Welcome To Website IAS

Hot news
Achievement

Independence Award

- First Rank - Second Rank - Third Rank

Labour Award

- First Rank - Second Rank -Third Rank

National Award

 - Study on food stuff for animal(2005)

 - Study on rice breeding for export and domestic consumption(2005)

VIFOTEC Award

- Hybrid Maize by Single Cross V2002 (2003)

- Tomato Grafting to Manage Ralstonia Disease(2005)

- Cassava variety KM140(2010)

Centres
Website links
Vietnamese calendar
Library
Visitors summary
 Curently online :  3
 Total visitors :  6313843

Exploring the areas of applicability of whole genome prediction methods for Asian rice (Oryza sativa L.)
Thursday, 2015/01/08 | 10:32:17

Akio Onogi · Osamu Ideta · Yuto Inoshita · Kaworu Ebana · Takuma Yoshioka · Masanori Yamasaki · Hiroyoshi Iwata

Theoretical and Applied Genetics, January 2015, Volume 128, Issue 1, pp 41-53

http://link.springer.com/journal/volumesAndIssues/122

 

Abstract

Key message

 

Our simulation results clarify the areas of applicability of nine prediction methods and suggest the factors that affect their accuracy at predicting empirical traits.

 

Abstract

 

Whole-genome prediction is used to predict genetic value from genome-wide markers. The choice of method is important for successful prediction. We compared nine methods using empirical data for eight phenological and morphological traits of Asian rice cultivars (Oryza sativa L.) and data simulated from real marker genotype data. The methods were genomic BLUP (GBLUP), reproducing kernel Hilbert spaces regression (RKHS), Lasso, elastic net, random forest (RForest), Bayesian lasso (Blasso), extended Bayesian lasso (EBlasso), weighted Bayesian shrinkage regression (wBSR), and the average of all methods (Ave). The objectives were to evaluate the predictive ability of these methods in a cultivar population, to characterize them by exploring the area of applicability of each method using simulation, and to investigate the causes of their different accuracies for empirical traits. GBLUP was the most accurate for one trait, RKHS and Ave for two, and RForest for three traits. In the simulation, Blasso, EBlasso, and Ave showed stable performance across the simulated scenarios, whereas the other methods, except wBSR, had specific areas of applicability; wBSR performed poorly in most scenarios. For each method, the accuracy ranking for the empirical traits was largely consistent with that in one of the simulated scenarios, suggesting that the simulation conditions reflected the factors that affected the method accuracy for the empirical results. This study will be useful for genomic prediction not only in Asian rice, but also in populations from other crops with relatively small training sets and strong linkage disequilibrium structures.

 

Back      Print      View: 843

[ Other News ]___________________________________________________
  • Auxin depletion from leaf primordia contributes to organ patterning
  • Phytochrome controls alternative splicing to mediate light responses in Arabidopsis
  • Maternal temperature history activates Flowering Locus T in fruits to control progeny dormancy according to time of year
  • Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655
  • Factor analytic mixed models for the provision of grower information from national crop variety testing programs
  • Investigation of terpene diversification across multiple sequenced plant genomes
  • Arabidopsis ribosomal proteins control vacuole trafficking and developmental programs through the regulation of lipid metabolism
  • Effect of the ahas Transgene on Biological Nitrogen Fixation and Yield of Soybean
  • Arabidopsis ROCK1 transports UDP-GlcNAc/UDP-GalNAc and regulates ER protein quality control and cytokinin activity
  • A peripheral endocannabinoid mechanism contributes to glucocorticoid-mediated metabolic syndrome
  • High-Resolution Linkage Map and Chromosome-Scale Genome Assembly for Cassava (Manihot esculenta Crantz) from 10 Populations
  • Analysis of the Transcriptome of Banana Fruit during Ripening
  • Nitric oxide negatively regulates abscisic acid signaling in guard cells by S-nitrosylation of OST1
  • Salt Tolerant Gene in Soybean Identified
  • Climate change decouples oceanic primary and export productivity and organic carbon burial
  • Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus
  • 5-Hydroxymethylcytosine Is Not Present in Appreciable Quantities in Arabidopsis DNA
  • Fine mapping of the qLOP2 and qPSR2 1 loci associated with chilling stress tolerance of wild rice seedlings
  • Natural diversity in daily rhythms of gene expression contributes to phenotypic variation
  • DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

 

Designed & Powered by WEBSO CO.,LTD