March 2017, Volume 59 Issue 3, Pages 158每224.


Cover Caption: Apple genetic variation and selection
Wild apples display higher levels of genetic diversity than cultivated apples. In this issue, Ma et al. (190每204) observed linkage disequilibrium (LD) decays quite rapidly in cultivated and wild apples. Most LD blocks unique to cultivated apples are located within QTL regions controlling fruit quality, suggesting that fruit quality has undergone selection during domestication. Introgression is also an important driving force during initial domestication. The wild apple photo is provided by Cuiying Li from Northwest A&F University.

 

          Letter to the Editor
An epiallele of rice AK1 affects photosynthetic capacity  
Author: Xiangjin Wei, Xianwei Song, Liya Wei, Shaoqing Tang, Jing Sun, Peisong Hu and Xiaofeng Cao
Journal of Integrative Plant Biology 2017 59(3): 158每163
Published Online: January 6, 2017
DOI: 10.1111/jipb.12518
      
    

Epigenetic gene variants, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Here, we identify a natural epiallele of OsAK1, which encodes a rice adenylate kinase. The Epi-ak1 plants show albino in young leaf and panicle with abnormal chloroplast structures. We found that no nucleotide sequence variation but hypermethylation at promoter region caused silencing of OsAK1 (Os08g01770) in Epi-ak1 plants. OsAK1 localizes to chloroplast and many genes associated with photosynthesis processes were downregulated in Epi-ak1. Thus, the work identified a novel rice epiallele caused by DNA methylation changes, shedding light on significant roles of DNA methylation on rice development.

Abstract (Browse 260)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
A naturally epigenetic gene variant, which carries hypermethylated cytosines at promoter of OsAK1 (Os08g01770), was identified in rice. The hypermethylation causes silencing of this gene and leads to albino in young leaf and panicle, shedding light on significant roles of DNA methylation on rice development.
          Invited Expert Review
Plant phosphatidylinositol-specific phospholipase C at the center of plant innate immunity  
Author: Ahmed M. Abd-El-Haliem and Matthieu H.A.J. Joosten
Journal of Integrative Plant Biology 2017 59(3): 164每179
Published Online: January 18, 2017
DOI: 10.1111/jipb.12520
      
    
Understanding plant resistance to pathogenic microbes requires detailed information on the molecular mechanisms controlling the execution of plant innate immune responses. A growing body of evidence places phosphoinositide-specific phospholipase C (PI-PLC) enzymes immediately downstream of activated immune receptors, well upstream of the initiation of early defense responses. An increase of the cytoplasmic levels of free Ca2+, lowering of the intercellular pH and the oxidative burst are a few examples of such responses and these are regulated by PI-PLCs. Consequently, PI-PLC activation represents an early primary signaling switch between elicitation and response involving the controlled hydrolysis of essential signaling phospholipids, thereby simultaneously generating lipid and non-lipid second messenger molecules required for a swift cellular defense response. Here, we elaborate on the signals generated by PI-PLCs and their respective downstream effects, while providing an inventory of different types of evidence describing the involvement of PI-PLCs in various aspects of plant immunity. We project the discussed information into a model describing the cellular events occurring after the activation of plant immune receptors. With this review we aim to provide new insights supporting future research on plant PI-PLCs and the development of plants with improved resistance.
Abstract (Browse 1131)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Plants are sessile organisms that respond to invading microbes with a swift immune response. Plants carry immune receptors, which immediately activate phosphoinositide-specific phospholipase C (PI-PLC) enzymes upon their activation. We present a model in which PI-PLCs mediate the hydrolysis of essential signaling phospholipids, thereby simultaneously generating the second messengers required for a swift cellular defense response.
          Molecular Ecology and Evolution
Fitness consequences of altering floral circadian oscillations for Nicotiana attenuata  
Author: Felipe Yon, Danny Kessler, Youngsung Joo, Lucas Cortés Llorca, Sang-Gyu Kim and Ian T. Baldwin
Journal of Integrative Plant Biology 2017 59(3): 180每189
Published Online: December 13, 2016
DOI: 10.1111/jipb.12511
      
    

Ecological interactions between flowers and pollinators are all about timing. Flower opening/closing and scent emissions are largely synchronized with pollinator activity, and a circadian clock regulates these rhythms. However, whether the circadian clock increases a plant's reproductive success by regulating these floral rhythms remains untested. Flowers of Nicotiana attenuata, a wild tobacco, diurnally and rhythmically open, emit scent and move vertically through a 140° arc to interact with nocturnal hawkmoths. We tethered flowers to evaluate the importance of flower positions for Manduca sexta-mediated pollinations; flower position dramatically influenced pollination. We examined the pollination success of phase-shifted flowers, silenced in circadian clock genes, NaZTL, NaLHY, and NaTOC1, by RNAi. Circadian rhythms in N. attenuata flowers are responsible for altered seed set from outcrossed pollen.

Abstract (Browse 1072)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Wild tobacco flowers rhythmically open, emit scent and move vertically through a 140∼ arc. Flower position dramatically influenced cross-pollination success and seed set with nocturnal hawkmoths. By waving their flowers, this plant engages in a botanical version of synchronized dancing with its pollinators and filters its partners in this dance.
Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple
Author: Baiquan Ma, Liao Liao, Qian Peng, Ting Fang, Hui Zhou, Schuyler S. Korban and Yuepeng Han
Journal of Integrative Plant Biology 2017 59(3): 190每204
Published Online: January 17, 2017
DOI: 10.1111/jipb.12522
      
    

Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphism with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2-value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.

Abstract (Browse 223)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Reduced representation genome sequencing reveals that a variety of horticultural traits, such as fruit quality, tree growth habit, and resistance to biotic stress, have probably undergone selection during apple domestication.
          Plant Reproduction Biology
Functional specialization of Nicotiana attenuata phytochromes in leaf development and flowering time
Author: Variluska Fragoso, Youngjoo Oh, Sang-Gyu Kim, Klaus Gase and Ian Thomas Baldwin
Journal of Integrative Plant Biology 2017 59(3): 205每224
Published Online: December 23, 2016
DOI: 10.1111/jipb.12516
      
    

Phytochromes mainly function in photoautotrophic organisms to adjust growth in response to fluctuating light signals. The different isoforms of plant phytochromes often display both conserved and divergent roles, presumably to fine-tune plant responses to environmental signals and optimize fitness. Here we describe the distinct, yet partially redundant, roles of phytochromes NaPHYA, NaPHYB1 and NaPHYB2 in a wild tobacco species, Nicotiana attenuata using RNAi-silenced phytochrome lines. Consistent with results reported from other species, silencing the expression of NaPHYA or NaPHYB2 in N. attenuata had mild or no influence on plant development as long as NaPHYB1 was functional; whereas silencing the expression of NaPHYB1 alone strongly altered flowering time and leaf morphology. The contribution of NaPHYB2 became significant only in the absence of NaPHYB1; plants silenced for both NaPHYB1 and NaPHYB2 largely skipped the rosette-stage of growth to rapidly produce long, slender stalks that bore flowers early: hallmarks of the shade-avoidance responses. The phenotyping of phytochrome-silenced lines, combined with sequence and transcript accumulation analysis, suggest the independent functional diversification of the phytochromes, and a dominant role of NaPHYB1 and NaPHYB2 in N. attenuata's vegetative and reproductive development.

Abstract (Browse 187)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
To understand how a wild tobacco species perceives light, we examined transgenic plants impaired in their ability to ※see§ particular wavelengths of light by silencing the expression of photoreceptor proteins, the phytochromes. The phytochromes were specialized in their function: B1 controlled leaf development while B2 controlled flower development.
 

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