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Oryza rufipogon

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https://www.readbyqxmd.com/read/28861103/integrated-rna-sequencing-and-qtl-mapping-to-identify-candidate-genes-from-oryza-rufipogon-associated-with-salt-tolerance-at-the-seedling-stage
#1
Shanshan Wang, Meng Cao, Xin Ma, Weikang Chen, Jie Zhao, Chuanqing Sun, Lubin Tan, Fengxia Liu
Soil salinity is a common abiotic stress affecting crop productivity. To identify favorable alleles from wild rice (Oryza rufipogon Griff.) that enhance salinity tolerance of rice (O. sativa L.), a set of introgression lines (ILs) were developed. The ILs were derived from an O. rufipogon accession collected from Chaling (Hunan Province, China) as the donor, and a widely grown O. sativa indica cultivar 93-11 as the recipient. Through evaluating the salt tolerance of 285 ILs at the seedling stage, a total of 10 quantitative trait loci (QTLs) related to salt tolerance were identified on chromosomes 1, 5, 7 and 9-12, with individual QTLs explaining 2-8% of phenotypic variance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28758676/assessment-and-genetic-analysis-of-heavy-metal-content-in-rice-grain-using-an-oryza-sativa-%C3%A3-o-rufipogon-backcross-inbred-line-population
#2
De-Run Huang, Ye-Yang Fan, Biao-Lin Hu, Ye-Qing Xiao, Da-Zhou Chen, Jie-Yun Zhuang
BACKGROUND: Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to character the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. RESULTS: The contents of Ni, As, Pb, Cr and Hg in milled rice showed significant decline as compared with those in brown rice, whereas the content of Cd showed little change...
July 31, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28754953/genetically-engineered-rice-endogenous-5-enolpyruvoylshikimate-3-phosphate-synthase-epsps-transgene-alters-phenology-and-fitness-of-crop-wild-hybrid-offspring
#3
Xiao Yang, Lei Li, Xiaoqi Jiang, Wei Wang, Xingxing Cai, Jun Su, Feng Wang, Bao-Rong Lu
Genetically engineered (GE) rice endogenous epsps (5-enolpyruvoylshikimate-3-phosphate synthase) gene overexpressing EPSPS can increase glyphosate herbicide-resistance of cultivated rice. This type of epsps transgene can enhance the fecundity of rice crop-weed hybrid offspring in the absence of glyphosate, stimulating great concerns over undesired environmental impacts of transgene flow to populations of wild relatives. Here, we report the substantial alteration of phenology and fitness traits in F1-F3 crop-wild hybrid descendants derived from crosses between an epsps GE rice line and two endangered wild rice (Oryza rufipogon) populations, based on the common-garden field experiments...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28700714/genome-wide-re-sequencing-of-newly-developed-rice-lines-from-common-wild-rice-oryza-rufipogon-griff-for-the-identification-of-nbs-lrr-genes
#4
Wen Liu, Fozia Ghouri, Hang Yu, Xiang Li, Shuhong Yu, Muhammad Qasim Shahid, Xiangdong Liu
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89...
2017: PloS One
https://www.readbyqxmd.com/read/28649256/evolutionary-insights-based-on-snp-haplotypes-of-red-pericarp-grain-size-and-starch-synthase-genes-in-wild-and-cultivated-rice
#5
Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu, Ashok K Singh, Nagendra K Singh
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28606528/molecular-structures-and-properties-of-starches-of-australian-wild-rice
#6
Tiparat Tikapunya, Wei Zou, Wenwen Yu, Prudence O Powell, Glen P Fox, Agnelo Furtado, Robert J Henry, Robert G Gilbert
Australian wild rices have significant genetic differences from domesticated rices, which might provide rices with different starch molecular structure and thus different functional properties. Molecular structure, gelatinization properties, and pasting behaviours of starch of three Australian wild rices (Oryza australiensis, taxa A (O. rufipogon like) and taxa B (O. meridionalis like)) were determined and compared to domesticated indica and japonica rice. These had higher amylose content, more shorter amylose chains and fewer short amylopectin chains, resulted in a high gelatinization temperature in these wild rices...
September 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28459834/genome-wide-analysis-of-rice-dehydrin-gene-family-its-evolutionary-conservedness-and-expression-pattern-in-response-to-peg-induced-dehydration-stress
#7
Giti Verma, Yogeshwar Vikram Dhar, Dipali Srivastava, Maria Kidwai, Puneet Singh Chauhan, Sumit Kumar Bag, Mehar Hasan Asif, Debasis Chakrabarty
Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28447321/erratum-to-population-dynamics-among-six-major-groups-of-the-oryza-rufipogon-species-complex-wild-relative-of-cultivated-asian-rice
#8
HyunJung Kim, Janelle Jung, Namrata Singh, Anthony Greenberg, Jeff J Doyle, Wricha Tyagi, Jong-Wook Chung, Jennifer Kimball, Ruaraidh Sackville Hamilton, Susan R McCouch
No abstract text is available yet for this article.
December 2017: Rice
https://www.readbyqxmd.com/read/28443109/novel-alleles-of-phosphorus-starvation-tolerance-1-gene-pstol1-from-oryza-rufipogon-confers-high-phosphorus-uptake-efficiency
#9
Kumari Neelam, Shiwali Thakur, Neha, Inderjit S Yadav, Kishor Kumar, Salwinder S Dhaliwal, Kuldeep Singh
Limited phosphorus availability in the soil is one of the major constraints to the growth and productivity of rice across Asian, African and South American countries, where 50% of the rice is grown under rain-fed systems on poor and problematic soils. With an aim to determine novel alleles for enhanced phosphorus uptake efficiency in wild species germplasm of rice Oryza rufipogon, we investigated phosphorus uptake1 (Pup1) locus with 11 previously reported SSR markers and sequence characterized the phosphorus-starvation tolerance 1 (PSTOL1) gene...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424372/effects-of-drought-stress-on-global-gene-expression-profile-in-leaf-and-root-samples-of-dongxiang-wild-rice-oryza-rufipogon
#10
Fantao Zhang, Yi Zhou, Meng Zhang, Xiangdong Luo, Jiankun Xie
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought stress response. The results indicated that 11,231 transcripts were differentially expressed in the leaves (4,040 up-regulated and 7,191 down-regulated) and 7,025 transcripts were differentially expressed in the roots (3,097 up-regulated and 3,928 down-regulated)...
April 19, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28352559/cytological-analysis-for-meiotic-patterns-in-wild-rice-oryza-rufipogon-griff
#11
Sutanu Sarkar, Somnath Bhattacharyya, Saikat Gantait
The present report explores the chromosomal patterns during meiosis as a fundamental cell division study in wild rice (Oryza rufipogon Griff.). Cytological assays revealed normal meiosis in most cases but in some instances meiotic abnormalities such as weak desynapsis, univalent and quadrivalent formation, translocation, spindle abnormalities and precocious movement of chromosomes were noticed. Interestingly, this wild species also has the bi-nucleoli in first meiotic stages alike the cultivated species of Oryza (O...
March 2017: Biotechnology Reports
https://www.readbyqxmd.com/read/28238052/estimation-of-loci-involved-in-non-shattering-of-seeds-in-early-rice-domestication
#12
Ryo Ishikawa, Akinori Nishimura, Than Myint Htun, Ryo Nishioka, Yumi Oka, Yuki Tsujimura, Chizuru Inoue, Takashige Ishii
Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1...
April 2017: Genetica
https://www.readbyqxmd.com/read/28176282/evolutionary-analysis-of-the-sub1-locus-across-the-oryza-genomes
#13
Railson Schreinert Dos Santos, Daniel da Rosa Farias, Camila Pegoraro, Cesar Valmor Rombaldi, Takeshi Fukao, Rod A Wing, Antonio Costa de Oliveira
BACKGROUND: Tolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made...
December 2017: Rice
https://www.readbyqxmd.com/read/28107426/identification-of-micrornas-in-response-to-drought-in-common-wild-rice-oryza-rufipogon-griff-shoots-and-roots
#14
Jing-Wen Zhang, Yan Long, Man-de Xue, Xing-Guo Xiao, Xin-Wu Pei
BACKGROUND: Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. RESULTS: In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where 'R' indicates the root tissue and 'L' indicates the shoot tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28087768/the-rice-paradox-multiple-origins-but-single-domestication-in-asian-rice
#15
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
April 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27990555/root-associated-bacterial-diversities-of-oryza-rufipogon-and-oryza-sativa-and-their-influencing-environmental-factors
#16
Lei Tian, Xue Zhou, Lina Ma, Shangqi Xu, Fahad Nasir, Chunjie Tian
Oryza rufipogon is the ancestor of human-cultivated Oryza sativa. However, little is known about the difference between the root-associated microorganisms of O. rufipogon and O. sativa. In this study, the root-associated bacteria of O. rufipogon, Leersia hexandra, and O. sativa from different latitudes in China were studied by DGGE analysis. Their bacterial community structures were compared by principal component analysis. The relationship between root-associated bacteria and soil properties was explored by canonical correspondence analysis...
May 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/27986805/emergence-of-a-novel-chimeric-gene-underlying-grain-number-in-rice
#17
Hao Chen, Yanyan Tang, Jianfeng Liu, Lubin Tan, Jiahuan Jiang, Mumu Wang, Zuofeng Zhu, Xianyou Sun, Chuanqing Sun
Grain number is an important factor in determining grain production of rice (Oryza sativa L.). The molecular genetic basis for grain number is complex. Discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. Here, we identified GRAINS NUMBER 2 (GN2), a novel gene that is responsible for rice grain number, from "Yuanjiang" common wild rice (O. rufipogon Griff.). Transgenic plants overexpressing GN2 showed less grain number, reduced plant height, and later heading date than control plants...
February 2017: Genetics
https://www.readbyqxmd.com/read/27941309/gene-interaction-at-seed-awning-loci-in-the-genetic-background-of-wild-rice
#18
Mai Ikemoto, Mitsuharu Otsuka, Pham Thien Thanh, Phuong Dang Thai Phan, Ryo Ishikawa, Takashige Ishii
Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2...
December 9, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27933072/development-and-evaluation-of-chromosome-segment-substitution-lines-carrying-overlapping-chromosome-segments-of-the-whole-wild-rice-genome
#19
Dewei Yang, Xinfu Ye, Xianghua Zheng, Chaoping Cheng, Ning Ye, Fenghuang Huang
Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27889940/sequencing-of-australian-wild-rice-genomes-reveals-ancestral-relationships-with-domesticated-rice
#20
Marta Brozynska, Dario Copetti, Agnelo Furtado, Rod A Wing, Darren Crayn, Glen Fox, Ryuji Ishikawa, Robert J Henry
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O...
June 2017: Plant Biotechnology Journal
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