Geodesic
Informational Support of the Breeding Experiment in Wheat in the WheatPGE System
Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012), pp. 410-424.

Voir la notice de l'article provenant de la source Math-Net.Ru

Modern breeding experiment in plants is based on the information about genome and genetic markers and should provide the collection and management of large amount of phenotypic information. In the current work we describe WheatPGE database that provide informational support of such experiments in wheat including high throughput phenotyping. The database is available at http://wheatdb.org. 
@article{MBB_2012_7_a2,
     author = {M. A. Genaev and A. V. Doroshkov and T. A. Pshenichnikova and E. V. Morozova and A. V. Simonov and D. A. Afonnikov},
     title = {Informational {Support} of the {Breeding} {Experiment} in {Wheat} in the {WheatPGE} {System}},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {410--424},
     publisher = {mathdoc},
     volume = {7},
     year = {2012},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2012_7_a2/}
}
TY  - JOUR
AU  - M. A. Genaev
AU  - A. V. Doroshkov
AU  - T. A. Pshenichnikova
AU  - E. V. Morozova
AU  - A. V. Simonov
AU  - D. A. Afonnikov
TI  - Informational Support of the Breeding Experiment in Wheat in the WheatPGE System
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2012
SP  - 410
EP  - 424
VL  - 7
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MBB_2012_7_a2/
LA  - ru
ID  - MBB_2012_7_a2
ER  - 
%0 Journal Article
%A M. A. Genaev
%A A. V. Doroshkov
%A T. A. Pshenichnikova
%A E. V. Morozova
%A A. V. Simonov
%A D. A. Afonnikov
%T Informational Support of the Breeding Experiment in Wheat in the WheatPGE System
%J Matematičeskaâ biologiâ i bioinformatika
%D 2012
%P 410-424
%V 7
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MBB_2012_7_a2/
%G ru
%F MBB_2012_7_a2
M. A. Genaev; A. V. Doroshkov; T. A. Pshenichnikova; E. V. Morozova; A. V. Simonov; D. A. Afonnikov. Informational Support of the Breeding Experiment in Wheat in the WheatPGE System. Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012), pp. 410-424. http://geodesic.mathdoc.fr/item/MBB_2012_7_a2/

[1] Houle D., Govindaraju D. R., Omholt S., “Phenomics: the next challenge”, Nat. Rev. Genet., 11:12 (2010), 855–866 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/nrg2897'>10.1038/nrg2897</ext-link>

[2] Benfey P. N., Mitchell-Olds T., “From genotype to phenotype: systems biology meets natural variation”, Science, 320:5875 (2008), 495–497 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.1153716'>10.1126/science.1153716</ext-link>

[3] Ajjawi I., Lu Y., Savage L. J., Bell S. M., Last R. L., “Large-scale reverse genetics in Arabidopsis: case studies from the Chloroplast 2010 Project”, Plant Physiol., 152:2 (2010), 529–540 <ext-link ext-link-type='doi' href='https://doi.org/10.1104/pp.109.148494'>10.1104/pp.109.148494</ext-link>

[4] Brachi B., Faure N., Horton M., Flahauw E., Vazquez A., Nordborg M., Bergelson J., Cuguen J., Roux F., “Linkage and association mapping of Arabidopsis thaliana flowering time in nature”, PLoS Genet., 6:5 (2010), e1000940 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pgen.1000940'>10.1371/journal.pgen.1000940</ext-link>

[5] Eberius M., Lima-Guerra J., “High-throughput plant phenotyping — data acquisition, transformation, and analysis”, Bioinformatics: Tools and Applications, eds. D. Edwards et al., Springer Science&Business Media, LLC, 2009, 259–278

[6] Hartmann A., Czauderna T., Hoffmann R., Stein N., Schreiber F., “HTPheno: an image analysis pipeline for high-throughput plant phenotyping”, BMC Bioinformatics, 12 (2011), 148 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1471-2105-12-148'>10.1186/1471-2105-12-148</ext-link>

[7] Doroshkov A. V., Arsenina S. I., Pshenichnikova T. A., Afonnikov D. A., “Primenenie kompyuternoi obrabotki izobrazhenii mikrofotografii lista dlya analiza opusheniya pshenitsy Triticum aestivum L”, Informatsionnyi vestnik VOGiS, 13:1 (2009), 218–226

[8] Vankadavath R. N., Hussain A. J., Bodanapu R., Kharshiing E., Basha P. O., Gupta S., Sreelakshmi Y., Sharma R., “Computer aided data acquisition tool for high-throughput phenotyping of plant populations”, Plant Methods, 5 (2009), 18 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1746-4811-5-18'>10.1186/1746-4811-5-18</ext-link>

[9] Joosen R. V., Kodde J., Willems L. A., Ligterink W., van der Plas L. H., Hilhorst H. W., “GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination”, Plant J., 62:1 (2010), 148–159 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1365-313X.2009.04116.x'>10.1111/j.1365-313X.2009.04116.x</ext-link>

[10] Lu Y., Savage L. J., Larson M. D., Wilkerson C. G., Last R. L., “Chloroplast 2010: a database for large-scale phenotypic screening of Arabidopsis mutants”, Plant Physiol., 155:4 (2011), 1589–1600 <ext-link ext-link-type='doi' href='https://doi.org/10.1104/pp.110.170118'>10.1104/pp.110.170118</ext-link>

[11] Fabre J., Dauzat M., Negre V., Wuyts N., Tireau A., Gennari E., Neveu P., Tisné S., Massonnet C., Hummel I., Granier C., “PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context”, BMC Plant Biol., 11 (2011), 77 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1471-2229-11-77'>10.1186/1471-2229-11-77</ext-link>

[12] Thorisson G. A., Muilu J., Brookes A. J., “Genotype-phenotype databases: challenges and solutions for the post-genomic era”, Nat Rev Genet., 10:1 (2009), 9–18 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/nrg2483'>10.1038/nrg2483</ext-link>

[13] Antofie A., Lateur M., Oger R., Patocchi A., Durel C. E., Van de Weg W. E., “A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase”, Bioinformatics, 23:7 (2007), 882–891 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bioinformatics/btm013'>10.1093/bioinformatics/btm013</ext-link>

[14] Milc J., Sala A., Bergamaschi S., Pecchioni N., “A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database”, Database, 2011 (2012), baq038 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/database/baq038'>10.1093/database/baq038</ext-link>

[15] Carollo V., Matthews D. E., Lazo G. R., Blake T. K., Hummel D. D., Lui N., Hane D. L., Anderson O. D., “GrainGenes 2.0. An improved resource for the small-grains community”, Plant Physiol., 139:2 (2005), 643–651 <ext-link ext-link-type='doi' href='https://doi.org/10.1104/pp.105.064485'>10.1104/pp.105.064485</ext-link>

[16] Sakurai T., Kondou Y., Akiyama K., Kurotani A., Higuchi M., Ichikawa T., Kuroda H., Kusano M., Mori M., Saitou T., Sakakibara H., Sugano S., Suzuki M., Takahashi H., Takahashi S., Takatsuji H., Yokotani N., Yoshizumi T., Saito K., Shinozaki K., Oda K., Hirochika H., Matsui M., “RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function”, Plant Cell Physiol., 52:2 (2011), 265–273 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/pcp/pcq190'>10.1093/pcp/pcq190</ext-link>

[17] Jung S., Menda N., Redmond S., Buels R. M., Friesen M., Bendana Y., Sanderson L. A., Lapp H., Lee T., MacCallum B., Bett K. E., Cain S., Clements D., Mueller L. A., Main D., “The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data”, Database, 2011 (2011), bar051 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/database/bar051'>10.1093/database/bar051</ext-link>

[18] Genaev M. A., Doroshkov A. V., Morozova E. V., Pshenichnikova T. A., Afonnikov D. A., “Kompyuternaya sistema WheatPGE dlya analiza vzaimosvyazi fenotip–genotip–okruzhayuschaya sreda u pshenitsy”, Vavilovskii zhurnal genetiki i selektsii, 15:4 (2011), 784–793

[19] Rogachev S. (data obrascheniya: 23.07.2012) <ext-link ext-link-type='uri' href='http://rsdn.ru/article/patterns/generic-mvc.xml'>http://rsdn.ru/article/patterns/generic-mvc.xml</ext-link>