Next generation mapping of enological traits in an F2 interspecific grapevine hybrid family

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Yang, Shanshan ^a   Fresnedo Ramírez, Jonathan ^b   Sun, Qi ^b   Manns, David C ^c   Sacks, Gavin L ^a   Mansfield, Anna Katharine ^c   Luby, James J ^d   Londo, Jason P ^e   Reisch, Bruce I ^a   Cadle Davidson, Lance E ^e   Fennell, Anne Y ^f,g  

^a Department of Obstetrics Gynecology   (United States)

^b School of Operations Research and Industrial Engineering   (United States)

^c New York State Agricultural Experiment Station   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

^f SOUTH DAKOTA STATE UNIVERSITY   (United States)

^g BioSNTR   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; CULTIVAR; FRUIT COLOR; GENE MAPPING; GENETIC LINKAGE; GENETIC MARKER; GENETIC TRAIT; GENOTYPE; HETEROZYGOSITY; INTERSPECIFIC HYBRID; MEASUREMENT ACCURACY; NONHUMAN; PLANT GENOME; PROGENY; QUANTITATIVE TRAIT LOCUS MAPPING; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; VITIS; VITIS RIPARIA; CHIMERA; FRUIT; GENETICS; HETEROZYGOTE; QUANTITATIVE TRAIT;

CHIMERA; FRUIT; HETEROZYGOTE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; VITIS;

EID: 84962327695     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0149560     Document Type: Article

References (75)

1. Bell S-J, Henschke PA. Implications of nitrogen nutrition for grapes, fermentation and wine. Aust J Grape Wine Res. 2005; 11(3): 242-95. doi:10.1111/j.1755-0238.2005.tb00028.x
2. Mahanil S, Ramming D, Cadle-Davidson M, Owens C., Garris A, Myles S, et al Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. Theoret Appl Genet. 2012; 124(1): 23-33. doi:10.1007/s00122-011-1684-7
3. Sacks GL, Acree TE, M.T. K, Vanden Heuvel JE, Wilcox WF, editors. Tell me about your childhood" - the role of the vineyard in determining wine flavour chemistry. 15th Australian wine industry technical conference; 2013; Sydney, New South Wales, Australia.
4. Ugliano M, Henschke P. Yeasts and wine flavour. In: Moreno-Arribas MV, Polo MC, editors. Wine chemistry and biochemistry: Springer New York; 2009. p. 313-92.
5. Reisch B, Owens C, Cousins P. Grape. In: Badenes ML, Byrne DH, editors. Fruit breeding. Handbook of plant breeding. Springer US; 2012. p. 225-262.
6. Young PR, Vivier MA Genetics and genomic approaches to improve grape quality for winemaking. In: Reynolds AG, editor. Managing wine quality: Woodhead Publishing; 2010. p. 316-364.
7. Di Gaspero G, Cattonaro F. Application of genomics to grapevine improvement. Aust J Grape Wine Res. 2010; 16:122-130. doi:10.1111/j.1755-0238.2009.00072.x
8. Sawler J, Reisch B, Aradhya MK, Prins B, Zhong GY, Schwaninger H, et al. Genomics assisted ancestry deconvolution in grape. PLoS One. 2013; 8(11): e80791. doi: 10.1371/journal.pone.0080791 PMID: 24244717
9. Jackson RS. Wine science: Principles and applications. 4th ed. San Diego: Academic Press; 2014.
10. Myles S. Improving fruit and wine: what does genomics have to offer? Trends Genet. 2013; 29(4): 190-196. doi: 10.1016/j.tig.2013.01.006 PMID: 23428114
11. Myles S, Boyko AR, Owens CL, Brown P.J., Grassi F., Aradhya MK, et al. Genetic structure and domestication history of the grape. Proc Natl Acad Sci USA. 2011; 108(9): 3530-3535. doi: 10.1073/pnas.1009363108 PMID: 21245334
12. Sun Q, Gates MJ, Lavin E.H., Acree TE, Sacks GL. Comparison of odor-active compounds in grapes and wines from Vitis vinifera and non-foxy American grape species. J Agric Food Chem. 2011; 59(19): 10657-10664. doi: 10.1021/jf2026204 PMID: 21879766
13. Boulton R, Singleton V, Bisson L., Kunkee R. Preparation of musts and juice. Principles and practices of winemaking: Springer US; 1999. p. 65-101.
14. Volschenkla H, Van Vuuren H, Viljoen-Bloom M. Malic acid in wine: origin, function and metabolism during vinification. SAfr J Enol Vitic. 2006; 27(2): 123-136.
15. Kliewer WM. Concentration of Tartrates, Malates, Glucose and Fructose in the Fruits of the Genus Vitis. Am J Enol Vitic. 1967; 18(2): 87-96.
16. Jackson D. Climate, monographs in cool climate viticulture-2. Daphne Brasell NZ. 2001.
17. Brice C, Sanchez I, Bigey F, Legras JL, Blondin B. A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genomics. 2014; 15:495. doi: 10.1186/1471-2164-15-495 PMID: 24947828
18. Stewart ACH. Nitrogen composition of interspecific hybrid and Vitis vinifera wine grapes from the Eastern United States. Ph.D. Dissertation. Purdue University; 2013. Available: http://docs.lib.purdue.edu/dissertations/AAI3592130/.
19. Song S, del Mar Hernández M, Provedo I, Menéndez C. Segregation and associations of enological and agronomic traits in Graciano × Tempranillo wine grape progeny (Vitis vinifera L.). Euphytica. 2014; 195(2): 259-277. doi:10.1007/s10681-013-0994-z
20. Chen J, Wang N, Fang L-C, Liang Z-C, Li S-H, Wu B-H. Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries. BMC Plant Biol. 2015; 15: 28. doi: 10.1186/s12870-015-0428-2 PMID: 25644551
21. Viana AP, Riaz S, Walker MA. Genetic dissection of agronomic traits within a segregating population of breeding table grapes. Genet Mol Res. 2013; 12(2): 951-964. doi: 10.4238/2013.April.2.11 PMID: 23613241
22. Huang Z, Ough CS Effect of Vineyard Locations, Varieties, and Rootstocks on the Juice Amino Acid Composition of Several CultivarsAm J Enol ViticAm J Enol Vitic. 1989; 40(2): 135-139.
23. Grattapaglia D, Bertolucci FL, Sederoff RR Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. TheorAppl Genet. 1995; 90(7-8): 933-947. doi: 10.1007/BF00222906 PMID: 24173047
24. Adam-Blondon A.F., Roux C, Claux D., Butterlin G, Merdinoglu D, This P. Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. TheorAppl Genet. 2004; 109(5): 1017-1027. doi: 10.1007/s00122-004-1704-y PMID: 15184982
25. Barba P, Cadle-Davidson L, Harriman J., Glaubitz JC, Brooks S, Hyma K, et al Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. TheorAppl Genet. 2014; 127(1): 73-84. doi: 10.1007/s00122-013-2202-x PMID: 24072208
26. Doligez A, Adam-Blondon AF, Cipriani G., Di Gaspero G, Laucou V, Merdinoglu D., et al. An integrated SSR map of grapevine based on five mapping populations. TheorAppl Genet. 2006; 113(3): 369-82. doi: 10.1007/s00122-006-0295-1 PMID: 16799809
27. Wang N, Fang LC, Xin H.P., Wang LJ, Li SH. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC Plant Biol. 2012; 12:148. doi: 10.1186/1471-2229-12-148 PMID: 22908993
28. Fennell A, Mathiason K, Luby J. Genetic segregation for indicators of photoperiod control of dormancy induction in Vitis species. Acta Hortic. 689. 2005; p. 533-540. doi:10.17660/ActaHortic.2005.689.66
29. Garris A, Clark L, Owens C, McKay S, Luby J, Mathiason K, et al. Mapping of photoperiod-induced growth cessation in the wild grape Vitis riparia. J Am Soc Hortic Sci. 2009; 134(2): 261-272.
30. Fennell AY, Schlauch KA, Gouthu S, Deluc L.G., Khadka V, Sreekantan L, et al. Short day transcriptomic programming during induction of dormancy in grapevine. Front. Plant Sci. 2015; 6:834. doi:10.3389/fpls.2015.00834
31. Mathiason K, He D, Grimplet J., Venkateswari J, Galbraith DW, Or E, et al Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. Funct Integr Genomics. 2009; 9(1): 81-96. doi: 10.1007/s10142-008-0090-y PMID: 18633655
32. Sreekantan L, Mathiason K, Grimplet J., Schlauch K, Dickerson JA, Fennell AY Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning. Plant Mol Biol. 2010; 73(1-2): 191-205. doi: 10.1007/s11103-010-9611-x PMID: 20151315
33. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, et al. TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS One. 2014; 9(2): e90346. doi: 10.1371/journal.pone.0090346 PMID: 24587335
34. Swarts K, Li HH, Navarro JAR, An D, Romay M.C., Hearne S., et al. Novel Methods: to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants. Plant Genome. 2014; 7(3). doi:10.3835/plantgenome2014.05.0023
35. Elshire RJ, Glaubitz JC, Sun Q, Poland J.A., Kawamoto K., Buckler ES, et al. A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS One. 2011; 6(5): e19379. doi: 10.1371/journal.pone.0019379 PMID: 21573248
36. Azuma A, Kobayashi S, Mitani N, Shiraishi M, Yamada M, Ueno T, et al. Genomic and genetic analysis of Myb-related genes that regulate anthocyanin biosynthesis in grape berry skin. Theor Appl Genet. 2008; 117(6): 1009-1019. doi: 10.1007/s00122-008-0840-1 PMID: 18651125
37. Cardoso S, Lau W, Dias J.E., Fevereiro P., Maniatis N. A Candidate-Gene Association Study for Berry Colour and Anthocyanin Content in Vitisvinifera L. PLoS One Sep 28. 2012; 7(9): e46021. doi: 10.1371/journal.pone.0046021 PMID: 23029369
38. Salmaso M, Malacarne G, Troggio M., Faes G, Stefanini M, Grando M.S., et al. A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes. Theor Appl Genet. 2008; 116(8): 1129-1143. doi: 10.1007/s00122-008-0741-3 PMID: 18347774
39. Castellari M, Versari A, Spinabelli U., Galassi S, Amati A. An improved HPLC method for the analysis of organic acids, carbohydrates, and alcohols in grape musts and wines. J Liq Chromatogr Relat Technol. 2000; 23(13): 2047-2056. doi:10.1081/Jlc-100100472
40. Jaillon O, Aury JM, Noel B, Policriti A., Clepet C, Casagrande A, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161): 463-467. doi: 10.1038/nature06148 PMID: 17721507
41. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-1760. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
42. Danecek P, Auton A, Abecasis G., Albers CA, Banks E, DePristo MA, et al The variant call format and VCFtools. Bioinformatics. 2011; 27(15): 2156-8. doi: 10.1093/bioinformatics/btr330 PMID: 21653522
43. Bradbury PJ, Zhang Z, Kroon D.E., Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19): 2633-2635. doi: 10.1093/bioinformatics/btm308 PMID: 17586829
44. Van Ooijen J. Join Map® 4. Software for the calculation of genetic linkage maps in experimental populations. Version 4.1. Wageningen, The Netherlands: Kyazma; 2006.
45. Wu R, Ma C-X, Painter I, Zeng Z-B. Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Popul Biol. 2002; 61(3): 349-363. doi:10.1006/tpbi.2002.1577
46. Van Ooijen J. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res. 2011; 93(5): 343-349. doi:10.1017/S0016672311000279
47. Broman KW, Wu H, Sen S., Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003; 19(7): 889-890. doi: 10.1093/Bioinformatics/Btg112 PMID: 12724300
48. R Core Team. R: A language and environment for statistical computing. Version 3.1.2. Vienna, Austria: R Foundation for statistical computing; 2014.
49. Boer MP, Malosetti M, Welham S.J., Thissen JTNM. Part 2: Statistical genetics and QTL estimation. In: Payne RW, Harding SA, Murray DA, Soutar DM, Baird DB, Glaser AI, et al., editors. The guide to Gen-Stat release 17. Hemel Hempstead, UK: VSN International; 2014.
50. VSN International. GenStat for Windows 17th edition. Hemel Hempstead, UK: VSN International; 2014.
51. Broman KW, Sen S. A guide to QTL mapping with R/qtl: Springer; 2009.
52. Li J, Ji L. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity. 2005; 95(3): 221-7. doi: 10.1038/Sj.Hdy.6800717 PMID: 16077740
53. Malosetti M, Voltas J, Romagosa I., Ullrich SE, van Eeuwijk FA. Mixed models including environmental covariablesforstudyingQTLby environment interaction. Euphytica. 2004; 137(1):139-145. doi:10.1023/B:Euph.0000040511.46388.Ef
54. Boer MP, Wright D, Feng L., Podlich DW, Luo L, Cooper M, et al A mixed-model quantitative trait loci (QTL) analysis for multiple-environment trial data using environmental covariables for QTL-by-environment interactions, with an example in maize. Genetics. 2007; 177(3): 1801-1813. doi: 10.1534/genetics.107.071068 PMID: 17947443
55. Lynch M, Walsh B. Genetics and analysis of quantitative traits. Sunderland, Mass. Sinauer; 1998.
56. Neto EC, Broman AT, Keller M.P., Attie AD, Zhang B, Zhu J, et al Modeling causality for pairs of phenotypes in system genetics. Genetics. 2013; 193(3): 1003-1013. doi: 10.1534/Genetics.112.147124/-/Dc1 PMID: 23288936
57. Neto EC, Yandell BS qtlhot: Inference for QTL Hotspots. 2013. R package version 0.9.0. Available: http://CRAN.R-project.org/package=qtlhot.
58. Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color. Science. 2004; 304(5673): 982. doi: 10.1126/science.1095011 PMID: 15143274
59. Myles S, Chia J-M, Hurwitz B, Simon C, Zhong GY, Buckler E, et al. Rapid genomic characterization of the genus Vitis. PLoSOne. 2010 January 13, 2010; 5(1): e8219. doi: 10.1371/journal.pone.0008219 PMID: 20084295
60. Plomion C, Durel C. Estimation of the average effects of specific alleles detected by the pseudo-testcross QTL mapping strategy. Genet Sel EVol. 1996; 28(3): 1-13. doi:10.1186/1297-9686-28-3-223
61. 2 populations. TheorAppl Genet. 1995; 90(1): 81-89. doi: 10.1007/BF00220999 PMID: 24173787
62. Staub JE, Serquen FC, Gupta M. Genetic markers, map construction, and their application in plant breeding. HortScience. 1996; 31(5): 729-741.
63. Van Ooijen J., Jansen J. Genetic mapping in experimental populations. Cambridge: Cambridge University Press; 2013.
64. Morgante M, De Paoli E, Radovic S. Transposable elements and the plant pan-genomes. Curr Opin Plant Biol. 2007; 10(2):149-155. doi: 10.1016/j.pbi.2007.02.001 PMID: 17300983
65. Ugliano M, Kolouchova R, Henschke PA Occurrence of hydrogen sulfide in wine and in fermentation: influence of yeast strain and supplementation of yeast available nitrogen. J Ind Microbiol Biotechnol. 2011; 38(3): 423-429. doi: 10.1007/s10295-010-0786-6 PMID: 20668912
66. Nisbet MA, Martinson TE, Mansfield AK Accumulation and Prediction of Yeast Assimilable Nitrogen in New York WinegrapeCultivars. Am J Enol Vitic. 2014; 65(3): 325-332. doi:10.5344/ajev.2014.13130
67. Kanellis A, Roubelakis-Angelakis K. Grape. Biochemistry of fruit ripening: Springer; 1993. p. 189-234.
68. Sweetman C, Deluc LG, Cramer G.R., Ford CM, Soole KL. Regulation of malate metabolism in grape berry and other developing fruits. Phytochemistry. 2009; 70(11-12): 1329-1344. doi: 10.1016/j.phytochem.2009.08.006 PMID: 19762054
69. Banerjee S, Yandell BS, Yi NJ Bayesian quantitative trait loci mapping for multiple traits. Genetics. 2008; 179(4): 2275-2289. doi: 10.1534/Genetics.108.088427 PMID: 18689903
70. Xu CW, Li ZK, Xu SZ Joint mapping of quantitative trait loci for multiple binary characters. Genetics. 2005; 169(2): 1045-1059. doi: 10.1534/Genetics.103.019406 PMID: 15489509
71. Yang RQ, Li JH, Xu SZ Mapping quantitative trait loci for traits defined as ratios. Genetica. 2008; 132 (3): 323-329. doi: 10.1007/S10709-007-9175-0 PMID: 17671840
72. Zhu W, Zhang H. Why do we test multiple traits in genetic association studies? J Korean Stat Soc. 2009; 38(1): 1-10. doi: 10.1016/j.jkss.2008.10.006 PMID: 19655045
73. Yang RQ, Jin TB, Li WB Mapping genome-wide QTL of ratio traits with Bayesian shrinkage analysis for its component traits. Genetica. 2010; 138(8): 853-860. doi: 10.1007/S10709-010-9468-6 PMID: 20556635
74. Khan SA, Beekwilder J, Schaart J.G., Mumm R., Soriano JM, Jacobsen E, et al. Differences in acidity of apples are probably mainly caused by a malic acid transporter gene on LG16. Tree Genet Genomes. 2013; 9(2): 475-487. doi:10.1007/S11295-012-0571-Y
75. Jiang C, Zeng ZB Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics. 1995; 140(3): 1111-1127. PMID: 7672582