August 2014, Volume 56 Issue 8, Pages 714每809.


Cover Caption: Time for Emerging
About the cover: The emergences of radicle and coleoptile during seed germination represent cumulated effects of underlying genetic networks. Studies in the past have identified genes regulating seed germination and seedling growth without distinguishing these two steps. Using a dynamic evaluation method, in this issue Xie et al (pp. 749每759) identified different QTLs for seed germination and for seedling establishment.

 

          Invited Expert Reviews
Unique and conserved features of floral evocation in legumes
Author: Lim Chee Liew, Mohan B. Singh and Prem L. Bhalla
Journal of Integrative Plant Biology 2014 56(8): 714每728
Published Online: February 20, 2014
DOI: 10.1111/jipb.12187
      
    

Legumes, with their unique ability to fix atmospheric nitrogen, play a vital role in ensuring future food security and mitigating the effects of climate change because they use less fossil energy and produce less greenhouse gases compared with N-fertilized systems. Grain legumes are second only to cereal crops as a source of human and animal food, and they contribute approximately one third of the protein consumed by the human population. The productivity of seed crops, such as grain legumes, is dependent on flowering. Despite the genetic variation and importance of flowering in legume production, studies of the molecular pathways that control flowering in legumes are limited. Recent advances in genomics have revealed that legume flowering pathways are divergent from those of such model species as Arabidopsis thaliana. Here, we discuss the current understanding of flowering time regulation in legumes and highlight the unique and conserved features of floral evocation in legumes.

 

Liew LC, Singh MB, Bhalla PL (2014) Unique and conserved features of floral evocation in legumes. J Integr Plant Biol 56: 714–728. doi: 10.1111/jipb.12187

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          Minireview
Plant pleiotropic drug resistance transporters: Transport mechanism, gene expression, and function  
Author: Mohammed Nuruzzaman, Ru Zhang, Hong-Zhe Cao and Zhi-Yong Luo
Journal of Integrative Plant Biology 2014 56(8): 729每740
Published Online: March 20, 2014
DOI: 10.1111/jipb.12196
      
    

Pleiotropic drug resistance (PDR) transporters belonging to the ABCG subfamily of ATP-binding cassette (ABC) transporters are identified only in fungi and plants. Members of this family are expressed in plants in response to various biotic and abiotic stresses and transport a diverse array of molecules across membranes. Although their detailed transport mechanism is largely unknown, they play important roles in detoxification processes, preventing water loss, transport of phytohormones, and secondary metabolites. This review provides insights into transport mechanisms of plant PDR transporters, their expression profiles, and multitude functions in plants.

 

Nuruzzaman M, Zhang R, Cao HZ, Luo ZY (2014) Plant pleiotropic drug resistance transporters: Transport mechanism, gene expression, and function. J Integr Plant Biol 56: 729–740. doi: 10.1111/jipb.12196

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          New Technology
Loop-mediated isothermal amplification of single pollen grains  
Author: Ali Bektaş and Ignacio Chapela
Journal of Integrative Plant Biology 2014 56(8): 741每748
Published Online: March 11, 2014
DOI: 10.1111/jipb.12191
      
    

The polymerase chain reaction (PCR) has been a reliable and fruitful method for many applications in ecology. Nevertheless, unavoidable technical and instrumental requirements of PCR have limited its widespread application in field situations. The recent development of isothermal DNA amplification methods provides an alternative to PCR, which circumvents key limitations of PCR for direct amplification in the field. Being able to analyze DNA in the pollen cloud of an ecosystem would provide very useful ecological information, yet would require a field-enabled, high-throughput method for this potential to be realized. Here, we demonstrate the applicability of the loop-mediated DNA amplification method (LAMP), an isothermal DNA amplification technique, to be used in pollen analysis. We demonstrate that LAMP can provide a reliable method to identify species from the pollen cloud, and that it can amplify successfully with sensitivity down to single pollen grains, thus opening the possibility of field-based, high-throughput analysis.

 

Bektaş A, Chapela I (2014) Loop坼mediated isothermal amplification of single pollen grains. J Integr Plant Biol 56: 741–748 doi: 10.1111/jipb.12191

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          Cell and Developmental Biology
Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice
Author: Lixia Xie, Zhengwei Tan, Yuan Zhou, Rongbao Xu, Laibao Feng, Yongzhong Xing and Xiaoquan Qi
Journal of Integrative Plant Biology 2014 56(8): 749每759
Published Online: February 27, 2014
DOI: 10.1111/jipb.12190
      
    

Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments.

 

Xie L, Tan Z, Zhou Y, Xu R, Feng L, Xing Y, Qi X (2014) Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. J Integr Plant Biol 56: 749–759. doi: 10.1111/jipb.12190

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          Molecular Ecology and Evolution
Prospects for discriminating Zingiberaceae species in India using DNA barcodes
Author: Meenakshi Ramaswamy Vinitha, Unnikrishnan Suresh Kumar, Kizhakkethil Aishwarya, Mamiyil Sabu and George Thomas
Journal of Integrative Plant Biology 2014 56(8): 760每773
Published Online: February 26, 2014
DOI: 10.1111/jipb.12189
      
    

We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in all the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two paraphyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.

 

Vinitha MR, Suresh Kumar U, Aishwarya K, Sabu M, Thomas G (2014) Prospects for discriminating Zingiberaceae species in India using DNA barcodes. J Integr Plant Biol 56: 760–773. doi: 10.1111/jipb.12189

Abstract (Browse 799)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Haplotype variation of Green Revolution gene Rht-D1 during wheat domestication and improvement
Author: Chihong Zhang, Lifeng Gao, Jiaqiang Sun, Jizeng Jia and Zhenglong Ren
Journal of Integrative Plant Biology 2014 56(8): 774每780
Published Online: March 20, 2014
DOI: 10.1111/jipb.12197
      
    

Green Revolution made a substantial contribution to wheat yields worldwide in the 1960s and 1970s. It is of great importance to analyze the haplotype variation of Rht-D1, the Green Revolution gene, during wheat (Triticum aestivum L.) domestication and breeding to understand its evolution and function in wheat breeding history. In this study, the Rht-D1 and its flanking regions were sequenced and single nucleotide polymorphisms were detected based on a panel of 45 accessions of Aegilops tauschii, 51 accessions of landraces and 80 accessions of commercial varieties. Genetic diversity in the wild accessions was much higher than that in the varieties and higher than that reported previously. Seven haplotypes (Hapl I to Hapl VII) of Rht-D1 were identified and their evolutionary relationships were proposed. In addition to the well-known Green Revolution allele Rht-D1b, Hapl VII (an allele Rht-D1k) was identified in early breeding varieties, which reduced plant height by 16%. The results suggested that Rht-D1k had been used in breeding before the Green Revolution and made a great contribution to wheat production worldwide. Based on the breeding history and molecular evidence, we proposed that the wheat Green Revolution in China and International Maize and Wheat Improvement Center (CIMMYT) occurred independently.

 

Zhang C, Gao L, Sun J, Jia J, Ren Z (2014) Haplotype variation of Green Revolution gene Rht坼D1 during wheat domestication and improvement. J Integr Plant Biol 56: 774–780 doi: 10.1111/jipb.12197

Abstract (Browse 888)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Physiology
Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon
Author: Richard Poiré, Vincent Chochois, Xavier R.R. Sirault, John P. Vogel, Michelle Watt and Robert T. Furbank
Journal of Integrative Plant Biology 2014 56(8): 781每796
Published Online: March 25, 2014
DOI: 10.1111/jipb.12198
      
    

This work evaluates the phenotypic response of the model grass (Brachypodium distachyon (L.) P. Beauv.) to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose–response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight (R2 > 0.92) and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response to nitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determination of genomic regions associated with superior nutrient use efficiency.

 

Poiré R, Chochois V, Sirault XRR, Vogel JP, Watt M, Furbank RT (2014) Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon. J Integr Plant Biol 56: 781–796. doi: 10.1111/jipb.12198

Abstract (Browse 836)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Plant-environmental Interactions
Early osmotic adjustment responses in drought-resistant and drought-sensitive oilseed rape
Author: Sarah Hatzig, L. Irina Zaharia, Suzanne Abrams, Marie Hohmann, Laurie Legoahec, Alain Bouchereau, Nathalie Nesi and Rod J. Snowdon
Journal of Integrative Plant Biology 2014 56(8): 797每809
Published Online: March 25, 2014
DOI: 10.1111/jipb.12199
      
    

The impact of osmotic stress on growth, physiology, and metabolism of winter oilseed rape (Brassica napus L.) was investigated by detailed analysis of biomass traits, hormone metabolites and osmolytes in two genetically unrelated drought-tolerant genotypes and two unrelated drought-sensitive genotypes. Seedlings were grown in vitro under controlled conditions and osmotic stress was simulated by applying a gradual treatment with polyethylene glycol (PEG 6000), followed by hypo-osmotic treatment of variants used for metabolite determination. The results provide a basis for the identification of reliable selection criteria for drought resistance in oilseed rape. The in vitro cultivation system established during this study enabled effective discrimination of early osmotic stress responses between drought-resistant and -susceptible oilseed rape genotypes that also show large differences in relative seed yield under drought conditions in the field. Clear physiological and metabolic differences were observed between the drought-resistant and drought-sensitive genotypes, suggesting that osmotic adjustment is a key component of drought response in oilseed rape. Unexpectedly, however, the drought-resistant genotypes did not show typical hormonal adjustment and osmolyte accumulation, suggesting that they possess alternative physiological mechanisms enabling avoidance of stress symptoms.

 

Hatzig S, Zaharia LI, Abrams S, Hohmann M, Legoahec L, Bouchereau A, Nesi N, Snowdon RJ (2014) Early osmotic adjustment responses in drought坼resistant and drought坼sensitive oilseed rape. J Integr Plant Biol 56: 797–809. doi: 10.1111/jipb.12199

Abstract (Browse 857)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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