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      Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

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          Abstract

          Rajeev Varshney, Ryohei Terauchi, and Susan McCouch summarize the current and future uses of next-generation sequencing technologies, both for developing crops with improved traits and for increasing the efficiency of modern plant breeding, as a step towards meeting the challenge of feeding a growing world population.

          Abstract

          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.

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          Most cited references 89

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          Prediction of total genetic value using genome-wide dense marker maps.

          Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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            Real-time DNA sequencing from single polymerase molecules.

            We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.
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              Genome-wide association studies of 14 agronomic traits in rice landraces.

              Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                plosbiol
                PLoS Biology
                Public Library of Science (San Francisco, USA )
                1544-9173
                1545-7885
                June 2014
                10 June 2014
                : 12
                : 6
                Affiliations
                [1 ]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
                [2 ]The University of Western Australia (UWA), Crawley, Western Australia, Australia
                [3 ]Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
                [4 ]Cornell University, Ithaca, New York, United States of America
                The University of North Carolina at Chapel Hill, United States of America
                Author notes

                The authors have declared that no competing interests exist.

                PBIOLOGY-D-14-00370
                10.1371/journal.pbio.1001883
                4051599
                24914810

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Counts
                Pages: 8
                Funding
                RKV thanks the Australia Indo-Strategic Research Fund (AISRF) and Department of Biotechnology, Government of India for sponsoring research at ICRISAT on the topics mentioned in the article. RT thanks the Programme for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry, Japan, Grant-in-aid for MEXT (Scientific Research on Innovative Areas 23113009) and JSPS KAKENHI (Grant No. 24248004). SMc thanks the National Science Foundation Plant Genome Research Program (Grant #1026555) and the Global Crop Diversity Trust. This study has been undertaken as a part of CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR consortium. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Essay
                Biology and Life Sciences

                Life sciences

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