Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits

[1]  R. Varshney,et al.  Genomic Selection for Crop Improvement , 2017, Springer International Publishing.

[2]  A. Fujiyama,et al.  Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes , 2016, PloS one.

[3]  M. Lund,et al.  Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds. , 2016, Journal of dairy science.

[4]  Yuan Yu,et al.  QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers , 2016, Tree Genetics & Genomes.

[5]  A. Fujiyama,et al.  A genomic approach to selecting robust and versatile SNP sets from next-generation sequencing data for genome-wide association study in citrus cultivars , 2016 .

[6]  P. Ollitrault,et al.  Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. , 2016, Annals of botany.

[7]  Takeshi Hayashi,et al.  Genomics-assisted breeding in fruit trees , 2016, Breeding science.

[8]  T. Shimada,et al.  Citrus breeding, genetics and genomics in Japan , 2016, Breeding science.

[9]  M. Bink,et al.  Accuracy and responses of genomic selection on key traits in apple breeding , 2015, Horticulture Research.

[10]  D. Bates,et al.  Linear Mixed-Effects Models using 'Eigen' and S4 , 2015 .

[11]  Jesse Poland,et al.  Breeding-assisted genomics. , 2015, Current opinion in plant biology.

[12]  T. Lacombe,et al.  Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine , 2014, PloS one.

[13]  Daniel Gianola,et al.  Kernel-based whole-genome prediction of complex traits: a review , 2014, Front. Genet..

[14]  Shizhong Xu,et al.  Predicting hybrid performance in rice using genomic best linear unbiased prediction , 2014, Proceedings of the National Academy of Sciences.

[15]  G. de los Campos,et al.  Genome-Wide Regression and Prediction with the BGLR Statistical Package , 2014, Genetics.

[16]  Karin M. Fredrikson,et al.  Complex history of admixture during citrus domestication revealed by genome analysis , 2014 .

[17]  Andrea Zuccolo,et al.  Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication , 2014, Nature Biotechnology.

[18]  J. Pérez-Ortín,et al.  Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast , 2013, Front. Genet..

[19]  Luis Varona,et al.  On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope , 2013, Genetics.

[20]  P. De Franceschi,et al.  Identifying a Carotenoid Cleavage Dioxygenase (ccd4) Gene Controlling Yellow/White Fruit Flesh Color of Peach , 2013, Plant Molecular Biology Reporter.

[21]  A. Korte,et al.  The advantages and limitations of trait analysis with GWAS: a review , 2013, Plant Methods.

[22]  R. Fernando,et al.  Genomic Prediction of Hybrid Wheat Performance , 2013 .

[23]  Takeshi Hayashi,et al.  Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia , 2013, Breeding science.

[24]  P. Pérez,et al.  BGLR: A Statistical Package for Whole Genome Regression and Prediction , 2013 .

[25]  Niranjan Nagarajan,et al.  The draft genome of sweet orange (Citrus sinensis) , 2012, Nature Genetics.

[26]  I. Matušíková,et al.  Callose: the plant cell wall polysaccharide with multiple biological functions , 2012, Acta Physiologiae Plantarum.

[27]  S. Korban,et al.  Association mapping in forest trees and fruit crops | 3 of 16 Association mapping in forest trees and fruit crops | 4047 , 2012 .

[28]  Marco C. A. M. Bink,et al.  Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.) , 2012, PloS one.

[29]  R. Wellmann,et al.  Bayesian models with dominance effects for genomic evaluation of quantitative traits. , 2012, Genetics research.

[30]  M. Calus,et al.  Reliability of direct genomic values for animals with different relationships within and to the reference population. , 2012, Journal of dairy science.

[31]  Yusheng Zhao,et al.  Accuracy of genomic selection in European maize elite breeding populations , 2011, Theoretical and Applied Genetics.

[32]  Jeffrey B. Endelman,et al.  Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP , 2011 .

[33]  Justin O Borevitz,et al.  Genome-wide association studies in plants: the missing heritability is in the field , 2011, Genome Biology.

[34]  M. Blaxter,et al.  Genome-wide genetic marker discovery and genotyping using next-generation sequencing , 2011, Nature Reviews Genetics.

[35]  Aaron J. Lorenz,et al.  Genomic Selection in Plant Breeding , 2011 .

[36]  D. Grattapaglia,et al.  Genomic selection in forest tree breeding , 2011, Tree Genetics & Genomes.

[37]  Alessandro Liverani,et al.  Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism , 2011, BMC Plant Biology.

[38]  Jean-Luc Jannink,et al.  Genomic selection in plant breeding: from theory to practice. , 2010, Briefings in functional genomics.

[39]  Trevor Hastie,et al.  Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.

[40]  Simon Fraser,et al.  LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms , 2006 .

[41]  M. Goddard,et al.  Reliability of Genomic Predictions Across Multiple Populations , 2009, Genetics.

[42]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[43]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[44]  B. Browning,et al.  A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. , 2009, American journal of human genetics.

[45]  R. Fernando,et al.  Genomic selection of purebreds for crossbred performance , 2009, Genetics Selection Evolution.

[46]  Takeshi Hayashi,et al.  Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms , 2009, Theoretical and Applied Genetics.

[47]  M. Goddard,et al.  Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus Cattle , 2008, Genetics.

[48]  T. Yoshioka,et al.  Citrus hybrid seedlings reduce initial time to flower when grafted onto shiikuwasha rootstock , 2008 .

[49]  M P L Calus,et al.  Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. , 2007, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.

[50]  Jinko Graham,et al.  hapassoc: Software for Likelihood Inference of Trait Associations with SNP Haplotypes and Other Attributes , 2006 .

[51]  M. McMullen,et al.  A unified mixed-model method for association mapping that accounts for multiple levels of relatedness , 2006, Nature Genetics.

[52]  T. Lacombe,et al.  Linkage disequilibrium in cultivated grapevine, Vitis vinifera L , 2006, Theoretical and Applied Genetics.

[53]  P. Gupta,et al.  Linkage disequilibrium and association studies in higher plants: Present status and future prospects , 2005, Plant Molecular Biology.

[54]  H. Hyodo,et al.  Accumulation of Carotenoids and Expression of Carotenoid Biosynthetic Genes during Maturation in Citrus Fruit1 , 2004, Plant Physiology.

[55]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[56]  E. Buckler,et al.  Structure of linkage disequilibrium in plants. , 2003, Annual review of plant biology.

[57]  D. Sengupta.  Linear models , 2003 .

[58]  Manos Mavrikakis,et al.  Electronic structure and catalysis on metal surfaces. , 2002, Annual review of physical chemistry.

[59]  J. Pritchard,et al.  Linkage disequilibrium in humans: models and data. , 2001, American journal of human genetics.

[60]  M. Goddard,et al.  Prediction of total genetic value using genome-wide dense marker maps. , 2001, Genetics.

[61]  M. Kita,et al.  Cloning and Expression of CitPDS1, a Gene Encoding Phytoene Desaturase in Citrus , 2001, Bioscience, biotechnology, and biochemistry.

[62]  C. Economos,et al.  Nutritional and health benefits of citrus fruits , 1999 .

[63]  N. Sakurai,et al.  Relationship between Fruit Softening and Wall Polysaccharides in Avocado (Persea americana Mill) Mesocarp Tissues , 1997 .

[64]  T. Barrette,et al.  Genetic dissection of carotenoid synthesis in arabidopsis defines plastoquinone as an essential component of phytoene desaturation. , 1995, The Plant cell.

[65]  Matthew P. Wand,et al.  Kernel Smoothing , 1995 .

[66]  A. Kanellis,et al.  Regulation of Glutamate Dehydrogenase and Glutamine Synthetase in Avocado Fruit during Development and Ripening , 1994, Plant physiology.

[67]  Donald J. Nevins,et al.  Changes in physical properties and cell wall polysaccharides of tomato (Lycopersicon esculentum) pericarp tissues , 1993 .

[68]  N. Okudai.  Recent Trend in Breeding Medium- and Late-Maturing Citrus in Japan , 1981 .

[69]  C. E. Rogers,et al.  Symbolic Description of Factorial Models for Analysis of Variance , 1973 .

[70]  Robert Willard Hodgson,et al.  Horticultural varieties of citrus , 1967 .

[71]  J. H. Ward.  Hierarchical Grouping to Optimize an Objective Function , 1963 .