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161.
Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice 总被引:6,自引:0,他引:6
Jiang N Bao Z Temnykh S Cheng Z Jiang J Wing RA McCouch SR Wessler SR 《Genetics》2002,161(3):1293-1305
A new and unusual family of LTR elements, Dasheng, has been discovered in the genome of Oryza sativa following database searches of approximately 100 Mb of rice genomic sequence and 78 Mb of BAC-end sequence information. With all of the cis-elements but none of the coding domains normally associated with retrotransposons (e.g., gag, pol), Dasheng is a novel nonautonomous LTR element with high copy number. Over half of the approximately 1000 Dasheng elements in the rice genome are full length (5.6-8.6 kb), and 60% are estimated to have amplified in the past 500,000 years. Using a modified AFLP technique called transposon display, 215 elements were mapped to all 12 rice chromosomes. Interestingly, more than half of the mapped elements are clustered in the heterochromatic regions around centromeres. The distribution pattern was further confirmed by FISH analysis. Despite clustering in heterochromatin, Dasheng elements are not nested, suggesting their potential value as molecular markers for these marker-poor regions. Taken together, Dasheng is one of the highest-copy-number LTR elements and one of the most recent elements to amplify in the rice genome. 相似文献
162.
Microsatellite marker development,mapping and applications in rice genetics and breeding 总被引:38,自引:0,他引:38
McCouch Susan R. Chen Xiuli Panaud Olivier Temnykh Svetlana Xu Yunbi Cho Yong Gu Huang Ning Ishii Takashige Blair Matthew 《Plant molecular biology》1997,35(1-2):89-99
Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10 000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trait locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice. 相似文献
163.
Y. Xu L. Zhu J. Xiao N. Huang S. R. McCouch 《Molecular genetics and genomics : MGG》1997,253(5):535-545
Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?/?japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129–629 markers. Segregation distortion was determined based on chi-square analysis (P?<?0.01) and was observed at 6.8–31.8% of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated. 相似文献
164.
The use of the antiplatelet agents abciximab and clopidogrel is now accepted therapy in percutaneous coronary intervention. We present a case in which these agents were used in a patient with idiopathic thrombocytopaenic purpura and a platelet count of 40x10(9)/l undergoing primary multivessel coronary stenting. This case shows that unstable coronary syndromes can occur in patients with thrombocytopaenia and that antiplatelet agents may be used safely in this context. 相似文献
165.
Yunbi Xu Dominique This Roman C. Pausch Wendy M. Vonhof Jason R. Coburn Jonathan P. Comstock Susan R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(6):1065-1081
Increasing the water use efficiency (WUE) of our major crop species is an important target of agricultural research. Rice
is a major water consumer in agriculture and it is also an attractive genetic model. We evaluated leaf-level WUE in young
rice seedlings using carbon isotope discrimination (∆13C) as an indicator of the trait. A survey of ∆13C was undertaken in 116 diverse germplasm accessions representing O. sativa, O. glaberrima and four wild Oryza species. O. sativa cultivars were classified into sub-populations based on SSR markers, and significant differences in ∆13C were observed among the five genetically defined groups. While individual accessions explained a greater proportion of the
variation than did sub-population, indica rice varieties had the lowest ∆13C values overall, indicating superior WUE, while temperate
japonica had the highest ∆13C. O sativa accessions had a similar or greater range of ∆13C values than wild Oryza species, while domesticated O. glaberrima had a narrower range. Correlation analysis identified leaf morphological and physiological traits that were significantly
associated with ∆13C, including longer leaves, more drooping leaves, higher tillering ability, and lower leaf nitrogen content. These trait associations
were investigated by quantitative trait locus (QTL) mapping using backcross inbred lines derived from a cross between Nipponbare
(temperate
japonica) and Kasalath (aus). Seven QTL for ∆13C were identified using composite interval analysis, located in five chromosomal regions. The QTL with the largest additive
effect came from Kasalath and co-localized with QTL for leaf length, tiller number and nitrogen content. 相似文献
166.
Addressing Research Bottlenecks to Crop Productivity 总被引:2,自引:0,他引:2
Matthew Reynolds Owen K. Atkin Malcolm Bennett Mark Cooper Ian C. Dodd M. John Foulkes Claus Frohberg Graeme Hammer Ian R. Henderson Bingru Huang Viktor Korzun Susan R. McCouch Carlos D. Messina Barry J. Pogson Gustavo A. Slafer Nicolas L. Taylor Peter E. Wittich 《Trends in plant science》2021,26(6):607-630
167.
Jennifer Spindel Hasina Begum Deniz Akdemir Parminder Virk Bertrand Collard Edilberto Redo?a Gary Atlin Jean-Luc Jannink Susan R. McCouch 《PLoS genetics》2015,11(2)
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute''s (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. 相似文献
168.
Satoshi Ogawa Michael Gomez Selvaraj Angela Joseph Fernando Mathias Lorieux Manabu Ishitani Susan McCouch Juan David Arbelaez 《Plant and Soil》2014,375(1-2):303-315
Aims
In rice, seminal root elongation plays an important role in acquisition of nutrients such as N and P, but the extent to which different N forms and P concentrations affect root growth is poorly understood. This study aimed to examine N- and P-mediated seminal root elongation response and to identify putative QTLs associated with seminal root elongation.Methods
Seminal root elongation was evaluated in 15 diverse wild and cultivated accessions of rice, along with 48 chromosome segment substitution lines (CSSLs) derived from a cross between the rice variety ‘Curinga’ and Oryza rufipogon (IRGC 105491). Root elongation in response to different forms of N (NH4 +, NO3 ? and NH4NO3) and concentrations of P was evaluated under hydroponic conditions, and associated putative QTL regions were identified.Results
The CSSL parents had contrasting root responses to N and P. Root elongation in O. rufipogon was insensitive to N source and concentration, whereas Curinga was responsive. In contrast to N, seminal root elongation and P concentration was positively correlated. Three putative QTLs for seminal root elongation in response to N were detected on chromosome 1, and one QTL on chromosome 3 was associated with low P concentration.Conclusions
Genetic variation in seminal root elongation and plasticity of nutrient response may be appropriate targets for marker-assisted selection to improve rice nutrient acquisition efficiency. 相似文献169.
Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
This article is part of the PLOS Biology Collection “The Promise of Plant Translational Research.”相似文献
170.
Miguel A. Piñ eros Brandon G. Larson Jon E. Shaff David J. Schneider Alexandre Xavier Falcã o Lixing Yuan Randy T. Clark Eric J. Craft Tyler W. Davis Pierre-Luc Pradier Nathanael M. Shaw Ithipong Assaranurak Susan R. McCouch Craig Sturrock Malcolm Bennett Leon V. Kochian 《植物学报(英文版)》2016,58(3):230-241
A plant's ability to maintain or improve its yield under limiting conditions,such as nutrient de ficiency or drought,can be strongly in fluenced by root system architecture(RSA),the three-dimensional distribution of the different root types in the soil. The ability to image,track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system,while allowing for aeration,solution replenishment and the imposition of nutrient treatments,as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modi fications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity(detection of fine roots and other root details),higher ef ficiency,and a broad array of growing conditions for plants that more closely mimic those found under field conditions. 相似文献