Toyota City, Dec 6, 2010 – (JCN Newswire) – Toyota Motor Corporation (TMC) announces that, based on joint development with the National Agricultural Research Center for Kyushu Okinawa Region (KONARC), TMC has created genetic-analysis technology that can substantially shorten the time needed to improve varieties of sugar cane and improve plant performance.
TMC developed a high-throughput DNA (deoxyribonucleic acid) analysis technology, based on which KONARC assessed sugar cane performance and TMC worked on genetic analysis. Combining the results created the new genetic-analysis technology.
Conventional agricultural plant improvement involves selecting and crossing parent varieties based on extensive past performance data, assessing progeny over the long term, and selecting new progeny with the desired property. In place of this, a revolutionary crop-improving technology – marker-assisted breeding – uses genetic information to predict performance and has been used in breeding rice and maize. However, sugar cane’s large genome size makes it difficult to genetically analyze, meaning marker-assisted breeding cannot easily be applied.
In response, TMC developed its high-throughput DNA analysis technology based on DNA microarray technology* that allows highly precise, high-throughput genotyping. With its new technology, TMC successfully created a sugar-cane genetic map five times more accurate than previous maps, making it possible to identify the positions of genes and to use that information to create better sugar cane.
TMC believes the development of the new genetic-analysis technology will constitute a major step toward achieving the goal of shortening the period needed for sugar-cane improvement by 50% and expects it will lead to increased sugar-cane yield through creating sugar-cane varieties with higher sugar content and improved disease resistance.
TMC and KONARC will present the new genetic-analysis technology at the 33rd Annual Meeting of the Molecular Biology Society of Japan to be held in Kobe from December 7.
TMC has been developing technologies to increase crop yield with the aim of supporting the expanded use of bio-fuels. The high-throughput DNA analysis technology that forms the core of the genetic-analysis technology announced today can be applied to not only sugar cane but to other varieties of plants that have a large genome. TMC believes that its high-throughput DNA analysis technology also holds potential foodstuff-production and environmental advantages. To enable broad use of this technology, TMC plans to make information concerning it open.
* A technology being developed for, among other uses, assessing human predispositions and cancer occurrence risks.
About Toyota
Supported by people around the world, Toyota Motor Corporation (TSE: 7203; NYSE: TM), has endeavored since its establishment in 1937 to serve society by creating better products. As of the end of March 2010, Toyota conducts its business worldwide with 51 overseas manufacturing companies in 26 countries and regions. Toyota’s vehicles are sold in more than 170 countries and regions. For more information, please visit www.toyota.co.jp/en/index.html.
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Dec 6, 2010
Source: Toyota
Toyota (TSE: 7203) (U.S: TM)
From the Japan Corporate News Network
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Topic: Research and development
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Large-scale SNP genotyping in crosses between outbred lines: how useful is it?
Heredity. 2010 Aug;105(2):173-82
Authors: Ledur MC, Navarro N, Pérez-Enciso M
Although genome-wide association (GWA) studies are not worth the effort in crosses between inbred lines, many crosses are actually made up of divergent yet outbred populations. Despite its relevance, however, this experimental setting has not been studied at a time when SNP microarrays are available in many species. To assess whether GWA can be useful in this setting, we performed combined coalescence--gene dropping simulations. We studied the influence of marker density, QTL effect and QTL allele frequency on power, false discovery rate (FDR) and accuracy. Our results suggest that GWA in outbred F(2) crosses is useful, especially in large populations. Under these circumstances, accuracy increased and FDR decreased as compared with classical linkage analysis. However, current SNP densities (in the order of 30-60 K SNPs/genome or equivalent to 10-20 SNPs per cM) may not be much better than linkage analysis and higher SNP densities may be required. SNP ascertainment had an important effect; the best option was to select SNPs as uniformly as possible without setting any restriction on allele frequency. Using only SNPs with fixed alternative alleles in each breed controlled false positive rate but was not useful to detect variability within lines. Finally, the most significant SNP was not necessarily the closest to the causal SNP, although the closest SNPs were usually above the significance threshold; thus, it is prudent to follow-up significant signals located in regions of interest even if they do not correspond to absolute maxima.
PMID: 19844266 [PubMed - in process]
J Anim Breed Genet. 2010 Oct;127(5):348-51. doi: 10.1111/j.1439-0388.2010.00864.x.
Gorbach DM, Makgahlela ML, Reecy JM, Kemp SJ, Baltenweck I, Ouma R, Mwai O, Marshall K, Murdoch B, Moore S, Rothschild MF.
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA, USA Agricultural Research Council, Private Bag X2, Irene, South Africa School of Biological Sciences, Biosciences Building, Liverpool, UK International Livestock Research Institute, Nairobi, Kenya 410 AgFor Centre, University of Alberta, Edmonton, AB, Canada.
Abstract
High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow-calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam-calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clustered with Holsteins, while animals from smaller farms were generally crosses between Holstein and Guernsey. Coefficients of relatedness were estimated and showed evidence of heavy use of one AI bull. We conclude that little native germplasm exists within the genotyped populations and mostly European ancestry remains.
PMID: 20831558 [PubMed - in process]
High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow-calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam-calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clust...
