September 2008, Volume 50 Issue 9, Pages 1057-1182.

Cover Caption:
INS localizes to the cytosol of Arabidopsis cells
Higher plants have been proposed to have two IAA biosynthetic pathways: one is tryptophan-dependent and another is tryptophan-independent. In this issue, Zhang et al. (pages 1070C1077) reported the isolation and characterization of the Arabidopsis indole synthase (INS), a homolog of Trp synthase (TSA1). Their results demonstrated that INS is different from TSA1 in the expression pattern, the subcellular localization and the functional complementation of E. coli trpA cells, implying that INS may participate in a non-tryptophan biosynthetic pathway (Cover design: Ying Wang).


          Invited Expert Reviews
Current Opinions on the Functions of Tocopherol Based on the Genetic Manipulation of Tocopherol Biosynthesis in Plants
Author: Yin Li, Zinan Wang, Xiaofen Sun and Kexuan Tang
Journal of Integrative Plant Biology 2008 50(9): 1057-1069
DOI: 10.1111/j.1744-7909.2008.00689.x
    As a member of an important group of lipid soluble antioxidants, tocopherols play a paramount role in the daily diet of humans and animals. Recently, genes required for tocochromanol biosynthesis pathway have been identified and cloned with the help of genomics-based approaches and molecular manipulation in the model organisms: Arabidopsis thaliana and Synechocystis sp. PCC 6803. At the basis of these foundations, genetic manipulation of tocochromanol biosynthesis pathway can give rise to strategies that enhance the level of tocochromanol content or convert the constitution of tocochromanol. In addition, genetic manipulations of the tocochromanol biosynthesis pathway provide help for the study of the function of tocopherol in plant systems. The present article summarizes recent advances and pays special attention to the functions of tocopherol in plants. The roles of tocopherol in the network of reactive oxygen species, antioxidants and phytohormones to maintain redox homeostasis and the functions of tocopherol as a signal molecule in chloroplast-to-nucleus signaling to regulate carbohydrate metabolism are also discussed.
Abstract (Browse 1256)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Cell and Developmental Biology
Arabidopsis Indole Synthase, a Homolog of Tryptophan Synthase Alpha, is an Enzyme Involved in the Trp-independent Indole-containing Metabolite Biosynthesis  
Author: Rui Zhang, Bing Wang, Jian Ouyang, Jiayang Li and Yonghong Wang
Journal of Integrative Plant Biology 2008 50(9): 1070-1077
DOI: 10.1111/j.1744-7909.2008.00729.x
    The plant tryptophan (Trp) biosynthetic pathway produces many secondary metabolites with diverse functions. Indole-3-acetic acid (IAA), proposed as a derivative from Trp or its precursors, plays an essential role in plant growth and development. Although the Trp-dependant and Trp-independent IAA biosynthetic pathways have been proposed, the enzymes, reactions and regulatory mechanisms are largely unknown. In Arabidopsis, indole-3-glycerol phosphate (IGP) is suggested to serve as a branchpoint component in the Trp-independent IAA biosynthesis. To address whether other enzymes in addition to Trp synthase (TSA1) catalyze IGP cleavage, we identified and characterized an indole synthase (INS) gene, a homolog of TSA1 in Arabidopsis. INS exhibits different subcellular localization from TSA1 owing to the lack of chloroplast transit peptide (cTP). In silico data show that the expression levels of INS and TSA1 in all examined organs are quite different. Histochemical staining of INS promoter-GUS transgenic lines indicates that INS is expressed in vascular tissue of cotyledons, hypocotyls, roots and rosette leaves as well as in flowers and siliques. INS is capable of complementing the Trp auxotrophy of Escherichia colitrpA strain, which is defective in Trp synthesis due to the deletion of TSA. This implies that INS catalyzes the conversion of IGP to indole and may be involved in the biosynthesis of Trp-independent IAA or other secondary metabolites in Arabidopsis.
Abstract (Browse 1874)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Global Identification of Significantly Expressed Genes in Developing Endosperm of Rice by Expression Sequence Tags and cDNA Array Approaches  
Author: Qichao Tu, Haitao Dong, Haigen Yao, Yongqi Fang, Cheng'en Dai, Hongmei Luo, Jian Yao, Dong Zhao and Debao Li
Journal of Integrative Plant Biology 2008 50(9): 1078-1088
DOI: 10.1111/j.1744-7909.2008.00714.x

Rice endosperm plays a very important role in seedling germination and determines the qualities of rice grain. Although studies on specific gene categories in endosperm have been carried out, global view of gene expression at a transcription level in rice endosperm is still limited. To gain a better understanding of the global and tissue-specific gene expression profiles in rice endosperm, a cDNA library from rice endosperm of immature seeds was sequenced. A cDNA array was constructed based on the tentative unique transcripts derived from expression sequence tag (EST) assembling results and then hybridized with cDNAs from five different tissues or organs including endosperm, embryo, leaf, stem and root of rice. Significant redundancy was found for genes encoding prolamin, glutelin, allergen, and starch synthesis proteins, accounting for ∼34% of the total ESTs obtained. The cDNA array revealed 87 significantly expressed genes in endosperm compared with the other four organs or tissues. These genes included 13 prolamin family proteins, 17 glutelin family proteins, 12 binding proteins, nine catalytic proteins and four ribosomal proteins, indicating a complicated biological processing in rice endosperm. In addition, Northern verification of 1,4-alpha-glucan branching enzyme detected two isoforms in rice endosperm, the larger one of which only existed in endosperm.

Abstract (Browse 2563)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Plant-environmental Interactions
Mapping Quantitative Trait Loci Associated with Aluminum Toxin Tolerance in NJRIKY Recombinant Inbred Line Population of Soybean (Glycine max)
Author: Bo Qi, Paul Korir, Tuanjie Zhao, Deyue Yu, Shouyi Chen and Junyi Gai
Journal of Integrative Plant Biology 2008 50(9): 1089-1095
DOI: 10.1111/j.1744-7909.2008.00682.x
    To investigate the genetic mechanism of Al-tolerance in soybean, a recombinant inbred line population (RIL) with 184 F2:7:11 lines derived from the cross of Kefeng No.1 Nannong 1138-2 (Al-tolerant Al-sensitive) were tested in pot experiment with sand culture medium in net room in Nanjing. Four traits, i.e. plant height, number of leaves, shoot dry weight and root dry weight at seedling stage, were evaluated and used to calculate the average membership index (FAi) as the indicator of Al-tolerance. The composite interval mapping (CIM) under WinQTL Cartographer v. 2.5 detected five QTLs (i.e. qFAi-1, qFAi-2, qFAi-3, qFAi-4 and qFAi-5), explaining 5.20%C9.07% of the total phenotypic variation individually. While with the multiple interval mapping (MIM) of the same software, five QTLs (qFAi-1, qFAi-5, qFAi-6, qFAi-7, and qFAi-8) explaining 5.7%C24.60% of the total phenotypic variation individually were mapped. Here qFAi-1 and qFAi-5 were detected by both CIM and MIM with the locations in a same flanking marker region, GMKF046-GMKF080 on B1 and satt278-sat_95 on L, respectively. While qFAi-2 under CIM and qFAi-6 under MIM both on D1b2 were located in neighboring regions with their confidence intervals overlapped and might be the same locus. Segregation analysis under major gene plus polygene inheritance model showed that Al-tolerance was controlled by two major genes (h2mg = 33.05%) plus polygenes (h2pg = 52.73%). Both QTL mapping and segregation analysis confirmed two QTLs responsible for Al-tolerance with relatively low heritability, and there might be a third QTL, confounded with the polygenes in segregation analysis.
Abstract (Browse 1126)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Effect of Salicylic Acid on Salinity-induced Changes in Brassica juncea
Author: Mohammad Yusuf, Syed Aiman Hasan, Barket Ali, Shamsul Hayat, Qazi Fariduddin and Aqil Ahmad
Journal of Integrative Plant Biology 2008 50(9): 1096-1102
DOI: 10.1111/j.1744-7909.2008.00697.x
    Seeds of Indian mustard (Brassica juncea L.) Czern & Coss were exposed to 0, 50, 100, 150 mM NaCl for 8 h. and seeds were sown in an earthen pot. These stressed seedlings were subsequently sprayed with 10 M salicylic acid (SA) at 30-day stage and were sampled at 60-day to assess the changes in growth, photosynthesis and antioxidant enzymes. The seedlings raised from the seeds treated with NaCl significantly reduced the growth, the activities of carbonic anhydrase and nitrate reductase and photosynythesis and the decrease was proportional to the increase in NaCl concentaration. However, the antioxidant enzymes (catalase, peroxidase and superoxide dismutase) and proline content was enhanced in response to NaCl and/or SA treatment, where their interaction had an additive effect. Moreover, the toxic effects generated by the lower concentration of NaCl (50 mM) were completely overcome by the application of SA. It was, therefore, concluded that SA ameliorated the stress generated by NaCl through the alleviated antioxidant system.
Abstract (Browse 2082)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Aluminum-activated Oxalate Secretion does not Associate with Internal Content among Some Oxalate Accumulators
Author: Jian Li Yang, Lei Zhang and Shao Jian Zheng
Journal of Integrative Plant Biology 2008 50(9): 1103-1107
DOI: 10.1111/j.1744-7909.2008.00687.x
    Although aluminum (Al)-activated secretion of oxalate has been considered to be an important Al-exclusion mechanism, whether it is a general response in oxalate accumulators and related to oxalate content in roots are still not clear. Here, we examined the oxalate secretion and oxalate content in some oxalate accumulators, and investigated the role of oxalate secretion in Al resistance. When oxalate content in amaranth roots was decreased by about 50% with the increased ratio of NH4+-N to NO3−-N in nutrient solution, the amount of Al-activated oxalate secretion still remained constant. There was no relationship between the content of the water soluble oxalate in four species of oxalate accumulators and the amount of the Al-activated oxalate secretion in roots. Furthermore, oxalate secretion is poorly associated with Al resistance among these species. Based on the above results, we concluded that although all of the oxalate accumulators tested could secrete oxalate rapidly, the density of anion channels in plasma membrane may play a more important role in Al-activated oxalate secretion.
Abstract (Browse 1218)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Physiology
QTL and QTL Environment Effects on Agronomic and Nitrogen Acquisition Traits in Rice
Author: Senapathy Senthilvel, Kunnummal Kurungara Vinod, Palaniappan Malarvizhi and Marappa Maheswaran
Journal of Integrative Plant Biology 2008 50(9): 1108-1117
DOI: 10.1111/j.1744-7909.2008.00713.x
    Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.
Abstract (Browse 1916)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Ecology and Evolution
Population Genetic Structure of the Medicinal Plant Vitex rotundifolia in China: Implications for its Use and Conservation
Author: Yuan Hu, Yu Zhu, Qiao-Yan Zhang, Hai-Liang Xin, Lu-Ping Qin, Bao-Rong Lu, Khalid Rahman and Han-Chen Zheng
Journal of Integrative Plant Biology 2008 50(9): 1118-1129
DOI: 10.1111/j.1744-7909.2008.00635.x
    Vitex rotundifolia L. is an important plant species used in traditional Chinese medicine. For its efficient use and conservation, genetic diversity and clonal variation of V. rotundifolia populations in China were investigated using inter-simple sequence repeat markers. Fourteen natural populations were included to estimate genetic diversity, and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure. The overall genetic diversity (GD) of V. rotundifolia populations in China was moderate (GD = 0.190), with about 40% within-population variation. Across all populations surveyed, the average within-population diversity was moderate (P = 22.6%; GD = 0.086). A relatively high genetic differentiation (Gst = 0.587) among populations was detected based on the analysis of molecular variance data. Such characteristics of V. rotundifolia are likely attributed to its sexual/asexual reproduction and limited gene flow. The genotypic diversity (D = 0.992) was greater than the average values of a clonal plant, indicating its significant reproduction through seedlings. Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m. Genetic diversity patterns of V. rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds, and by sampling individuals in a population at >20 m spatial intervals to avoid collecting individuals with identical or similar genotypes.
Abstract (Browse 2066)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide Characterization of Long Terminal Repeat -retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons
Author: Hai-Yue Sun, Hong-Yan Dai, Gui-Ling Zhao, Yue Ma, Chun-Qing Ou, He Li, Lin-Guang Li and Zhi-Hong Zhang
Journal of Integrative Plant Biology 2008 50(9): 1130-1139
DOI: 10.1111/j.1744-7909.2008.00717.x
    The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1-copia and Ty3-gypsy group retrotransposons was observed, but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (∼5 000) and Ty3-gypsy (∼26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1-copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.
Abstract (Browse 1253)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Spatial Patterns and Interspecific Associations of Three Canopy Species at Different Life Stages in a Subtropical Forest, China
Author: Lin Li, Shi-Guang Wei, Zhong-Liang Huang, Wan-Hui Ye and Hong-Lin Cao
Journal of Integrative Plant Biology 2008 50(9): 1140-1150
DOI: 10.1111/j.1744-7909.2008.00690.x
    Spatial patterns of species at different life stages are an important aspect for understanding causal mechanisms that facilitate species co-existence. Using Ripley's univariate L(t) and bivariate L12(t) functions, we analyzed the spatial patterns and interspecific associations of three canopy species at different life history stages in a 20-ha subtropical forest plot in Dinghushan Nature Reserve. Based on diameter at breast height (DBH), four life stages were distinguished. Castanopsis chinensis and Schima superba showed a unimodal DBH distribution. Engelhardtia roxburghiana showed a bimodal curve. L(t) function analysis showed significantly aggregated distributions of all three species at later life stages and random distribution at early life stages at some scales. From the analysis of L12(t) function, the results showed the positive association was a dominant pattern for most species pairs at most scales but the intensity of association decreases with the increase of life stages. Juveniles of the three species had no negative intra- and interspecific associations with the older life stages. Only premature trees were suppressed by overmature trees at some scales. Considering these results, we found three canopy-dominant species that lacked regeneration. There was no direct competition occurring between understorey individuals. Young trees can grow well under conspecific species with two other species. Longevity and lack of regeneration led to a large number of trees stored in mature and overmature stages, therefore, intra- and inter-competition can be strong at later life stages. Based on diameter at breast height (DBH), four life stages were distinguished. Castanopsis chinensis and Schima superba showed a unimodal DBH distribution. Engelhardtia roxburghiana showed a bimodal curve. L(t) function analysis showed significantly aggregated distributions of all three species at later life stages and random distribution at early life stages at some scales. From the analysis of L12(t) function, the results showed the positive association was a dominant pattern for most species pairs at most scales but the intensity of association decreases with the increase of life stages. Juveniles of the three species had no negative intra- and interspecific with the older life stages. Only premature trees were suppressed by overmature trees at some scales. Considering these results, we found three canopy dominant species lack of regeneration. There was no direct competition occurring between understorey individuals. Young trees can grow well under conspecific species and other two species. Longevity and lack of regeneration led to large number of trees stored in mature and overmature stages, therefore, intra- and inter-competition can be strong at later life stages.
Abstract (Browse 1256)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Effects of Population Size on Reproductive Success of the Endangered and Endemic Species Primula merrilliana
Author: Jian-Wen Shao, Xiao-Ping Zhang, Zhong-Xing Zhang and Guo-Ping Zhu
Journal of Integrative Plant Biology 2008 50(9): 1151-1160
DOI: 10.1111/j.1744-7909.2008.00655.x
    The reproductive ability related to the population size of the endangered and endemic species Primula merrilliana Schltr. was investigated. In 26 populations observed, only four contain more than 500 flowering individuals, whereas most of them (53.8%) consist of less than 100 flowering individuals. Though the ratio of pin and thrum plants keeps its balance at 1:1 for all populations, the frequency of pin and thrum flowers was significantly biased in most small populations. Population size strongly affected reproductive success; plants in small populations produced significantly fewer flowers and fruits per plant and fewer seeds per fruit, and therefore fewer seeds per plant. The floral density was another important factor that influenced the reproductive success of P. merrilliana, because four main reproductive success parameters (fruits per plant, seeds per fruit, seeds per plant, and the proportion of flowers setting fruit) were all positively correlated with floral density. The size of plants and the number of leaves per plant (measure of habitat quality) were not influenced by the variation of population size, suggesting that the reduced fecundity in small populations may not be a consequence of lower habitat quality. Inbreeding depression and pollen limitation as a result of less attractiveness in small populations are therefore likely explanations for these patterns.
Abstract (Browse 1849)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Covariance of Floral and Vegetative Traits in Four Species of Ranunculaceae: A Comparison between Specialized and Generalized Pollination Systems
Author: Jin-Liu Meng, Xian-Hui Zhou, Zhi-Gang Zhao and Guo-Zhen Du
Journal of Integrative Plant Biology 2008 50(9): 1161-1170
DOI: 10.1111/j.1744-7909.2008.00722.x
    Theory predicts that tighter correlation between floral traits and weaker relationship between floral and vegetative traits more likely occur in specialized flowers than generalized flowers, favoring by precise fit with pollinators. However, traits and trait correlations frequently vary under different environments. Through detecting spatiotemporal variation in phenotypic traits (floral organ size and vegetative size) and trait correlations in four Ranunculaceae species, we examined four predictions. Overall, our results supported these predictions to a certain degree. The mean coefficient of variation (CV) of floral traits in two specialized species (Delphinium kamaonense and Aconitum gymnandrum) was marginally significantly lower than that of another two generalized species (Trollius ranunculoides and Anemone obtusiloba). The two specialized species also showed marginally significantly smaller CV in floral traits than vegetative size across the two species. The absolute mean correlation between floral and vegetative traits, or that between floral traits in species with specialized flowers was not significantly lower, or higher than that in generalized plants, weakly supporting the predictions. Furthermore, we documented a large variation in trait correlations of four species among different seasons and populations. Study of covariance of floral and vegetative traits will benefit from the contrast of results obtained from generalized and specialized pollination systems.
Abstract (Browse 1287)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Demographic Genetic Structure of Cryptomeria japonica var. sinensis in Tianmushan Nature Reserve, China
Author: Yan Chen, Shu-Zhen Yang, Ming-Shui Zhao, Bi-Ye Ni, Liang Liu and Xiao-Yong Chen
Journal of Integrative Plant Biology 2008 50(9): 1171-1177
DOI: 10.1111/j.1744-7909.2008.00725.x
    Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeria japonica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.599 9 respectively, lower than other conifers with the same life history characteristics. FST was 0.002 0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event(s). The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.
Abstract (Browse 1863)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Discovery of Gynoecium Color Polymorphism in an Aquatic Plant
Author: Shuang-Quan Huang and Xiao-Xin Tang
Journal of Integrative Plant Biology 2008 50(9): 1178-1182
DOI: 10.1111/j.1744-7909.2008.00720.x
    Flower color polymorphism exhibited by natural populations provides an opportunity for understanding the evolutionary mechanisms contributing to the diversity of floral morphology. However, little is known about the color polymorphism of female organs in flowering plants. Here we report gynoecium color polymorphism in Butomus umbellatus (Butomaceae), an emergent, aquatic monocot. Populations from Mishan, northeastern China comprised two morphs; gynoecia are either pink, as observed in other areas, or white. We measured floral traits and female fecundity in the two gynoecium color morphs in the field. There was no significant difference in plant height, pedicel length, and flower size including petal, sepal and gynoecium between the two morphs, but plants with pink gynoecia had wider inflorescence stalks, larger inner whorl anthers and produced more pollen and ovules than those with white gynoecia. Correspondingly, we found that seed production was significantly higher in the pink than in the white morph. This new finding suggested selection against white gynoecia in part because of low fecundity, consistent with the rarity of the white gynoecium morph in this species.
Abstract (Browse 1254)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
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