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Lei Tian, Shaohua Shi, Lina Ma, Fahad Nasir, Xiujun Li, Lam-Son Phan Tran, Chunjie Tian
The plants and root-associated microbiomes are closely related. Plant metabolic substances can serve as a nutrient source for the microbiome, and in return, the microbiome can regulate the production of plant metabolic substances. Wild rice (Oryza rufipogon), as the ancestor of cultivated rice (Oryza sativa), has changed several metabolic pathways and root-associated microbiome during evolution. Thus, the study of the different associations between metabolic pathways and root-associated microbiomes in wild and cultivated rice varieties is important for rice breeding...
April 13, 2018: Plant Physiology and Biochemistry: PPB
Ali M Moner, Agnelo Furtado, Ian Chivers, Glen Fox, Darren Crayn, Robert J Henry
In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia...
April 2018: Ecology and Evolution
Lei Tian, Shaohua Shi, Fahad Nasir, Chunling Chang, Weiqiang Li, Lam-Son Phan Tran, Chunjie Tian
BACKGROUND: Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to current cultivated rice varieties, no prior studies have compared the immune and transcriptional responses in the roots of wild and cultivated rice to M...
April 20, 2018: Rice
Lan Qi, Yingbin Ding, Xiaoming Zheng, Rui Xu, Lizhen Zhang, Yanyan Wang, Xiaoning Wang, Lifang Zhang, Yunlian Cheng, Weihua Qiao, Qingwen Yang
A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311...
April 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Qian-Wen Deng, Xiang-Dong Luo, Ya-Ling Chen, Yi Zhou, Fan-Tao Zhang, Biao-Lin Hu, Jian-Kun Xie
BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response...
March 15, 2018: Biological Research
Balwant Singh, Nisha Singh, Shefali Mishra, Kabita Tripathi, Bikram P Singh, Vandna Rai, Ashok K Singh, Nagendra K Singh
Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches...
2018: Frontiers in Plant Science
Li Jing, Xu Rui, Wang Chunchao, Qi Lan, Zheng Xiaoming, Wang Wensheng, Ding Yingbin, Zhang Lizhen, Wang Yanyan, Cheng Yunlian, Zhang Lifang, Qiao Weihua, Yang Qingwen
Heading date (HD) and panicle length (PL) are important traits that affect rice breeding and are controlled by pleiotropic genes. Some alleles associated with HD and PL from wild relatives might differ from those in cultivated rice. In this study, a main effect HD quantitative trait locus from wild rice, qHD7.2, was identified using a chromosomal segment substitution line (CSSL) population. First, qHD7.2 was determined to be located near RM172 on chromosome 7 based on association analysis of phenotype data from six environments and 181 polymorphic molecular markers...
February 13, 2018: Scientific Reports
Rashmita Samal, Pritesh Sundar Roy, Auromira Sahoo, Meera Kumari Kar, Bhaskar Chandra Patra, Bishnu Charan Marndi, Jwala Narasimha Rao Gundimeda
The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufipogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i...
February 9, 2018: Scientific Reports
Lan Qi, Yan Sun, Jing Li, Long Su, Xiaoming Zheng, Xiaoning Wang, Kaimian Li, Qingwen Yang, Weihua Qiao
Grain size and weight are important determinants of rice yield. The identification of beneficial genes from wild rice that have been lost or weakened in cultivated rice has become increasingly important for modern breeding strategies. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) of wild rice, Oryza rufipogon with the indica cultivar 9311 genetic background. Four grain-related traits, i.e., grain length (GL), grain width (GW), length-width ratio (LWR), and thousand grain weight (TGW), were screened across six environments...
December 2017: Breeding Science
Qiang Zhao, Qi Feng, Hengyun Lu, Yan Li, Ahong Wang, Qilin Tian, Qilin Zhan, Yiqi Lu, Lei Zhang, Tao Huang, Yongchun Wang, Danlin Fan, Yan Zhao, Ziqun Wang, Congcong Zhou, Jiaying Chen, Chuanrang Zhu, Wenjun Li, Qijun Weng, Qun Xu, Zi-Xuan Wang, Xinghua Wei, Bin Han, Xuehui Huang
The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the O. sativa japonica Nipponbare reference genome. Here we constructed a pan-genome dataset of the O. sativa-O. rufipogon species complex through deep sequencing and de novo assembly of 66 divergent accessions...
February 2018: Nature Genetics
Marcelo Pillonetto, Lavinia N Arend, Helisson Faoro, Helena R S D'Espindula, Jochen Blom, Theo H M Smits, Marcelo T Mira, Fabio Rezzonico
The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA-DNA hybridization support the existence of a second species within the genus Phytobacter...
January 2018: International Journal of Systematic and Evolutionary Microbiology
V Vishnu Prasanth, M Suchandranath Babu, Ramana K Basava, V G N Tripura Venkata, Satendra K Mangrauthia, S R Voleti, Sarla Neelamraju
Wild species and derived introgression lines (ILs) are a good source of genes for improving complex traits such as heat tolerance. The effect of heat stress on 18 yield traits was studied in four treatments in two seasons, under field conditions by subjecting 37 ILs and recurrent parents Swarna and KMR3, N22 mutants, and wild type and 2 improved rice cultivars to heat stress using polycover house method in wet season and late sowing method in dry season. Normal grown unstressed plants were controls. Both correlation and path coefficient analysis showed that the major contributing traits for high yield per plant (YPP) under heat stress conditions were tiller number, secondary branches in panicle, filled grain number, and percent spikelet fertility...
2017: Frontiers in Plant Science
Hua Cui, Chunlian Wang, Tengfei Qin, Feifei Xu, Yongchao Tang, Ying Gao, Kaijun Zhao
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region...
2017: PloS One
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
Michael J Thomson, Namrata Singh, Maria S Dwiyanti, Diane R Wang, Mark H Wright, Francisco Agosto Perez, Genevieve DeClerck, Joong Hyoun Chin, Geraldine A Malitic-Layaoen, Venice Margarette Juanillas, Christine J Dilla-Ermita, Ramil Mauleon, Tobias Kretzschmar, Susan R McCouch
BACKGROUND: Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups...
August 30, 2017: Rice
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 characterise 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 a significant decline as compared with those in brown rice, whereas the content of Cd showed little change...
March 2018: Journal of the Science of Food and Agriculture
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
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
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
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
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