Genetical genomics of quality related traits in potato tubers using proteomics

BMC Plant Biology

Volumn 18, Issue 1, 2018, Pages

  Acharjee, Animesh ^a,b,c   Chibon, Pierre Yves ^a   Kloosterman, Bjorn ^a,f   America, Twan ^a,d   Renaut, Jenny ^e   Maliepaard, Chris ^a   Visser, Richard G F ^a,d  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^c UNIVERSITY HOSPITALS BIRMINGHAM NHS FOUNDATION TRUST   (United Kingdom)

^d CENTRE FOR BIOSYSTEMS GENOMICS   (Netherlands)

^e LUXEMBOURG INSTITUTE OF SCIENCE AND TECHNOLOGY   (Luxembourg)

^f KEYGENE N V   (Netherlands)

Author keywords

Genetical genomics; Potato quality traits; Protein QTL; Proteomics

Indexed keywords

STARCH;

CARBOHYDRATE METABOLISM; FOOD QUALITY; GENETICS; GENOMICS; METABOLISM; PHENOTYPE; PHYSIOLOGY; PLANT TUBER; POTATO; PROTEOMICS;

CARBOHYDRATE METABOLISM; FOOD QUALITY; GENOMICS; PHENOTYPE; PLANT TUBERS; PROTEOMICS; SOLANUM TUBEROSUM; STARCH;

EID: 85043485025     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-018-1229-1     Document Type: Article

References (40)

1. Prat S, Frommer WB, Höfgen R, Keil M, Kossmann J, Köster-Töpfer M, et al. Gene expression during tuber development in potato plants. FEBS Lett. 1990;268:334-8.
2. Visser RGF, Vreugdenhil D, Hendriks T, Jacobsen E. Gene expression and carbohydrate content during stolon to tuber transition in potatoes (Solanum Tuberosum). Physiol Plantarum. 1994;90:285-92.
3. Scott GJBR, Rosegrant M, Bokanga M. Roots and tubers in the global food system: a vision statement to the year 2020.2000; Lima (Peru).
4. Salvato F, Havelund JF, Chen M, Rao RS, Rogowska-Wrzesinska A, Jensen ON, et al. The potato tuber mitochondrial proteome. Plant Physiol. 2014;164:637-53.
5. Kosová K, Vítámvás P, Urban MO, Klíma M, Roy A, Prášil IT, et al. Biological networks underlying Abiotic stress tolerance in temperate crops--a proteomic perspective. Int J Mol Sci. 2015;16:20913-42.
6. Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F. Targeted proteomics approach for precision plant breeding. J Proteome Res. 2016;15:638-46.
7. Bündig C, Jozefowicz AM, Mock HP, Winkelmann T. Proteomic analysis of two divergently responding potato genotypes (Solanum Tuberosum L.) following osmotic stress treatment in vitro. J Proteome. 2016;30:227-41.
8. Folgado R, Panis B, Sergeant K, Renaut J, Swennen R, Hausman JF. Unravelling the effect of sucrose and cold pretreatment on cryopreservation of potato through sugar analysis and proteomics. Cryobiology. 2015;71:432-41.
9. Acharjee A, Kloosterman B, de Vos RCH, Werij JS, Bachem CWB, Visser RGF, et al. Data integration and network reconstruction with omics data using random Forest regression in potato. Anal Chim Acta. 2011;705:56-63.
10. Acharjee A, Kloosterman B, Visser RG, Maliepaard C. Integration of multi-omics data for prediction of phenotypic traits using random forest. BMC Bioinformatics. 2016;5:180.
11. Jansen RC, Nap JP. Genetical genomics: the added value from segregation. Trends Genet. 2001;17:388-91.
12. Doerge RW. Mapping and analysis of quantitative trait loci in experimental populations. Nature review. Genetics. 2002;3:43-52.
13. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 2003;422:297-302.
14. Keurentjes JB, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, et al. The genetics of plant metabolism. Nat Genet. 2006;38:842-9.
15. Kliebenstein DJ. Metabolomics and plant quantitative trait locus analysis-the optimum genetical genomics platform, concepts in plant Metabolomics, Springer; 2007.
16. Mason KE, Hilmer JK, Maaty WS, Reeves BD, Grieco PA, Bothner B, et al. Proteomic comparison of near-isogenic barley (Hordeum Vulgare L.) germplasm differing in the allelic state of a major senescence QTL identifies numerous proteins involved in plant pathogen defense. Plant Physiol Biochem. 2016;109:114-27.
17. Wang J, Chen P, Wang D, Shannon G, Zeng A, Orazaly M, et al. Identification and mapping of stable QTL for protein content in soybean seeds. Mol Breed. 2015;35:92.
18. Qi Z, Hou M, Han X, Liu C, Jiang H, Xin D, et al. Identification of quantitative trait loci (QTLs) for seed protein concentration in soybean and analysis for additive effects and epistatic effects of QTLs under multiple environments. Plant Breed. 2014;133:499-507.
19. Bourgeois M, Jacquin F, Cassecuelle F, Savois V, Belghazi M, Aubert G, et al. A PQTL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition. Proteomics. 2011;11:1581-94.
20. Chen S, Ding G, Wang Z, Cai H, Xu F. Proteomic and comparative genomic analysis reveals adaptability of Brassica Napus to phosphorus-deficient stress. J Proteome. 2015;117:106-19.
21. Gan L, Zhang CY, Wang XD, Wang H, Long Y, Yin YT, et al. Proteomic and comparative genomic analysis of two Brassica Napus lines differing in oil content. J Proteome Res. 2013;12:4965-78.
22. Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire C, et al. Genetical genomics: spotlight on QTL hot spots. PLoS Genet. 2008;4:1-4.
23. Acharjee A. Systems biology and statistical data integration of omics data sets, PhD thesis, Wageningen University, 2003.
24. Celis-Gamboa C. The life cycle of the potato (Solanum tuberosum L.): from crop physiology to genetics. PhD thesis, Wageningen University, 2002.
25. Broman KW, Sen S. A guide to QTL mapping with R/qtl, Springer; 2009.
26. Li J, Ji L. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity. 2005;95:221-7.
27. Haley CS, Knott SA. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity. 1992;69:315-24.
28. Kloosterman B, Anithakumari AM, Chibon PY, Oortwijn M, van der Linden GC, Visser RGF, et al. Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population. BMC Plant Biol. 2012;12:17.
29. Anithakumari AM, Tang J, van Eck HJ, Visser RG, Leunissen JA, Vosman B, et al. A pipeline for high throughput detection and mapping of SNPs from EST databases. Mol Breed. 2010;26:65-75.
30. Chen X, Hackett CA, Niks RE, Hedley PE, Booth C, Druka A, et al. An eQTL analysis of partial resistance to Puccinia Hordei in barley. PLoS One. 2010;5:e8598.
31. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc. 1995;57:289-300.
32. Liu YW, Han CH, Lee MH, Hsu FL, Hou WC. Patatin, the tuber storage protein of potato (Solanum Tuberosum L.), exhibits antioxidant activity in vitro. J Agric Food Chem. 2003;51:4389-93.
33. Brown CR, Kim TS, Ganga HK, De Jong D, Jahn M, et al. Segregation of total carotenoid in high level potato germplasm and its relationship to beta-carotene hydroxylase polymorphism. Am J Potato Res. 2006;83:365-72.
34. Werij JS, Kloosterman B, Celis-Gamboa C, de Vos CH, America T, Visser RG, et al. Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis. Theor Appl Genet. 2007;115:245-52.
35. Chan EK, Rowe HC, Kliebenstein DJ. Understanding the evolution of defense metabolites in Arabidopsis Thaliana using genome-wide association mapping. Genetics. 2010;185:991-1007.
36. Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, Ward JL, et al. System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet. 2009;41:166-7.
37. Hurtado Lopez PX Investigating genotype by environment and QTL by environment interactions for developmental traits in potato, PhD thesis, 2012; Wageningen University, Plant breeding department.
38. Kloosterman B, Oortwijn M, Uitdewilligen J, America T, de Vos R, Visser RGF, et al. From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy. BMC Genomics. 2010;11:158.
39. Wolters AM, Uitdewilligen JG, Kloosterman BA, Hutten RC, Visser RG, van Eck HJ, et al. Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers. Plant Mol Biol. 2010;73:659-71.
40. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, et al. A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot. 2004;55:1671-85.