Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs

Synthesis beyond limit

<p>Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.</p

Pseudorapidity dependence of long-range two-particle correlations in pPb collisions at root sNN=5.02 TeV

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Revisiting rice breeding methods – evaluating the use of rapid generation advance (RGA) for routine rice breeding

Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency

Search for the standard model Higgs boson decaying into two photons in pp collisions at root s=7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a center-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 fb(-1). Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1 sigma. The global significance of observing an excess with a local significance >= 3.1 sigma anywhere in the search range 110-150 GeV is estimated to be 1.8 sigma. More data are required to ascertain the origin of this excess. (C) 2012 CERN. Published by Elsevier B.V. All rights reserved. RI Lokhtin, Igor/D-7004-2012; Perfilov, Maxim/E-1064-2012; Belyaev, Andrey/E-1540-2012; Dudko, Lev/D-7127-2012; Boos, Eduard/D-9748-2012; Snigirev, Alexander/D-8912-2012; Tomei, Thiago/E-7091-2012; Focardi, Ettore/E-7376-2012; Raidal, Martti/F-4436-2012; Palla, Fabrizio/F-4727-2012; Gregores, Eduardo/F-8702-2012; Novaes, Sergio/D-3532-2012; Padula, Sandra /G-3560-2012; Lujan Center, LANL/G-4896-2012; Tinoco Mendes, Andre David/D-4314-2011; Flix, Josep/G-5414-2012; Fruhwirth, Rudolf/H-2529-2012; Chen, Jie/H-6210-2011; Torassa, Ezio/I-1788-201

First measurement of hadronic event shapes in pp collisions at root s=7 TeV

Hadronic event shapes have been measured in proton-proton collisions at root s = 7 TeV, with a data sample collected with the CMS detector at the LHC. The sample corresponds to an integrated luminosity of 3.2 pb(-1). Event-shape distributions, corrected for detector response, are compared with five models of QCD multijet production. (C) 2011 CERN. Published by Elsevier B.V. All rights reserved

Inclusive search for a vector-like T quark with charge 2/3 in pp collisions at root s=8 TeV

A search is performed for a massive new vector-like quark T, with charge 2/3, that is pair produced together with its antiparticle in proton-proton collisions. The data were collected by the CMS experiment at the Large Hadron Collider in 2012 at root s = 8 TeV and correspond to an integrated luminosity of 19.5 fb(-1). The T quark is assumed to decay into three different final states, bW, tZ, and tH. The search is carried out using events with at least one isolated lepton. No deviations from standard model expectations are observed, and lower limits are set on the T quark mass at 95% confidence level. The lower limit lies between 687 and 782 GeV for all possible values of the branching fractions into the three different final states assuming strong production. These limits are the most stringent constraints to date on the existence of such a quark. (C) Published by Elsevier B.V