven. Such genes have potential applications in developing future hybrid breeding systems.
Peptide aptamers: The versatile role of specific protein function inhibitors in plant biotechnology  
Author: Monica Colombo, Chiara Mizzotti, Simona Masiero, Martin M. Kater and Paolo Pesaresi
Journal of Integrative Plant Biology 2015 57(11): 892每901
Published Online: May 13, 2015
DOI: 10.1111/jipb.12368
      
    

In recent years, peptide aptamers have emerged as novel molecular tools that have attracted the attention of researchers in various fields of basic and applied science, ranging from medicine to analytical chemistry. These artificial short peptides are able to specifically bind, track, and inhibit a given target molecule with high affinity, even molecules with poor immunogenicity or high toxicity, and represent a remarkable alternative to antibodies in many different applications. Their use is on the rise, driven mainly by the medical and pharmaceutical sector. Here we discuss the enormous potential of peptide aptamers in both basic and applied aspects of plant biotechnology and food safety. The different peptide aptamer selection methods available both in vivo and in vitro are introduced, and the most important possible applications in plant biotechnology are illustrated. In particular, we discuss the generation of broad-based virus resistance in crops, “reverse genetics” and aptasensors in bioassays for detecting contaminations in food and feed. Furthermore, we suggest an alternative to the transfer of peptide aptamers into plant cells via genetic transformation, based on the use of cell-penetrating peptides that overcome the limits imposed by both crop transformation and Genetically Modified Organism commercialization. 

 

Colombo M, Mizzotti C, Masiero S, Kater MM, Pesaresi P (2015) Peptide aptamers: The versatile role of specific protein function inhibitors in plant biotechnology. J Integr Plant Biol 57: 892–901 doi: 10.1111/jipb.12368

Abstract (Browse 819)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Large amounts of chemicals, harmful for the environment and human health, are massively used in agriculture to guarantee yield and to extend the shelf life of products. In this review, we discuss the use of artificial short peptides as a healthy and eco-friendly alternative for the food and feed industry.
Roles of lignin biosynthesis and regulatory genes in plant development  
Author: Jinmi Yoon, Heebak Choi and Gynheung An
Journal of Integrative Plant Biology 2015 57(11): 902每912
Published Online: August 22, 2015
DOI: 10.1111/jipb.12422
      
    

Lignin is an important factor affecting agricultural traits, biofuel production, and the pulping industry. Most lignin biosynthesis genes and their regulatory genes are expressed mainly in the vascular bundles of stems and leaves, preferentially in tissues undergoing lignification. Other genes are poorly expressed during normal stages of development, but are strongly induced by abiotic or biotic stresses. Some are expressed in non-lignifying tissues such as the shoot apical meristem. Alterations in lignin levels affect plant development. Suppression of lignin biosynthesis genes causes abnormal phenotypes such as collapsed xylem, bending stems, and growth retardation. The loss of expression by genes that function early in the lignin biosynthesis pathway results in more severe developmental phenotypes when compared with plants that have mutations in later genes. Defective lignin deposition is also associated with phenotypes of seed shattering or brittle culm. MYB and NAC transcriptional factors function as switches, and some homeobox proteins negatively control lignin biosynthesis genes. Ectopic deposition caused by overexpression of lignin biosynthesis genes or master switch genes induces curly leaf formation and dwarfism.

 

Yoon J, Choi H, An G (2015) Roles of lignin biosynthesis and regulatory genes in plant development. J Integr Plant Biol 57: 902–912 doi: 10.1111/jipb.12422

Abstract (Browse 588)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Lignin is an important factor affecting agricultural traits. Alterations in lignin levels affect plant development. Defective lignin deposition is also associated with phenotypes of seed shattering or brittle culm. MYB and NAC transcriptional factors function as switches, and some homeobox proteins negatively control lignin biosynthesis genes.
Rice tissue-specific promoters and condition-dependent promoters for effective translational application  
Author: Hee-Jeong Jeong and Ki-Hong Jung
Journal of Integrative Plant Biology 2015 57(11): 913每924
Published Online: April 17, 2015
DOI: 10.1111/jipb.12362
      
    

Rice (Oryza sativa) is one of the most important staple food crops for more than half of the world's population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types: constitutive, spatiotemporal, and condition-dependent. Transcriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumulated molecules during cellular functions or energy consumption. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue-specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters (50 promoters in total) and six groups of condition-dependent promoters (27 promoters). These promoters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity.

 

Jeong HJ, Jung KH (2015) Rice tissue-specific promoters and condition-dependent promoters for effective translational application. J Integr Plant Biol 57: 913–924 doi: 10.1111/jipb.12362

Abstract (Browse 890)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
To maximize the effect of plant biotechnology using transgenic plants, it is better to use condition-dependent or tissue-specific promoters because use of a constitutive promoter often leads to a negative effect such as growth retardation. We introduce four groups of 50 tissue-specific promoters and six groups of 27 condition-dependent promoters.
          Research Articles
Micro-trichome as a class I homeodomain-leucine zipper gene regulates multicellular trichome development in Cucumis sativus  
Author: Jun-Long Zhao, Jun-Song Pan, Yuan Guan, Wei-Wei Zhang, Bei-Bei Bie, Yun-Li Wang, Huan-Le He, Hong-Li Lian and Run Cai
Journal of Integrative Plant Biology 2015 57(11): 925每935
Published Online: March 4, 2015
DOI: 10.1111/jipb.12345
      
    

Plant trichomes serve as a highly suitable model for investigating cell differentiation at the single-cell level. The regulatory genes involved in unicellular trichome development in Arabidopsis thaliana have been intensively studied, but genes regulating multicellular trichome development in plants remain unclear. Here, we characterized Cucumis sativus (cucumber) trichomes as representative multicellular and unbranched structures, and identified Micro-trichome (Mict), using map-based cloning in an F2 segregating population of 7,936 individuals generated from a spontaneous mict mutant. In mict plants, trichomes in both leaves and fruits, are small, poorly developed, and denser than in the wild type. Sequence analysis revealed that a 2,649-bp genomic deletion, spanning the first and second exons, occurred in a plant-specific class I homeodomain-leucine zipper gene. Tissue-specific expression analysis indicated that Mict is strongly expressed in the trichome cells. Transcriptome profiling identified potential targets of Mict including putative homologs of genes known in other systems to regulate trichome development, meristem determinacy, and hormone responsiveness. Phylogenic analysis charted the relationships among putative homologs in angiosperms. Our paper represents initial steps toward understanding the development of multicellular trichomes.

 

Zhao JL, Pan JS, Guan Y, Zhang WW, Bie BB, Wang YL, He HL, Lian HL, Cai R (2015) Micro-trichome as a class I homeodomain-leucine zipper gene regulates multicellular trichome development in Cucumis sativus. J Integr Plant Biol 57: 925–935 doi: 10.1111/jipb.12345

Abstract (Browse 946)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Trichomes of cucumber are representative multicellular and unbranched structures. We identified Micro-trichome (Mict) as a novel class I homeodomain-leucine zipper gene using map-based cloning. Mict represses trichome spacing and is strongly expressed in trichomes. Further, transcriptome profiling and phylogenic analysis were utilized to identifie potential targets and to chart the relationships among putative homologsin angiosperms respectively.
An ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5 gene mutation confers light green peel in cucumber  
Author: Qian Zhou, Shenhao Wang, Bowen Hu, Huiming Chen, Zhonghua Zhang and Sanwen Huang
Journal of Integrative Plant Biology 2015 57(11): 936每942
Published Online: March 26, 2015
DOI: 10.1111/jipb.12355
      
    

The peel color of fruit is an important commercial trait in cucumber, but the underlying molecular basis is largely unknown. A mutant showing light green exocarp was discovered from ethyl methane sulfonate (EMS) mutagenized cucumber line 406 with dark green exocarp. Genetic analysis showed the mutant phenotype is conferred by a single recessive gene, here designated as lgp (light green peel). By re-sequencing of bulked segregants, we identified the candidate gene Csa7G051430 encoding ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5 (ARC5) that plays a vital role in chloroplast division in Arabidopsis. A single nucleotide polymorphism (SNP) causing amino acid alteration in the conserved GTPase domain of Csa7G051430 showed co-segregation with the altered phenotype. Furthermore, the transient RNA interference of this gene resulted in reduced number and enlarged size of chloroplasts, which were also observed in the lgp mutant. This evidence supports that the non-synonymous SNP in Csa7G051430 is the causative mutation for the light green peel. This study provides a new allele for cucumber breeding for light green fruits and additional resource for the study of chloroplast development.

 

Zhou Q, Wang S, Hu B, Chen H, Zhang Z, Huang S (2015) An ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5 gene mutation confers light green peel in cucumber. J Integr Plant Biol 57: 936–942 doi: 10.1111/jipb.12355

Abstract (Browse 1102)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
We discovered a cucumber EMS mutant showing distinct light green exocarp. By combining whole genome sequencing with genetic mapping, we identified Csa7G051430, a homolog of Arabidopsis ARC5, as the candidate gene responsible for the altered peel color. The mutation caused abnormal chloroplast development in exocarp cells.
Maize orthologs of rice GS5 and their trans-regulator are associated with kernel development  
Author: Jie Liu, Min Deng, Huan Guo, Sharif Raihan, Jingyun Luo, Yuancheng Xu, Xiaofei Dong and Jianbing Yan
Journal of Integrative Plant Biology 2015 57(11): 943每953
Published Online: August 17, 2015
DOI: 10.1111/jipb.12421
      
    

Genome information from model species such as rice can assist in the cloning of genes in a complex genome, such as maize. Here, we identified a maize ortholog of rice GS5 that contributes to kernel development in maize. The genome-wide association analysis of the expression levels of ZmGS5, and 15 of its 26 paralogs, identified a trans-regulator on chromosome 7, which was a BAK1-like gene. This gene that we named as ZmBAK1-7 could regulate the expression of ZmGS5 and three of the paralogs. Candidate-gene association analyses revealed that these five genes were associated with maize kernel development-related traits. Linkage analyses also detected that ZmGS5 and ZmBAK1-7 co-localized with mapped QTLs. A transgenic analysis of ZmGS5 in Arabidopsis thaliana L. showed a significant increase in seed weight and cell number, suggesting that ZmGS5 may have a conserved function among different plant species that affects seed development.

 

Liu J, Deng M, Guo H, Raihan S, Luo J, Xu Y, Dong X, Yan J (2015) Maize orthologs of rice GS5 and their trans-regulator are associated with kernel development. J Integr Plant Biol 57: 943–953 doi: 10.1111/jipb.12421

Abstract (Browse 949)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
ZmGS5 and ZmBAK1-7 were associated with maize kernel development-related traits in association mapping population and also co-localized with mapped QTLs in this study. ZmBAK1-7 could regulate the expression of ZmGS5. A transgenic analysis of ZmGS5 in Arabidopsis showed a significant increase in seed weight and cell number.
GID1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice  
Author: Hao Du, Yu Chang, Fei Huang and Lizhong Xiong
Journal of Integrative Plant Biology 2015 57(11): 954每968
Published Online: November 22, 2014
DOI: 10.1111/jipb.12313
      
    

Plant responses to abiotic stresses are coordinated by arrays of growth and developmental programs. Gibberellic acid (GA) and abscisic acid (ABA) play critical roles in the developmental programs and environmental responses, respectively, through complex signaling and metabolism networks. However, crosstalk between the two phytohormones in stress responses remains largely unknown. In this study, we report that GIBBERELLIN-INSENSITIVE DWARF 1 (GID1), a soluble receptor for GA, regulates stomatal development and patterning in rice (Oryza sativa L.). The gid1 mutant showed impaired biosynthesis of endogenous ABA under drought stress conditions, but it exhibited enhanced sensitivity to exogenous ABA. Scanning electron microscope and infrared thermal image analysis indicated an increase in the stomatal conductance in the gid1 mutant under drought conditions. Interestingly, the gid1 mutant had increased levels of chlorophyll and carbohydrates under submergence conditions, and showed enhanced reactive oxygen species (ROS)-scavenging ability and submergence tolerance compared with the wild-type. Further analyses suggested that the function of GID1 in submergence responses is partially dependent on ABA, and GA signaling by GID1 is involved in submergence tolerance by modulating carbohydrate consumption. Taken together, these findings suggest GID1 plays distinct roles in stomatal response and submergence tolerance through both the ABA and GA signaling pathways in rice.

 

Du H, Chang Y, Huang F, Xiong L (2015) GID1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice. J Integr Plant Biol 57: 954–968 doi: 10.1111/jipb.12313

Abstract (Browse 1102)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
GID1 modulates stomatal development and negatively regulates the ABA response. GID1 is also involved in the control of chlorophyll degradation, ROS production, and carbohydrate consumption under submergence stress condition. Our results provide evidence that GID1 plays crucial roles in regulating stress responses through ABA-independent pathways under drought stress condition and GA-dependent pathways under submergence stress condition in rice.
Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice  
Author: Kwanho Jeong, Nicolas Mattes, Sheryl Catausan, Joong Hyoun Chin, Uta Paszkowski and Sigrid Heuer
Journal of Integrative Plant Biology 2015 57(11): 969每979
Published Online: October 15, 2015
DOI: 10.1111/jipb.12435
      
    

Phosphorus (P) is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal (AM) fungi and expression of different P transporter genes. Plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes (AM1, AM3, AM14) and P transporter genes for the direct Pi uptake (PT2, PT6) and AM-mediated pathway (PT11, PT13) were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which also maintained grain yield under P-deficient field conditions.

 

Jeong K, Mattes N, Catausan S, Chin JH, Paszkowski U, Heuer S (2015) Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice. J Integr Plant Biol 57: 969–979 doi: 10.1111/jipb.12435

Abstract (Browse 665)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
A comparative study of root colonization with Arbuscular mycorrhizal (AM) fungi and AM-marker gene expression was conducted using seven rice varieties. Surprisingly, delayed root colonization was observed in rainfed rice compared with irrigated rice. IR66 had highest expression of the phosphorus transporter OsPT6 and was tolerant to low-P field conditions.
          New Technology
Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform  
Author: Yang L邦, Xiao Cui, Rui Li, Piaopiao Huang, Jie Zong, Danqing Yao, Gang Li, Dabing Zhang and Zheng Yuan
Journal of Integrative Plant Biology 2015 57(11): 980每991
Published Online: March 21, 2015
DOI: 10.1111/jipb.12354
      
    

DNA markers play important roles in plant breeding and genetics. The Insertion/Deletion (InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor-intensive. We developed an end-to-end computational solution (InDel Markers Development Platform, IMDP) to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequences alignment pipeline (AGA-pipe) and next-generation re-sequencing data mapping pipeline (NGS-pipe). With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA-pipe and NGS-pipe, we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction (PCR) analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, to make them available to the public, we have integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, http://202.120.45.71/). The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

 

Lu Y, Cui X, Li R, Huang P, Zong J, Yao D, Li G, Zhang D, Yuan Z (2015) Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform. J Integr Plant Biol 57: 980–991 doi: 10.1111/jipb.12354

Abstract (Browse 1126)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide discovery of InDel polymorphisms offers a practical approach for basic research and molecular marker-assisted selection (MAS). In this study, we developed IMDP program under LONI processing pipeline environment to identify InDel markers from both assembled genome sequences and next-generation re-sequencing data. And all these markers were deposited in RIMD database.
 

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