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Plant Biotechnology Journal

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https://www.readbyqxmd.com/read/30407717/resequencing-of-cv-cri-12-family-reveals-haplotype-block-inheritance-and-recombination-of-agronomically-important-genes-in-artificial-selection
#1
Xuke Lu, Xiaoqiong Fu, Delong Wang, Junyi Wang, Xiugui Chen, Meirong Hao, Junjuan Wang, Kyle A Gervers, Lixue Guo, Shuai Wang, Zujun Yin, Weili Fan, Chunwei Shi, Xiaoge Wang, Jun Peng, Chao Chen, Ruifeng Cui, Na Shu, Binglei Zhang, Mingge Han, Xiaojie Zhao, Min Mu, John Z Yu, Wuwei Ye
Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles in domesticated and undomesticated cotton varieties is limited. Given the complexity and limited amount of genomic information since the completion of four cotton genomes, characterizing significant variations and haplotype block inheritance under artificial selection has been challenging. Here we sequenced G. hirsutum L.cv CRI-12 (the cotton variety with the largest acreage in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China...
November 8, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30407713/hybridisation-based-target-enrichment-of-phenology-genes-to-dissect-the-genetic-basis-of-yield-and-adaptation-in-barley
#2
Camilla Beate Hill, Tefera Tolera Angessa, Lee-Anne McFawn, Debbie Wong, Josquin Tibbits, Xiao-Qi Zhang, Kerrie Forrest, David Moody, Paul Telfer, Sharon Westcott, Dean Diepeveen, Yanhao Xu, Cong Tan, Matthew Hayden, Chengdao Li
Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes...
November 8, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30367555/enhanced-genome-editing-in-rice-using-single-transcript-unit-crispr-lbcpf1-systems
#3
Rongfang Xu, Ruiying Qin, Hao Li, Juan Li, Jianbo Yang, Pengcheng Wei
A variety of sequence-specific nucleases (SSNs) have been successfully used for plant genome editing. Clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) systems, which were developed from microbial adaptive immune systems, are preferred SSN tools due to their simplicity and versatility. The majority of plant genome editing studies have exploited a CRISPR-Cas9 system from Streptococcus pyogenes (SpCas9) to achieve site-specific mutagenesis and perform fragment insertion or replacement in organisms ranging from algae to higher plants...
October 27, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30338631/characterization-of-a-semidominant-dwarfing-procera-allele-identified-in-a-screen-for-crispr-cas9-induced-suppressors-of-loss-of-function-alleles
#4
Zhiguo Zhu, Xiaojun Kang, Vai S Lor, David Weiss, Neil Olszewski
Gibberellin (GA) is a plant hormone that regulates important growth processes including germination, flowering, and fruit development. DELLA proteins inhibit GA responses. GA signaling increases through GA triggered destruction of the DELLA protein. Several mutants with reduced stature due to mutations that stabilize the DELLA protein are known. Many of these mutations cause deletions within the DELLA domain. Here we report several new dwarfing alleles of the tomato DELLA protein, PROCERA, generated using the CRISPR/Cas9 system to create intragenic suppressors of two pro loss-of-function alleles...
October 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30328278/integrated-transcriptome-small-rna-and-degradome-sequencing-approaches-provide-insights-into-ascochyta-blight-resistance-in-chickpea
#5
Vanika Garg, Aamir W Khan, Himabindu Kudapa, Sandip M Kale, Annapurna Chitikineni, Sun Qiwei, Mamta Sharma, Chuanying Li, Baohong Zhang, Xin Liu, P B Kavi Kishor, Rajeev K Varshney
Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs)...
October 16, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30325102/crispr-plant-v2-an-online-resource-for-highly-specific-guide-rna-spacers-based-on-improved-off-target-analysis
#6
Bastian Minkenberg, Jianwei Zhang, Kabin Xie, Yinong Yang
Since the beginning of CRISPR/Cas9's use for genome-editing, reports of off-targets have caused concerns among users. Previous studies identified three main types of off-targets. The first type of off-targets are sequences at other 5'-NGG-3' protospacer adjacent motifs (PAMs) that are identical or have a small number of mismatches or substitutions (Fu et al., 2013; Tsai et al., 2015). The second type of off-targets are sequences at other 5'-NGG-3' PAMs that have insertions or deletions compared to the gRNA spacer or the targeted DNA (Lin et al...
October 16, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30321482/a-metabolome-based-core-hybridization-strategy-for-the-prediction-of-rice-grain-weight-across-environments
#7
Zhiwu Dan, Yunping Chen, Yanghong Xu, Junran Huang, Jishuai Huang, Jun Hu, Guoxin Yao, Yingguo Zhu, Wenchao Huang
Marker-based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilized two independent F1 hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method...
October 15, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30320953/optimizing-the-identification-of-causal-variants-across-varying-genetic-architectures-in-crops
#8
Chenyong Miao, Jinliang Yang, James C Schnable
Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures, and linkage disequilibrium patterns...
October 15, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30315621/insight-into-the-evolution-and-functional-characteristics-of-the-pan-genome-assembly-from-sesame-landraces-and-modern-cultivars
#9
Jingyin Yu, Agnieszka A Golicz, Kun Lu, Komivi Dossa, Yanxin Zhang, Jinfeng Chen, Linhai Wang, Jun You, Dingding Fan, David Edwards, Xiurong Zhang
Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties...
October 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30302894/mutagenesis-of-kiwifruit-centroradialis-like-genes-transforms-a-climbing-woody-perennial-with-long-juvenility-and-axillary-flowering-into-a-compact-plant-with-rapid-terminal-flowering
#10
Erika Varkonyi-Gasic, Tianchi Wang, Charlotte Voogd, Subin Jeon, Revel S M Drummond, Andrew P Gleave, Andrew C Allan
Annualization of woody perennials has the potential to revolutionize the breeding and production of fruit crops and rapidly improve horticultural species. Kiwifruit (Actinidia chinensis) is a recently domesticated fruit crop with a short history of breeding and tremendous potential for improvement. Previously, multiple kiwifruit CENTRORADIALIS (CEN)-like genes have been identified as potential repressors of flowering. In this study, CRISPR/Cas9- mediated manipulation enabled functional analysis of kiwifruit CEN-like genes AcCEN4 and AcCEN...
October 10, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30291759/whole-genome-sequencing-reveals-rare-off-target-mutations-and-considerable-inherent-genetic-or-and-somaclonal-variations-in-crispr-cas9-edited-cotton-plants
#11
Jianying Li, Hakim Manghwar, Lin Sun, Pengcheng Wang, Guanying Wang, Hanyan Sheng, Jie Zhang, Hao Liu, Lei Qin, Hangping Rui, Bo Li, Keith Lindsey, Henry Daniell, Shuangxia Jin, Xianlong Zhang
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and three negative (Ne) control and three wild-type (WT) plants. In total, 4188-6404 unique single-nucleotide polymorphisms (SNPs) and 312-745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared to WT, negative and cotton reference genome sequences...
October 6, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30267599/simultaneous-regulation-of-f5h-in-comt-rnai-transgenic-switchgrass-alters-effects-of-comt-suppression-on-syringyl-lignin-biosynthesis
#12
Zhenying Wu, Nengfei Wang, Hiroshi Hisano, Yingping Cao, Fengyan Wu, Wenwen Liu, Yan Bao, Zeng-Yu Wang, Chunxiang Fu
Ferulate 5-hydroxylase (F5H) catalyses the hydroxylation of coniferyl alcohol and coniferaldehyde for the biosynthesis of syringyl (S) lignin in angiosperms. However, the coordinated effects of F5H with caffeic acid O-methyltransferase (COMT) on the metabolic flux towards S units are largely unknown. We concomitantly regulated F5H expression in COMT-down-regulated transgenic switchgrass (Panicum virgatum L.) lines and studied the coordination of F5H and COMT in lignin biosynthesis. Down-regulation of F5H in COMT-RNAi transgenic switchgrass plants further impeded S lignin biosynthesis and, consequently, increased guaiacyl (G) units and reduced 5-OH G units...
September 29, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30256509/dna-methylome-analysis-provides-evidence-that-the-expansion-of-the-tea-genome-is-linked-to-te-bursts
#13
Lei Wang, Yan Shi, Xiaojun Chang, Shengli Jing, Qunjie Zhang, Chenjiang You, Hongyu Yuan, Haifeng Wang
DNA methylation is essential for gene regulation, imprinting and silencing of transposable elements (TEs). Although bursts of transposable elements are common in many plant lineages, how plant DNA methylation is related to transposon bursts remains unclear. Here we explore the landscape of DNA methylation of tea, a species thought to have experienced a recent transposon burst event. This species possesses more transposable elements than any other sequenced asterids (potato, tomato, coffee, pepper and tobacco)...
September 26, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30256508/the-grapevine-vitis-vinifera-lysm-receptor-kinases-vvlyk1-1-and-vvlyk1-2-mediate-chitooligosaccharide-triggered-immunity
#14
Daphnée Brulé, Clizia Villano, Laura J Davies, Lucie Trdá, Justine Claverie, Marie-Claire Héloir, Annick Chiltz, Marielle Adrian, Benoît Darblade, Pablo Tornero, Lena Stransfeld, Freddy Boutrot, Cyril Zipfel, Ian B Dry, Benoit Poinssot
Chitin, a major component of fungal cell walls, is a well-known pathogen-associated molecular pattern (PAMP) that triggers defense responses in several mammal and plant species. Here we show that two chitooligosaccharides, chitin and chitosan, act as PAMPs in grapevine (Vitis vinifera) as they elicit immune signaling events, defense gene expression, and resistance against fungal diseases. To identify their cognate receptors, the grapevine family of LysM receptor kinases (LysM-RKs) was annotated and their gene expression profiles characterized...
September 26, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30230695/molecular-tools-enabling-pennycress-thlaspi-arvense-as-a-model-plant-and-oilseed-cash-cover-crop
#15
Michaela McGinn, Winthrop B Phippen, Ratan Chopra, Sunil Bansal, Brice A Jarvis, Mary E Phippen, Kevin M Dorn, Maliheh Esfahanian, Tara J Nazarenus, Edgar B Cahoon, Timothy P Durrett, M David Marks, John C Sedbrook
Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, which makes translational research straightforward...
September 19, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30230168/development-and-evaluation-of-novel-salt-tolerant-eucalyptus-trees-by-molecular-breeding-using-an-rna-binding-protein-gene-derived-from-common-ice-plant-mesembryanthemum-crystallinum-l
#16
Ngoc-Ha Thi Tran, Taichi Oguchi, Nobuhumi Akatsuka, Etsuko Matsunaga, Akiyoshi Kawaoka, Akiyo Yamada, Yoshihiro Ozeki, Kazuo N Watanabe, Akira Kikuchi
The breeding of plantation forestry trees for the possible afforestation of marginal land would be one approach to addressing global warming issues. Here, we developed novel transgenic Eucalyptus trees (Eucalyptus camaldulensis Dehnh.) harbouring an RNA-Binding-Protein (McRBP) gene derived from a halophyte plant, common ice plant (Mesembryanthemum crystallinum L.). We conducted screened-house trials of the transgenic Eucalyptus using two different stringency salinity stress conditions to evaluate the plants' acute and chronic salt stress tolerances...
September 19, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30220108/resequencing-core-accessions-of-a-pedigree-identifies-derivation-of-genomic-segments-and-key-agronomic-trait-loci-during-cotton-improvement
#17
Xiongfeng Ma, Zhenyu Wang, Wei Li, Yuzhou Zhang, Xiaojian Zhou, Yangai Liu, Zhongying Ren, Xiaoyu Pei, Kehai Zhou, Wensheng Zhang, Kunlun He, Fei Zhang, Junfang Liu, Wenyu Ma, Guanghui Xiao, Daigang Yang
Upland cotton (Gossypium hirsutum) is the world's largest source of natural fiber and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fiber yields, yet the genome-wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we re-sequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps...
September 16, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30220095/zinc-finger-nuclease-mediated-targeting-of-multiple-transgenes-to-an-endogenous-soybean-genomic-locus-via-non-homologous-end-joining
#18
Nicholas D Bonawitz, W Michael Ainley, Asuka Itaya, Sivarama R Chennareddy, Tobias Cicak, Katherine Effinger, Ke Jiang, Tejinder Kumar Mall, Pradeep Reddy Marri, J Pon Samuel, Nagesh Sardesai, Matthew Simpson, Otto Folkerts, Rodrigo Sarria, Steven R Webb, Delkin O Gonzalez, Daina H Simmonds, Dayakar R Pareddy
Emerging genome editing technologies hold great promise for the improvement of agricultural crops. Several related genome editing methods currently in development utilize engineered, sequence-specific endonucleases to generate DNA double strand breaks (DSBs) at user-specified genomic loci. These DSBs subsequently result in small insertions/deletions (indels), base substitutions or incorporation of exogenous donor sequences at the target site, depending on the application. Targeted mutagenesis in soybean (Glycine max) via non-homologous end joining (NHEJ)-mediated repair of such DSBs has been previously demonstrated with multiple nucleases, as has homology-directed repair (HDR)-mediated integration of a single transgene into target endogenous soybean loci using CRISPR/Cas9...
September 16, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30191675/changes-to-the-core-and-flanking-sequences-of-g-box-elements-lead-to-increases-and-decreases-in-gene-expression-in-both-native-and-synthetic-soybean-promoters
#19
Ning Zhang, Leah K McHale, John J Finer
Cis-regulatory elements in promoters are major determinants of binding specificity of transcription factors (TFs) for transcriptional regulation. To improve our understanding of how these short DNA sequences regulate gene expression, synthetic promoters consisting of both classical (CACGTG) and variant G-box core sequences along with different flanking sequences derived from the promoters of three different highly expressing soybean genes, were constructed and used to regulate a green fluorescent protein (gfp) gene...
September 6, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30191657/maternal-control-of-seed-weight-in-rapeseed-brassica-napus-l-the-causal-link-between-the-size-of-pod-mother-source-and-seed-offspring-sink
#20
Na Li, Dongji Song, Wei Peng, Jiepeng Zhan, Jiaqin Shi, Xinfa Wang, Guihua Liu, Hanzhong Wang
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, primarily via the regulation of cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight...
September 6, 2018: Plant Biotechnology Journal
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