August 2013, Volume 55 Issue 8, Pages 681¨C784.

Cover Caption: Vernalization-Related Genes in Brachypodium
About the cover: Temperate plants often require vernalization to flower, but genes involved in vernalization memory are very much unknown. In this issue, Huan et al. (pp. 696¨C709) performed transcriptome analyses in vernalization in Brachypodium distachyon seedlings using RNA-Seq, and uncovered a group of vernalization-related genes. Comparative analyses of vernalization-related genes in barley revealed several conserved and species-specific genes involved.


          Cell and Developmental Biology
PHOSPHATIDYLSERINE SYNTHASE1 is Required for Inflorescence Meristem and Organ Development in Arabidopsis  
Author: Chengwu Liu, Hengfu Yin, Peng Gao, Xiaohe Hu, Jun Yang, Zhongchi Liu, Xiangdong Fu and Da Luo
Journal of Integrative Plant Biology 2013 55(8): 682-695
Published Online: August 11, 2013
DOI: 10.1111/jipb.12045

Phosphatidylserine (PS), a quantitatively minor membrane phospholipid, is involved in many biological processes besides its role in membrane structure. One PS synthesis gene, PHOSPHATIDYLSERINE SYNTHASE1 (PSS1), has been discovered to be required for microspore development in Arabidopsis thaliana L. but how PSS1 affects postembryonic development is still largely unknown. Here, we show that PSS1 is also required for inflorescence meristem and organ development in Arabidopsis. Disruption of PSS1 causes severe dwarfism, smaller lateral organs and reduced size of inflorescence meristem. Morphological and molecular studies suggest that both cell division and cell elongation are affected in the pss1-1 mutant. RNA in situ hybridization and promoter GUS analysis show that expression of both WUSCHEL (WUS) and CLAVATA3 (CLV3) depend on PSS1. Moreover, the defect in meristem maintenance is recovered and the expression of WUS and CLV3 are restored in the pss1-1 clv1-1 double mutant. Both SHOOTSTEMLESS (STM) and BREVIPEDICELLUS (BP) are upregulated, and auxin distribution is disrupted in rosette leaves of pss1-1. However, expression of BP, which is also a regulator of internode development, is lost in the pss1-1 inflorescence stem. Our data suggest that PSS1 plays essential roles in inflorescence meristem maintenance through the WUS-CLV pathway, and in leaf and internode development by differentially regulating the class I KNOX genes.

Liu C, Yin H, Gao P, Hu X, Yang J, Liu Z, Fu X, Luo D (2012) PHOSPHATIDYLSERINE SYNTHASE1 is required for inflorescence meristem and organ development in Arabidopsis. J. Integr. Plant Biol. 55(8), 682–695.

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Transcriptome-wide Analysis of Vernalization Reveals Conserved and Species-specific Mechanisms in Brachypodium
Author: Qing Huan, Zhiwei Mao, Jingyu Zhang, Yunyuan Xu and Kang Chong
Journal of Integrative Plant Biology 2013 55(8): 696-709
Published Online: June 12, 2013
DOI: 10.1111/jipb.12050

Several temperate cereals need vernalization to promote flowering. Little, however, is known about the vernalization-memory-related genes, and almost no comparative analysis has been performed. Here, RNA-Seq was used for transcriptome analysis in non-vernalized, vernalized and post-vernalized Brachypodium distachyon (L.) Beauv. seedlings. In total, the expression of 1,665 genes showed significant changes (fold change ≥4) in response to vernalization. Among them, 674 putative vernalization-memory-related genes with a constant response to vernalization were significantly enriched in transcriptional regulation and monooxygenase-mediated biological processes. Comparative analysis of vernalization-memory-related genes with barley demonstrated that the oxidative-stress response was the most conserved pathway between these two plant species. Moreover, Brachypodium preferred to regulate transcription and protein phosphorylation processes, while vernalization-memory-related genes, whose products are cytoplasmic membrane-bound-vesicle-located proteins, were preferred to be regulated in barley. Correlation analysis of the vernalization-related genes with barley revealed that the vernalization mechanism was conserved between these two plant species. In summary, vernalization, including its memory mechanism, is conserved between Brachypodium and barley, although several species-specific features also exist. The data reported here will provide primary resources for subsequent functional research in vernalization.

Huan Q, Mao Z, Zhang J, Xu Y, Chong K (2013) Transcriptomeİ\wide analysis of vernalization reveals conserved and speciesİ\specific mechanisms in Brachypodium. J. Integr. Plant Biol. 55(8), 696–709.

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          Plant Reproduction Biology
The ATP-binding Cassette Transporter OsABCG15 is Required for Anther Development and Pollen Fertility in Rice  
Author: Bai-Xiao Niu, Fu-Rong He, Ming He, Ding Ren, Le-Tian Chen and Yao-Guang Liu
Journal of Integrative Plant Biology 2013 55(8): 710-720
Published Online: June 17, 2013
DOI: 10.1111/jipb.12053

Plant male reproductive development is a complex biological process, but the underlying mechanism is not well understood. Here, we characterized a rice (Oryza sativa L.) male sterile mutant. Based on map-based cloning and sequence analysis, we identified a 1,459-bp deletion in an adenosine triphosphate (ATP)-binding cassette (ABC) transporter gene, OsABCG15, causing abnormal anthers and male sterility. Therefore, we named this mutant osabcg15. Expression analysis showed that OsABCG15 is expressed specifically in developmental anthers from stage 8 (meiosis II stage) to stage 10 (late microspore stage). Two genes CYP704B2 and WDA1, involved in the biosynthesis of very-long-chain fatty acids for the establishment of the anther cuticle and pollen exine, were downregulated in osabcg15 mutant, suggesting that OsABCG15 may play a key function in the processes related to sporopollenin biosynthesis or sporopollenin transfer from tapetal cells to anther locules. Consistently, histological analysis showed that osabcg15 mutants developed obvious abnormality in postmeiotic tapetum degeneration, leading to rapid degredation of young microspores. The results suggest that OsABCG15 plays a critical role in exine formation and pollen development, similar to the homologous gene of AtABCG26 in Arabidopsis. This work is helpful to understand the regulatory network in rice anther development.

Niu BX, He FR, He M, Ren D, Chen LT, Liu YG (2013) The ATPİ\binding cassette transporter OsABCG15 is required for anther development and pollen fertility in rice. J. Integr. Plant Biol. 55(8), 710–720.

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          Plant-environmental Interactions
Photosynthetic and Molecular Markers of CO2-mediated Photosynthetic Downregulation in Nodulated Alfalfa
Author: Álvaro Sanz-Sáez, Gorka Erice, Iker Aranjuelo, Ricardo Aroca, Juan Manuel Ruíz-Lozano, Jone Aguirreolea, Juan José Irigoyen and Manuel Sanchez-Diaz
Journal of Integrative Plant Biology 2013 55(8): 721-734
Published Online: June 24, 2013
DOI: 10.1111/jipb.12047

Elevated CO2 leads to a decrease in potential net photosynthesis in long-term experiments and thus to a reduction in potential growth. This process is known as photosynthetic downregulation. There is no agreement on the definition of which parameters are the most sensitive for detecting CO2 acclimation. In order to investigate the most sensitive photosynthetic and molecular markers of CO2 acclimation, the effects of elevated CO2, and associated elevated temperature were analyzed in alfalfa plants inoculated with different Sinorhizobium meliloti strains. Plants (Medicago sativa L. cv. AragÓn) were grown in summer or autumn in temperature gradient greenhouses (TGG). At the end of the experiment, all plants showed acclimation in both seasons, especially under elevated summer temperatures. This was probably due to the lower nitrogen (N) availability caused by decreased N2-fixation under higher temperatures. Photosynthesis measured at growth CO2 concentration, rubisco in vitro activity and maximum rate of carboxylation were the most sensitive parameters for detecting downregulation. Severe acclimation was also related with decreases in leaf nitrogen content associated with declines in rubisco content (large and small subunits) and activity that resulted in a drop in photosynthesis. Despite the sensitivity of rubisco content as a marker of acclimation, it was not coordinated with gene expression, possibly due to a lag between gene transcription and protein translation.

Sanz-Sáez Á, Erice G, Aranjuelo I, Aroca R, Ruíz-Lozano JM, Aguirreolea J, Irigoyen JJ, Sanchez-Diaz M (2013) Photosynthetic and molecular markers of CO2-mediated photosynthetic downregulation in nodulated alfalfa. J. Integr. Plant Biol. 55(8), 721–734.

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          Molecular Physiology
Genome-wide Association Analysis of Ten Chilling Tolerance Indices at the Germination and Seedling Stages in Maize
Author: Juan Huang, Jianhua Zhang, Wenzhen Li, Wei Hu, Lichao Duan, Yang Feng, Fazhan Qiu and Bing Yue
Journal of Integrative Plant Biology 2013 55(8): 735-744
Published Online: August 11, 2013
DOI: 10.1111/jipb.12051

Maize seedlings are very sensitive to chilling, especially during the transition phase from heterotrophic to autotrophic growth. Genetic dissection of the genetic basis of chilling tolerance would provide useful information for genetic improvement of maize inbreds. In this study, genome-wide association analysis was conducted to explore the genetic architecture of maize chilling tolerance at the seed germination and seedling stages with an association panel of 125 inbreds. Ten tolerance indices (ratios of the performance of 10 germination rates and seedling growth-related traits under chilling stress and control conditions) were investigated to assess the ability of chilling tolerance of the inbreds, and a total of 43 single nucleotide polymorphisms associated with chilling tolerance were detected, with none of them being related to chilling tolerance at both the germination and seedling stages simultaneously. Correlation analysis also revealed that the genetic basis of chilling tolerance at the seed germination stage is generally different from that at the seedling stage. In addition, a total of 40 candidate genes involving 31 of the 43 single nucleotide polymorphisms were predicted, and were grouped into five categories according to their functions. The possible roles of these candidate genes in chilling tolerance were also discussed.

Huang J, Zhang J, Li W, Hu W, Duan L, Feng Y, Qiu F, Yue B (2013) Genomeİ\wide association analysis of 10 chilling tolerance indices at the germination and seedling stages in maize. J. Integr. Plant Biol. 55(8), 735–744.

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Association Analysis for Quality Traits in a Diverse Panel of Chinese Sesame (Sesamum indicum L.) germplasm
Author: Wenliang Wei, Yanxin Zhang, Haixia Lv, Donghua Li, Linhai Wang and Xiurong Zhang
Journal of Integrative Plant Biology 2013 55(8): 745-758
Published Online: August 11, 2013
DOI: 10.1111/jipb.12049

The main objective of this study was to evaluate the potential of a sesame (Sesamum indicum L.) panel for association analysis, and investigate the genetic basis of oil content (OC), protein content, oleic acid concentration, and linoleic acid concentration using association mapping. A panel of 216 sesame accessions was phenotyped in a multi-environment trial and fingerprinted with 608 polymorphic loci produced by 79 primers, including simple sequence repeats (SSRs), sequence-related amplified polymorphisms (SRAPs), and amplified fragment length polymorphisms (AFLPs). Population structure analysis revealed two subgroups in the population. The Q model performed better for its ability to re-identify associations for the four traits at highly significant P-values compared to the other three mixed models. And a total of 35 and 25 associations for the four traits in 2010 and 2011 were identified, respectively, with the Q model after Bonferroni correction. Among those associations, only one for OC was re-identified in two environments, and several markers associated simultaneously with multiple traits were discovered. These results suggest the power and stability of the Q model for association analysis of nutritional traits in this sesame panel for its slight population stratification and familial relationship, which could aid in dissecting complex traits, and could help to develop strategies for improving nutritional quality.

Wei W, Zhang Y, Lv H, Li D, Wang L, Zhang X (2013) Association analysis for quality traits in a diverse panel of Chinese sesame (Sesamum indicum L.) germplasm. J. Integr. Plant Biol. 55(8), 745–758.

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          Molecular Ecology and Evolution
Mapping Heterotic Loci for Yield and Agronomic Traits Using Chromosome Segment Introgression Lines in Cotton
Author: Xian Guo, Yuping Guo, Jun Ma, Fang Wang, Mizhen Sun, Lijuan Gui, Jiajia Zhou, Xianliang Song, Xuezhen Sun and Tianzhen Zhang
Journal of Integrative Plant Biology 2013 55(8): 759-774
Published Online: August 11, 2013
DOI: 10.1111/jipb.12054
In the present study, a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F1 populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL). A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBS-D7-1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects (partial-, full-, over-dominant) were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.

Guo X, Guo Y, Ma J, Wang F, Sun M, Gui L, Zhou J, Song X, Sun X, Zhang T (2013) Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton. J. Integr. Plant Biol. 55(8), 759–774.

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Response of Rice to Insect Elicitors and the Role of OsJAR1 in Wound and Herbivory-induced JA-Ile Accumulation
Author: Kaori Fukumoto, Kabir Md Alamgir, Yuko Yamashita, Izumi C. Mori, Hideyuki Matsuura and Ivan Galis
Journal of Integrative Plant Biology 2013 55(8): 775-784
Published Online: August 11, 2013
DOI: 10.1111/jipb.12057

Plants produce jasmonic acid (JA) and its amino acid conjugate, jasmonoyl-L-isoleucine (JA-Ile) as major defense signals in response to wounding and herbivory. In rice (Oryza sativa), JA and JA-Ile rapidly increased after mechanical damage, and this increase was further amplified when the wounds were treated with oral secretions from generalist herbivore larvae, lawn armyworms (Spodoptera mauritia), revealing for the first time active perception mechanisms of herbivore-associated elicitor(s) in rice. In the rice genome, two OsJAR genes can conjugate JA and Ile and form JA-Ile in vitro; however, their function in herbivory-induced accumulation of JA-Ile has not been investigated. By functional characterization of TOS17 retrotransposon-tagged Osjar1 plants and their response to simulated herbivory, we show that OsJAR1 is essential for JA-Ile production in herbivore-attacked, field-grown plants. In addition, OsJAR1 was required for normal seed development in rice under field conditions. Our results suggest that OsJAR1 possesses at least two major functions in rice defense and development that cannot be complemented by the additional OsJAR2 gene function, although this gene previously showed overlapping enzyme activity in vitro.

Fukumoto K, Alamgir KM, Yamashita Y, Mori IC, Matsuura H, Galis I (2013) Response of rice to insect elicitors and the role of OsJAR1 in wound and herbivoryİ\induced JAİ\Ile accumulation. J. Integr. Plant Biol. 55(8), 775–784.

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