May 2016, Volume 58 Issue 5, Pages 441每513.

Cover Caption: Natural Variation of H3K27me3 in Hybrid
What is the biological consequence of natural variations in histone modification in plants? In this issue, genomewide H3K27me3 modification and expression analyses were performed in two Arabidopsis accessions and their hybrid. Results showed that variations of H3K27me3 histone modification between these two accessions correlates negatively with gene expression levels, resulting in allelic bias of the H3K27me3 modification in hybrid. The heterosis in hybrid was compromised upon mutation of CLF that regulates the H3K27me3 modification (see Yang et al., 466每474, for details).


          Cell and Developmental Biology
ANAC005 is a membrane-associated transcription factor and regulates vascular development in Arabidopsis  
Author: Jun Zhao, Jiang-Shu Liu, Fu-Ning Meng, Zhen-Zhen Zhang, Hao Long, Wen-Hui Lin, Xiao-Min Luo, Zhi-Yong Wang and Sheng-Wei Zhu
Journal of Integrative Plant Biology 2016 58(5): 442每451
Published Online: July 14, 2015
DOI: 10.1111/jipb.12379

Vascular tissues are very important for providing both mechanical strength and long-distance transport. The molecular mechanisms of regulation of vascular tissue development are still not fully understood. In this study we identified ANAC005 as a membrane-associated NAC family transcription factor that regulates vascular tissue development. Reporter gene assays showed that ANAC005 was expressed mainly in the vascular tissues. Increased expression of ANAC005 protein in transgenic Arabidopsis caused dwarf phenotype, reduced xylem differentiation, decreased lignin content, repression of a lignin biosynthetic gene and genes related to cambium and primary wall, but activation of genes related to the secondary wall. Expression of a dominant repressor fusion of ANAC005 had overall the opposite effects on vascular tissue differentiation and lignin synthetic gene expression. The ANAC005-GFP fusion protein was localized at the plasma membrane, whereas deletion of the last 20 amino acids, which are mostly basic, caused its nuclear localization. These results indicate that ANAC005 is a cell membrane-associated transcription factor that inhibits xylem tissue development in Arabidopsis.

Abstract (Browse 1101)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
ANAC005, a NAC family transcription factor, expresses mainly in vascular tissues. It localizes in cell membrane, whereas deletion of the last 20 amino acids caused its nuclear localization. Moreover, ANAC005 reduce xylem differentiation and decrease lignin synthesis.
Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers
Author: Hui Wang, Pawan Khera, Bingyan Huang, Mei Yuan, Ramesh Katam, Weijian Zhuang, Karen Harris-Shultz, Kim M. Moore, Albert K. Culbreath, Xinyou Zhang, Rajeev K. Varshney, Lianhui Xie and Baozhu Guo
Journal of Integrative Plant Biology 2016 58(5): 452每465
Published Online: July 15, 2015
DOI: 10.1111/jipb.12380

Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

Abstract (Browse 834)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Assessing the peanut genetic diversity and population structure by country-wise analysis revealed that alleles per locus in three countries were similar. The groupings were related to peanut market types and geographic origin, which could be used by breeding programs to broaden the genetic base.
          Functional Omics and Systems Biology
Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid  
Author: Mei Yang, Xuncheng Wang, Hao Huang, Diqiu Ren, Yan'e Su, Pan Zhu, Danmeng Zhu, Liumin Fan, Liangbi Chen, Guangming He and Xing Wang Deng
Journal of Integrative Plant Biology 2016 58(5): 466每474
Published Online: October 24, 2015
DOI: 10.1111/jipb.12443

Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in allelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, especially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27, altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.

Abstract (Browse 1073)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
We performed genome-wide analyses of H3K27me3 modification and gene expression for two Arabidopsis accessions and their hybrid. H3K27me3 modification patterns were different in two accessions. Moreover, a negative correlation of H3K27me3 modification variation with gene expression variation was observed between these two accessions.
          Molecular Physiology
Evaluation of high yielding soybean germplasm under water limitation  
Author: Silvas J. Prince, Mackensie Murphy, Raymond N. Mutava, Zhengzhi Zhang, Na Nguyen, Yoon Ha Kim, Safiullah M. Pathan, Grover J. Shannon, Babu Valliyodan and Henry T. Nguyen
Journal of Integrative Plant Biology 2016 58(5): 475每491
Published Online: July 14, 2015
DOI: 10.1111/jipb.12378

Limited information is available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits was measured at multiple crop stages ranging from early vegetative to pod filling. The phenotypic root traits, and biomass accumulation data are collected at pod filling stage. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In sandy soil, PI458020 was found to have a thicker lateral root system and higher yield under water limitation. The genotypes identified in this study could be used to enhance drought tolerance of elite soybean cultivars through improved root traits specific to target environments.

Abstract (Browse 1109)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Understanding the root system of agronomic crops and their adaptive changes in morphology based on water availability is vital to developing high yielding lines with tolerance of drought conditions. We have identified high yielding soybean lines with adapted shoot and root traits specific to different soil and rain fall conditions.
          Plant-environmental Interactions
OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice
Author: Chiming Guo, Chengke Luo, Lijia Guo, Min Li, Xiaoling Guo, Yuxia Zhang, Liangjiang Wang and Liang Chen
Journal of Integrative Plant Biology 2016 58(5): 492每502
Published Online: July 14, 2015
DOI: 10.1111/jipb.12376

Domain of unknown function 1644 (DUF1644) is a highly conserved amino acid sequence motif present only in plants. Analysis of expression data of the family of DUF1644-containing genes indicated that they may regulate responses to abiotic stress in rice. Here we present our discovery of the role of OsSIDP366, a member of the DUF1644 gene family, in response to drought and salinity stresses in rice. Transgenic rice plants overexpressing OsSIDP366 showed enhanced drought and salinity tolerance and reduced water loss as compared to that in the control, whereas plants with downregulated OsSIDP366 expression levels using RNA interference (RNAi) were more sensitive to salinity and drought treatments. The sensitivity to abscisic acid (ABA) treatment was not changed in OsSIDP366-overexpressing plants, and OsSIDP366 expression was not affected in ABA-deficient mutants. Subcellular localization analysis revealed that OsSIDP366 is presented in the cytoplasmic foci that colocalized with protein markers for both processing bodies (PBs) and stress granules (SGs) in rice protoplasts. Digital gene expression (DGE) profile analysis indicated that stress-related genes such as SNAC1, OsHAK5 and PRs were upregulated in OsSIDP366-overexpressing plants. These results suggest that OsSIDP366 may function as a regulator of the PBs/SGs and positively regulate salt and drought resistance in rice.

Abstract (Browse 959)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
OsSIDP366 is a member of DUF1644 family in rice which co-localizes with processing bodies and stress granules.Over-expression of OsSIDP366 enhances drought and salt tolerance, reduces water loss rate and up-regulates stress-related genes in rice, suggesting the positive role of OsSIDP366 in abiotic stress response.
Suppression of the homeobox gene HDTF1 enhances resistance to Verticillium dahliae and Botrytis cinerea in cotton
Author: Wei Gao, Lu Long, Li Xu, Keith Lindsey, Xianlong Zhang and Longfu Zhu
Journal of Integrative Plant Biology 2016 58(5): 503每513
Published Online: September 26, 2015
DOI: 10.1111/jipb.12432

Development of pathogen-resistant crops, such as fungus-resistant cotton, has significantly reduced chemical application and improved crop yield and quality. However, the mechanism of resistance to cotton pathogens such as Verticillium dahliae is still poorly understood. In this study, we characterized a cotton gene (HDTF1) that was isolated following transcriptome profiling during the resistance response of cotton to V. dahliae. HDTF1 putatively encodes a homeodomain transcription factor, and its expression was found to be down-regulated in cotton upon inoculation with V. dahliae and Botrytis cinerea. To characterise the involvement of HDTF1 in the response to these pathogens, we used virus-induced gene silencing (VIGS) to generate HDTF1-silenced cotton. VIGS reduction in HDTF1 expression significantly enhanced cotton plant resistance to both pathogens. HDTF1 silencing resulted in activation of jasmonic acid (JA)-mediated signaling and JA accumulation. However, the silenced plants were not altered in the accumulation of salicylic acid (SA) or the expression of marker genes associated with SA signaling. These results suggest that HDTF1 is a negative regulator of the JA pathway, and resistance to V. dahliae and B. cinerea can be engineered by activation of JA signaling.

Abstract (Browse 666)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
HDTF1, a member of the PINTOX class homeobox gene family, was cloned and characterized. Silencing of HDTF1 enhanced cotton resistance to V. dahliae and B. cinerea. In addition, we revealed that HDTF1 is a negative regulator of JA signaling pathway, and it could be used as a candidate gene in cotton disease resistance breeding.


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