January 2018, Volume 60 Issue 1, Pages 1每78.

Cover Caption: Genetic diversity and evolution of lotus
Temperate and tropical lotuses display high-levels of genetic diversity and ecological adaptation. In this issue, Huang et al. (pp. 2每15) showed that genomic regions carrying genes involved in circadian clock and energy metabolism are highly differentiated. Photos of these lotus flowers were captured in Wuhan Botanical Garden.


          Functional Omics and Systems Biology
Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)  
Author: Longyu Huang, Mei Yang, Ling Li, Hui Li, Dong Yang, Tao Shi and Pingfang Yang
Journal of Integrative Plant Biology 2018 60(1): 2每15
Published Online: October 20, 2017
DOI: 10.1111/jipb.12606

Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.

Abstract (Browse 595)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Temperate and tropical lotus display high levels of genetic differentiation corresponding to ecological adaptation. Those genes contained in the highly differentiated genomic regions include those involving circadian clock and energy metabolism. Some of these candidate genes could be useful for molecular breeding of lotus lineages with long florescence in temperate zone.
          Plant-abiotic Interactions
Long-distance ABA transport can mediate distal tissue responses by affecting local ABA concentrations  
Author: Wenrao Li, Carlos de Ollas and Ian C Dodd
Journal of Integrative Plant Biology 2018 60(1): 16每33
Published Online: October 20, 2017
DOI: 10.1111/jipb.12605

Environmental stresses that perturb plant water relations influence abscisic acid (ABA) concentrations, but it is unclear whether long-distance ABA transport contributes to changes in local ABA levels. To determine the physiological relevance of ABA transport, we made reciprocal- and self-grafts of ABA-deficient flacca mutant and wild-type (WT) tomato plants, in which low phosphorus (P) conditions decreased ABA concentrations while salinity increased ABA concentrations. Whereas foliar ABA concentrations in the WT scions were rootstock independent under conditions, salinity resulted in long-distance transport of ABA: flacca scions had approximately twice as much ABA when grafted on WT rootstocks compared to flacca rootstocks. Root ABA concentrations were scion dependent: both WT and flacca rootstocks had less ABA with the flacca mutant scion than with the WT scion under conditions. In WT scions, whereas rootstock genotype had limited effects on stomatal conductance under conditions, a flacca rootstock decreased leaf area of stressed plants, presumably due to attenuated root-to-shoot ABA transport. In flacca scions, a WT rootstock decreased stomatal conductance but increased leaf area of stressed plants, likely due to enhanced root-to-shoot ABA transport. Thus, long-distance ABA transport can affect responses in distal tissues by changing local ABA concentrations.

Abstract (Browse 520)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Since phosphorus and salt stresses change ABA concentrations throughout the plant, wild-type and ABA-deficient mutant tomatoes were reciprocally grafted to compare local versus long-distance ABA effects. Rootstock genotype affected stomatal conductance, leaf area and shoot biomass, while scion genotype affected root biomass, by changing local ABA concentrations in distal tissues.
          Plant-biotic Interactions
Graft-accelerated virus-induced gene silencing facilitates functional genomics in rose flowers  
Author: Huijun Yan, Shaochuan Shi, Nan Ma, Xiaoqian Cao, Hao Zhang, Xianqin Qiu, Qigang Wang, Hongying Jian, Ningning Zhou, Zhao Zhang and Kaixue Tang
Journal of Integrative Plant Biology 2018 60(1): 34每44
Published Online: September 12, 2017
DOI: 10.1111/jipb.12599

Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors. Virus-induced gene silencing (VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose, called ‘graft-accelerated VIGS’, where axillary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR1, RhAG, and RhNUDX1 in rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.

Abstract (Browse 340)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
We report the establishment of a novel, rapid and efficient method for gene knocking-down in rose, which facilitates functional analysis of genes involved in color, fragrance as well as development of rose flowers.
          Plant Reproduction Biology
Defective Kernel 39 encodes a PPR protein required for seed development in maize  
Author: Xiaojie Li, Wei Gu, Silong Sun, Zongliang Chen, Jing Chen, Weibin Song, Haiming Zhao and Jinsheng Lai
Journal of Integrative Plant Biology 2018 60(1): 45每64
Published Online: October 5, 2017
DOI: 10.1111/jipb.12602

RNA editing is a posttranscriptional process that is important in mitochondria and plastids of higher plants. All RNA editing specific trans-factors reported so far belong to PLS-class of pentatricopeptide repeat (PPR) proteins. Here, we report the map-based cloning and molecular characterization of a defective kernel mutant dek6 in maize. Loss of Dek6 function leads to delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality. Dek6 encodes an E sub-class PPR protein that targets to both mitochondria and chloroplasts, and is involved in RNA editing in mitochondrial NADH dehydrogenase3 (nad3) at nad3-247 and nad3-275. C to U editing of nad3-275 is not conserved and even lost in Arabidopsis, consisting with the idea that no close DEK6 homologs present in Arabidopsis. However, the amino acids generated by editing nad3-247 and nad3-275 are highly conserved in many other plant species, and the reductions of editing at these two sites decreased the activity of mitochondria NADH dehydrogenase complex I, indicating that the alteration of amino acid sequence is necessary for Nad3 function. Our results indicate that Dek6 encodes an E sub-class PPR protein that is involved in RNA editing of multiple sites and is necessary for seed development of maize.

Abstract (Browse 403)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Maize PPR protein Defective kernel 6 was involved in RNA editing in mitochondria NADH dehydrogenase3 to correct Nad3 codons to conserved amino acids. Mutation in Dek6 decreased the activity of mitochondria NADH dehydrogenase complex I and led to the defective kernel phenotype of dek6.
AGO18b negatively regulates determinacy of spikelet meristems on the tassel central spike in maize  
Author: Wei Sun, Xiaoli Xiang, Lihong Zhai, Dan Zhang, Zheng Cao, Lei Liu and Zuxin Zhang
Journal of Integrative Plant Biology 2018 60(1): 65每78
Published Online: September 6, 2017
DOI: 10.1111/jipb.12596

The maize tassel represents an indeterminate male inflorescence. The number of primordia that a given inflorescence meristem produces is related to its determinacy, i.e., capacity for continued meristem activity. Transcription factors (TFs) controlling determinacy in tassel axillary meristems are well studied in maize, and small RNAs are known to influence tassel development by repressing targets, including tassel-related TFs. As core components of the RNA-inducible silence complex (RISC), Argonaute (AGO) proteins are required for small RNA-mediated repression. Here, we characterized the biological function of AGO18b, a tassel-enriched AGO. The abundance of AGO18b transcripts gradually increased during tassel development from inception to gametogenesis and were enriched in the inflorescence meristem and axillary meristems of the tassel. Repressing AGO18b expression resulted in more spikelets, which contributed to a longer central spike of the tassel. Additionally, the transcripts of several HD-ZIP III TFs that were canonical targets of microRNA166 (miR166) accumulated in the AGO18b-repressed lines. We propose that AGO18b is a negative regulator of the determinacy of inflorescence and axillary meristems, and that it acts by interacting with the miR166-HD-ZIP III TF regulatory pathway.

Abstract (Browse 436)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This study demonstrated that maize Argonaute (AGO) protein AGO18b is specifically enriched in the inflorescence meristem and axillary meristems of the tassel, and functions as a negative regulator of spikelet number on the tassel central spike by interacting with the microRNA166-mediated regulatory pathway.



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