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Journal of Integrative Plant Biology

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https://www.readbyqxmd.com/read/30421576/analysis-of-the-chromatin-binding-affinity-of-retrotransposases-reveals-novel-roles-in-diploid-and-tetraploid-cotton
#1
Jing Lin, Ying Cai, Gai Huang, Yan Yang, Yang Li, Kun Wang, Zhiguo Wu
LTR-retrotransposable elements are major components of diploid (Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes that have undergone dramatic increases in copy number during the course of evolution. However, little is known about the biological functions of LTR-retrotransposable elements in cotton. Here, we show that a copia-like LTR-retrotransposable element has maintained considerable activity in both G. arboreum and G. hirsutum. We identified two functional domains of the retrotransposon and analyzed their expression levels in various cotton tissues, including leaves, ovules, and germinating seeds...
November 12, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30421569/a-leaf-shape-mutant-provides-insight-into-pinoid-serine-threonine-kinase-function-in-cucumber-cucumis-sativus-l
#2
Mengfei Song, Feng Cheng, Jing Wang, Qingzhen Wei, Wenyuan Fu, Xiaqing Yu, Ji Li, Jinfeng Chen, Qunfeng Lou
Optimizing leaf shape is a major challenge in efforts to develop an ideal plant type. Cucumber leaf shapes are diverse; however, the molecular regulatory mechanisms underlying leaf shape formation are unknown. In this study, we obtained a round leaf mutant (rl) from an ethyl methanesulfonate-induced mutagenesis population. Genetic analysis revealed that a single recessive gene, rl, is responsible for this mutation. A modified MutMap analysis combined linkage mapping identified a single nucleotide polymorphism within a candidate gene, Csa1M537400, as the mutation underlying the trait...
November 12, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30421518/a-reductionist-approach-to-dissecting-grain-weight-and-yield-in-wheat
#3
REVIEW
Jemima Brinton, Cristobal Uauy
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among then, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate...
November 12, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30415497/systems-model-guided-rice-yield-improvements-based-on-genes-controlling-source-sink-and-flow
#4
REVIEW
Pan Li, Tiangen Chang, Shuoqi Chang, Xiang Ouyang, Mingnan Qu, Qingfeng Song, Langtao Xiao, Shitou Xia, Qiyun Deng, Xin-Guang Zhu
A large number of genes related to source, sink and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink and flow...
November 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30415491/arabidopsis-anac092-regulates-auxin-mediated-root-development-by-binding-to-the-arf8-and-pin4-promoters
#5
Dandan Xi, Xu Chen, Yuxia Wang, Ruiling Zhong, Jianmei He, Jiabin Shen, Feng Ming
Auxin is an important plant hormone that is essential for growth and development due to its effects on organogenesis, morphogenesis, tropisms, and apical dominance. The functional diversity of auxin highlights the importance of its biosynthesis, transport, and associated responses. In this study, we show that a NAC transcription factor, ANAC092 (also named AtNAC2 and ORESARA1), known to positively regulate leaf senescence and contribute to abiotic stress responses, also affects primary root development. Plants overexpressing ANAC092 had altered root meristem lengths and shorter primary roots compared with the wild-type control...
November 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30414306/grain-length-and-awn-1-negatively-regulates-grain-size-in-rice
#6
LETTER
Tao Wang, Ting Zou, Zhiyuan He, Guoqiang Yuan, Tao Luo, Jun Zhu, Yueyang Liang, Qiming Deng, Shiquan Wang, Aiping Zheng, Huainian Liu, Lingxia Wang, Ping Li, Shuangcheng Li
Grain size is an important factor determining yield in rice. Here, we identified a recessive mutant gene, grain length and awn 1 (gla1), which caused a significant increase in grain length and weight, and was associated with long awns. The gla1 mutation was mapped to a single-nucleotide polymorphism in a gene encoding a cytoplasmically-localized mitogen-activated protein kinase (MAPK) phosphatase. Overexpression of GLA1 caused a decrease in grain length, and the GLA1 protein interacted with OsMAPK6. These results suggest that GLA1 may serve as a negative regulator of the OsMAPKK4-OsMAPK6 cascade, controlling grain size via the dephosphorylation of OsMAPK6...
November 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30414305/domestication-and-crop-evolution-of-wheat-and-barley-genes-genomics-and-future-directions
#7
REVIEW
Matthew Haas, Mona Schreiber, Martin Mascher
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms...
November 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30387552/the-crispr-cas-revolution-continues-from-efficient-gene-editing-for-crop-breeding-to-plant-synthetic-biology
#8
REVIEW
Jochen Kumlehn, Janine Pietralla, Goetz Hensel, Michael Pacher, Holger Puchta
Since the discovery that nucleases of the bacterial CRISPR/Cas system can be used as easily programmable tools for genome engineering, their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double strand break induction, resulting in mutations by non-homologous recombination...
November 2, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30387549/decrease-in-dna-methylation-1-ddm1-is-required-for-the-formation-of-m-chh-islands-in-maize
#9
Jin Cheng Long, Ai Ai Xia, Jing Han Liu, Ju Li Jing, Ya Zhong Wang, Chuang Ye Qi, Yan He
DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development...
November 2, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30325110/genetic-pathways-controlling-inflorescence-architecture-and-development-in-wheat-and-barley
#10
REVIEW
Adam Gauley, Scott A Boden
Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally fruitful. The identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets...
October 16, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30302942/arabidopsis-big1-and-big5-are-crucial-for-male-gametophyte-transmission
#11
LETTER
Yiping Suo, Jirong Huang
Arabidopsis contains five Brefeldin A-inhibited guanine nucleotide exchange factors (BIGs), which play a critical role in vesicle biogenesis for protein traffic from the Golgi to the plasma membrane. Biological processes regulated by BIG1-BIG4 are postulated to be distinct from those by BIG5. However, we show that the self-pollinated BIG1+/- big5 silique do not produce homozygous seeds, and some pollen tubes from BIG1+/- big5 anthers grew slowly in vitro and failed to target nearby ovules in vivo. We identified the big1 big5 homozygote from the progeny of BIG1+/- big5 plants transformed with BIG5, whose expression is driven by a pollen-specific promoter pLat52, indicating that male gametophyte transmission is blocked in the double mutant...
October 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30302902/short-panicle-3-controls-panicle-architecture-by-upregulating-apo2-rfl-and-increasing-cytokinin-content-in-rice
#12
Yong Huang, Xufeng Bai, Meifang Luo, Yongzhong Xing
Inflorescence architecture is a major determinant of spikelet numbers per panicle, a key component of grain yield in rice. In this study, Short Panicle 3 (SP3) was identified from a short panicle 3 (sp3) mutant in which T-DNA was inserted in the promoter of SP3, resulting in a knockdown mutation. SP3 encodes a DNA binding with one finger (Dof) transcriptional activator. Quantitative real time (qRT)-PCR and RNA in situ hybridization assays confirmed that SP3 is preferentially expressed in the young rice inflorescence, specifically in the branch primordial regions...
October 10, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30280512/endoplasmic-reticulum-stress-induced-accumulation-of-vamp721-722-requires-calreticulin-1-and-calreticulin-2-in-arabidopsis
#13
LETTER
Soohong Kim, Yunjin Choi, Chian Kwon, Hye Sup Yun
Excessive demand for translation and protein folding in the endoplasmic reticulum (ER) can cause ER stress in plants. Here, we show that CALRETICULIN 1 (CRT1) and CRT2 are critical components in the accumulation of VESICLE-ASSOCIATED MEMBRANE PROTEIN 721 (VAMP721) and VAMP722 during ER stress responses. We show that CRT2 interacts with VAMP722 and that CRT1/2 post-translationally maintain elevated VAMP721/722 levels under ER stress. The greater growth inhibition in VAMP721/722-deficient plants, induced by tunicamycin, suggests that plants under ER stress maintain physiological homeostasis, at least in part, by regulating VAMP721/722 levels, as VAMP721/722 are known to participate in various biological processes...
October 2, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30267474/big-grain3-encoding-a-purine-permease-regulates-grain-size-via-modulating-cytokinin-transport-in-rice
#14
Yunhua Xiao, Dapu Liu, Guoxia Zhang, Shaopei Gao, Linchuan Liu, Fan Xu, Ronghui Che, Yiqin Wang, Hongning Tong, Chengcai Chu
Grain size is an important agronomic trait affecting grain yield, but the underlying molecular mechanisms remain to be elucidated. Here, we isolated a dominant mutant, big grain3 (bg3-D), which exhibits a remarkable increase of grain size caused by activation of the PURINE PERMEASE gene, OsPUP4. BG3/OsPUP4 is predominantly expressed in vascular tissues and is specifically suppressed by exogenous cytokinin application. Hormone profiling revealed that the distribution of different cytokinin forms, in roots and shoots of the bg3-D mutant, is altered...
September 29, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30267471/ref6-promotes-lateral-root-formation-through-de-repression-of-pin1-3-7-genes
#15
LETTER
Xiaolei Wang, Jiong Gao, Shan Gao, Zhongpeng Li, Benke Kuai, Guodong Ren
The H3K27 methyltransferase CLF inhibits lateral root (LR) formation through depositing the repressive H3K27me3 mark to the chromatin of PIN1, a key polar auxin transporter gene. Here, we show that the H3K27me3 demethylase REF6 promotes lateral root primordium initiation and LR emergence. REF6 directly binds to the chromatin of PIN1/3/7. Dysfunction in REF6 results in increased levels of H3K27me3 on PIN1/3/7 and suppressed expression of PIN genes. Genetic analysis of the clf ref6 double mutant revealed an antagonistic action between CLF and REF6, in terms of LR formation...
September 29, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30255554/the-circadian-clock-contributes-to-diurnal-patterns-of-plant-indirect-defense-in-nature
#16
LETTER
Youngsung Joo, Jay K Goldberg, Lucille Chretien, Sang-Gyu Kim, Ian T Baldwin, Meredith C Schuman
The plant circadian clock regulates the rhythms of plant metabolism. Many herbivore-induced plant volatiles (HIPVs) fluctuate, diurnally, but the role of the circadian clock in the emission of HIPVs and their ecological consequences remains largely unknown. Here, we show that the timing of herbivore attack can alter the outcome of tri-trophic interactions, and this is mediated by the circadian clock, under both field and glasshouse conditions. Although most HIPV emissions did not have a circadian rhythm, the circadian clock modulated HIPV emissions in a time-dependent manner...
September 25, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30255551/streptomyces-lydicus-a01-affects-soil-microbial-diversity-improving-growth-and-resilience-in-tomato
#17
Qiong Wu, Caige Lu, Mi Ni, Hongli Wang, Weicheng Liu, Jie Chen
The actinomycete Streptomyces lydicus A01 promotes tomato seedling growth; however, the underlying mechanism is unclear. In this study, we investigated whether changes in soil microbial diversity, following Streptomyces lydicus A01 treatment, were responsible for the increased tomato seedling growth. Eukaryotic 18S ribosomal DNA (rDNA) sequencing showed that S. lydicus A01-treated and untreated soil shared 193 operational taxonomic units (OTUs), whereas bacterial 16S rDNA sequencing identified 1,219 shared OTUs between the treated and untreated soil...
September 25, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30253066/genomic-divergence-in-cotton-germplasm-related-to-maturity-and-heterosis
#18
Shoupu He, Gaofei Sun, Longyu Huang, Daigang Yang, Panhong Dai, Dayun Zhou, Yuzhen Wu, Xiongfeng Ma, Xiongming Du, Shoujun Wei, Jun Peng, Meng Kuang
Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high-quality single-nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton)...
September 25, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30246370/brassinosteroids-function-in-spikelet-differentiation-and-degeneration-in-rice
#19
Weiyang Zhang, Kuanyu Zhu, Zhiqin Wang, Hao Zhang, Junfei Gu, Lijun Liu, Jianchang Yang, Jianhua Zhang
Brassinosteroids (BRs) play crucial roles in many aspects of plant development. However, their function in spikelet differentiation and degeneration in rice (Oryza sativa L.) remains unclear. Here, we investigated the roles of these phytohormones in spikelet development in field-grown rice subjected to five different nitrogen (N) fertilization treatments during panicle differentiation. BR levels and expression of genes involved in BR biosynthesis and signal transduction were measured in spikelets. Pollen fertility and the number of differentiated spikelets were closely associated with 24-epicastasterone (24-epiCS) and 28-homobrassinolide (28-homoBL) levels in spikelets...
September 24, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/30226297/tazim-a1-negatively-regulates-flowering-time-in-common-wheat-triticum-aestivum-l
#20
Hong Liu, Tian Li, Yamei Wang, Jun Zheng, Huifang Li, Chenyang Hao, Xueyong Zhang
Flowering time is a critical determinant of regional adaptation for crops and has strong effects on crop yields. Here, we report that TaZIM-A1, an atypical GATA-like transcription factor, is a negative regulator of flowering in wheat. TaZIM-A1 possessed weak transcriptional repression activity, with its CCT domain functioning as the major inhibitory region. TaZIM-A1 expression exhibited a typical circadian oscillation pattern under various light regimes. Overexpression of TaZIM-A1 caused a delay in flowering time and a decrease in thousand-kernel weight (TKW) in wheat under long-day conditions...
September 18, 2018: Journal of Integrative Plant Biology
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