keyword
https://read.qxmd.com/read/38470483/root-microbiota-analysis-of-oryza-rufipogon-and-oryza-sativa-reveals-an-orientation-selection-during-the-domestication-process
#1
JOURNAL ARTICLE
Liqun Jiang, Da Ke, Bingrui Sun, Jing Zhang, Shuwei Lyu, Hang Yu, Pingli Chen, Xingxue Mao, Qing Liu, Wenfeng Chen, Zhilan Fan, Li Huang, Sanjun Yin, Yizhen Deng, Chen Li
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice ( Oryza sativa ) was domesticated from the ancestor species Oryza rufipogon . Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained...
March 12, 2024: Microbiology Spectrum
https://read.qxmd.com/read/38418937/transcription-factor-encoding-gene-osc1-regulates-leaf-sheath-color-through-anthocyanidin-metabolism-in-oryza-rufipogon-and-oryza-sativa
#2
JOURNAL ARTICLE
Liqun Jiang, Shuwei Lyu, Hang Yu, Jing Zhang, Bingrui Sun, Qing Liu, Xingxue Mao, Pingli Chen, Dajian Pan, Wenfeng Chen, Zhilan Fan, Chen Li
Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath)...
February 28, 2024: BMC Plant Biology
https://read.qxmd.com/read/38337902/physiological-responses-to-salt-stress-at-the-seedling-stage-in-wild-oryza-rufipogon-griff-and-cultivated-oryza-sativa-l-rice
#3
JOURNAL ARTICLE
Jacopo Trotti, Isabella Trapani, Federica Gulino, Maurizio Aceto, Miles Minio, Caterina Gerotto, Erica Mica, Giampiero Valè, Roberto Barbato, Cristina Pagliano
Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+ /K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status...
January 26, 2024: Plants (Basel, Switzerland)
https://read.qxmd.com/read/38230514/genetic-architecture-of-ecological-divergence-between-oryza-rufipogon-and-oryza-nivara
#4
JOURNAL ARTICLE
Qing-Lin Meng, Cheng-Gen Qiang, Ji-Long Li, Mu-Fan Geng, Ning-Ning Ren, Zhe Cai, Mei-Xia Wang, Zi-Hui Jiao, Fu-Min Zhang, Xian-Jun Song, Song Ge
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species...
January 17, 2024: Molecular Ecology
https://read.qxmd.com/read/38136960/genetic-and-transcriptome-analyses-of-callus-browning-in-chaling-common-wild-rice-oryza-rufipogon-griff
#5
JOURNAL ARTICLE
Lingyi Qiu, Jingjing Su, Yongcai Fu, Kun Zhang
Callus browning during tissue culture of indica rice is genotype dependent, thus limiting the application of genetic transformation for editing-assisted breeding and elucidation of gene function. Here, using 124 introgression lines (HCLs) derived from a cross between the indica rice 9311 and Chaling common wild rice and 2059 SNPs for single-point and interval analysis, we identified two major QTLs, qCBT7 on chromosome 7 and qCBT10 on chromosome 10, related to callus browning, explaining 8-13% of callus browning...
November 27, 2023: Genes
https://read.qxmd.com/read/38106511/wild-and-cultivated-allele-effects-on-rice-phenotypic-traits-in-reciprocal-backcross-populations-between-oryza-rufipogon-and-two-cultivars-o-sativa-nipponbare-and-ir36
#6
JOURNAL ARTICLE
Phuong Dang Thai Phan, Akinori Nishimura, Chika Yamamoto, Pham Thien Thanh, Toshihiro Niwa, Yaddehige Priya Jayantha Amarasinghe, Ryo Ishikawa, Takashige Ishii
A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of Oryza rufipogon W630 and two major cultivars, O. sativa Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations...
September 2023: Breeding Science
https://read.qxmd.com/read/38085356/different-contributions-of-prog1-and-tac1-to-the-angular-kinematics-of-the-main-culm-and-tillers-of-wild-rice-oryza-rufipogon
#7
JOURNAL ARTICLE
Yoshiki Tokuyama, Miku Omachi, Shiori Kushida, Kiwamu Hikichi, Shuhei Okada, Kazumitsu Onishi, Takashige Ishii, Yuji Kishima, Yohei Koide
PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified...
December 12, 2023: Planta
https://read.qxmd.com/read/38003501/comparative-genomic-analysis-of-asian-cultivated-rice-and-its-wild-progenitor-oryza-rufipogon-has-revealed-evolutionary-innovation-of-the-pentatricopeptide-repeat-gene-family-through-gene-duplication
#8
JOURNAL ARTICLE
Li-Ying Feng, Pei-Fan Lin, Rong-Jing Xu, Hai-Qi Kang, Li-Zhi Gao
The pentatricopeptide repeat ( PPR ) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon , and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11...
November 14, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/37994910/-actinoallomurus-soli-sp-nov-and-actinoallomurus-rhizosphaericola-sp-nov-two-novel-actinobacteria-isolated-from-rhizosphere-soil-of-oryza-rufipogon-griff
#9
JOURNAL ARTICLE
Tanatorn Chantavorakit, Supattra Muangham, Teo Wee Fei Aaron, Kannika Duangmal, Kui Hong
The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice ( Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T . Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus , while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives...
November 2023: International Journal of Systematic and Evolutionary Microbiology
https://read.qxmd.com/read/37965031/phylogenetic-analysis-of-endogenous-viral-elements-in-the-rice-genome-reveals-local-chromosomal-evolution-in-oryza-aa-genome-species
#10
JOURNAL ARTICLE
Nozomi Saito, Sunlu Chen, Katsuya Kitajima, Zhitong Zhou, Yohei Koide, Jaymee R Encabo, Maria Genaleen Q Diaz, Il-Ryong Choi, Kanako O Koyanagi, Yuji Kishima
INTRODUCTION: Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae . These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica ) and the closely related wild species Oryza rufipogon ...
2023: Frontiers in Plant Science
https://read.qxmd.com/read/37958759/genome-wide-identification-evolution-and-expression-analysis-of-the-wd40-subfamily-in-oryza-genus
#11
JOURNAL ARTICLE
Simin Ke, Yifei Jiang, Mingao Zhou, Yangsheng Li
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp...
October 30, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/37847396/qglf5-from-oryza-rufipogon-griff-improves-kernel-shape-plant-architecture-and-yield-in-rice
#12
JOURNAL ARTICLE
Yijun Wang, Xiaoya Liang, Gaoyang Gong, Guiquan Zhang, Hongyuan Zhao, Zhenwu Zheng, Chihang Wang, Haitao Zhu, Jinyan Huang, Zhan Li, Suhong Bu, Guifu Liu, Shaokui Wang, Zupei Liu
A novel QTL qGLF5 from Oryza rufipogon Griff. improves yield per plant and plant architecture in rice. Kernel size and plant architecture are critical agronomic traits that are key targets for improving crop yield. From the single-segment substitution lines of Oryza rufipogon Griff. in the indica cultivar Huajingxian74 (HJX74) background, we identified a novel quantitative trait locus (QTL), named qGLF5, which improves kernel shape, plant architecture, and yield per plant in rice. Compared with the control HJX74, the plant height, panicles per plant, panicle length, primary branches per panicle, secondary branches per panicle, and kernels per plant of the near-isogenic line-qGLF5 (NIL-qGLF5) are significantly increased...
October 17, 2023: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://read.qxmd.com/read/37833950/microrna2871b-of-dongxiang-wild-rice-oryza-rufipogon-griff-negatively-regulates-cold-and-salt-stress-tolerance-in-transgenic-rice-plants
#13
JOURNAL ARTICLE
Wanling Yang, Yong Chen, Rifang Gao, Yaling Chen, Yi Zhou, Jiankun Xie, Fantao Zhang
Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21-24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions...
September 25, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/37743422/population-structure-and-genetic-differentiation-analyses-reveal-high-level-of-diversity-and-allelic-richness-in-crop-wild-relatives-of-aa-genome-species-of-rice-oryza-sativa-l-in-india
#14
JOURNAL ARTICLE
Aswin Mahendran, Mahesh C Yadav, Shailesh Tiwari, Rakesh Kumar Bairwa, S Gopala Krishnan, Mukesh Kumar Rana, Rakesh Singh, Tapan Kumar Mondal
Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O...
September 25, 2023: Journal of Applied Genetics
https://read.qxmd.com/read/37737275/a-de-novo-evolved-gene-contributes-to-rice-grain-shape-difference-between-indica-and-japonica
#15
JOURNAL ARTICLE
Rujia Chen, Ning Xiao, Yue Lu, Tianyun Tao, Qianfeng Huang, Shuting Wang, Zhichao Wang, Mingli Chuan, Qing Bu, Zhou Lu, Hanyao Wang, Yanze Su, Yi Ji, Jianheng Ding, Ahmed Gharib, Huixin Liu, Yong Zhou, Shuzhu Tang, Guohua Liang, Honggen Zhang, Chuandeng Yi, Xiaoming Zheng, Zhukuan Cheng, Yang Xu, Pengcheng Li, Chenwu Xu, Jinling Huang, Aihong Li, Zefeng Yang
The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties...
September 22, 2023: Nature Communications
https://read.qxmd.com/read/37731231/the-discovery-and-utilization-of-favorable-genes-in-oryza-longistaminata
#16
REVIEW
Xiao-Ping Lian, Guang-Fu Huang, Yu-Jiao Zhang, Jing Zhang, Feng-Yi Hu, Shi-Lai Zhang
Asian cultivated rice has been domesticated from ancestors of the wild rice species Oryza rufipogon . During this process, important changes have occurred in many agronomic traits, such as plant height, grain shattering, and panicle shape, and the yield has also greatly increased. However, many favored traits (e.g., stress resistance) have been lost. The genome of O. longistaminata is of the same AA type as O. sativa , harboring many genes conferring resistance to biotic and abiotic stresses, and it is considered as a potential gene pool for genetic improvement of O...
September 20, 2023: Yi Chuan, Hereditas
https://read.qxmd.com/read/37726366/novel-genes-and-alleles-of-the-btb-poz-protein-family-in-oryza-rufipogon
#17
JOURNAL ARTICLE
Swarupa Nanda Mandal, Jacobo Sanchez, Rakesh Bhowmick, Oluwatobi R Bello, Coenraad R Van-Beek, Benildo G de Los Reyes
The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O...
September 19, 2023: Scientific Reports
https://read.qxmd.com/read/37668809/substitution-mapping-and-allelic-variations-of-the-domestication-genes-from-o-rufipogon-and-o-nivara
#18
JOURNAL ARTICLE
Zhangqiang Wang, Zisheng Guo, Tuo Zou, Zhe Zhang, Jianan Zhang, Ping He, Ruifeng Song, Ziqiang Liu, Haitao Zhu, Guiquan Zhang, Xuelin Fu
BACKGROUND: Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. RESULTS: In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74...
September 5, 2023: Rice
https://read.qxmd.com/read/37619981/detection-of-locally-adapted-genomic-regions-in-wild-rice-oryza-rufipogon-using-environmental-association-analysis
#19
JOURNAL ARTICLE
James A Bedford, Mark Carine, Mark A Chapman
Oryza rufipogon is the wild progenitor of cultivated rice O. sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress tolerant varieties and genes that could limit future climate-changed induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors...
August 24, 2023: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/37596418/saccharopolyspora-oryzae-sp-nov-isolated-from-rhizosphere-soil-of-the-wild-rice-species-oryza-rufipogon
#20
JOURNAL ARTICLE
Sirikarn Kammanee, Supattra Muangham, Waranya Butdee, Chollachai Klaysubun, Yasuhiro Igarashi, Kannika Duangmal
A novel actinobacterium, designated as strain WRP15-2T , was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98...
August 18, 2023: Journal of Antibiotics
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