Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

Molecular Breeding

Volumn 36, Issue 4, 2016, Pages

  McCallum, Susan ^a   Graham, Julie ^a   Jorgensen, Linzi ^a   Rowland, Lisa J ^b   Bassil, Nahla V ^c   Hancock, James F ^d   Wheeler, Edmund J ^e   Vining, Kelly ^f   Poland, Jesse A ^g   Olmstead, James W ^h   Buck, Emily ⁱ   Wiedow, Claudia ⁱ   Jackson, Eric ^j   Brown, Allan ^k   Hackett, Christine A ^l  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c USDA ARS National Clonal Germplasm Repository   (United States)

^d MICHIGAN STATE UNIVERSITY   (United States)

^e MBG Marketing   (United States)

^f OREGON STATE UNIVERSITY   (United States)

^g KANSAS STATE UNIVERSITY   (United States)

^h UNIVERSITY OF FLORIDA   (United States)

ⁱ New Zealand Institute for Plant and Food Research Limited Plant and Food Research   (New Zealand)

^j Wheat Innovation Center   (United States)

^k NORTH CAROLINA STATE UNIVERSITY   (United States)

^l BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

more..

Author keywords

Autotetraploid; Genotyping by sequencing; TetraploidMap; Vaccinium corymbosum

Indexed keywords

BIOMARKERS; DNA SEQUENCES; GENES; PLANTS (BOTANY);

AUTOTETRAPLOID; GENETIC MAP; GENOTYPING; GENOTYPING BY SEQUENCING; POLYMORPHIC MARKERS; SIMPLE SEQUENCE REPEATS; SIMPLE SEQUENCE-REPEAT MARKERS; SINGLE NUCLEOTIDES; TETRAPLOIDMAP; VACCINIUM CORYMBOSUM;

ALIGNMENT;

EID: 84961618740     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-016-0443-5     Document Type: Article

References (53)

1. Al-Janabi SM, Honeycutt RJ, McClelland M, Sobral BWS (1992) A genetic linkage map of Saccharum spontaneum L. ‘SES 208’. Genetics 134:1249–1260
2. Barba P, Cadle-Davidson L, Harriman J, Glaubitz JC, Brooks S, Hyma K, Reisch B (2014) Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theor Appl Genet 127:73–84
3. Bielenberg DG, Rau B, Fan S, Gasic K, Abbott A.G, Reighard GL, Okie WR, Wells CE (2015) Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in peach [Prunus persica (L.) Batsch]. PLoS ONE 10(10):e0139406
4. Boches PS, Bassil NV, Rowland LJ (2005) Microsatellite markers for Vaccinium from EST and genomic libraries. Mol Ecol Notes 5:657–660
5. Bradshaw JE, Hackett CA, Pande B, Waugh R, Bryan GJ (2008) QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet 116:193–211
6. Brazelton C (2013) World Acreage and Production. North American Blueberry Council. http://www.chilealimentos.com/2013/phocadownload/Aprocesados_congelados/nabc_2012-world-blueberry-acreage-production.pdf. Accessed 9 Feb 2015
7. Bushakra JM, Bryant DW, Dossett M, Vining KJ, Van Buren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV (2015) A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag4 conferring resistance to the aphid Amphorophora agathonica. Theor Appl Genet 128(8):1631–1646
8. Butruille DV, Boiteux LS (2000) Selection–mutation balance in polysomic tetraploids: impact of double reduction and gametophytic selection on the frequency of subchromosomal localization of deleterious mutations. Proc Natl Acad Sci USA 97:6608–6613
9. Camp WH (1945) The North American blueberries with notes on other groups of Vacciniaceae. Brittonia 5:203–275
10. Castro P, Stafne ET, Clark JR, Lewers KS (2013) Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry. Theor Appl Genet 126(10):2521–2532
11. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
12. Dhanaraj AL, Slovin JP, Rowland LJ (2004) Analysis of gene expression associated with cold acclimation in blueberry floral buds using expressed sequence tags. Plant Sci 166:863–872
13. Die JV, Rowland LJ (2013) Superior cross-species reference genes: a blueberry case study. PLoS ONE 8(9):e73354
14. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379
15. Gallais A (2003) Quantitative genetics and breeding methods in autopolyploid plants. INRA Editions, Paris
16. Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D (2011) An Autotetraploid Linkage Map of Rose (Rosa hybrida) Validated Using the Strawberry (Fragaria vesca) Genome Sequence. PloS ONE 6(5):e20463
17. Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S (2014) Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3: Genes|Genomes|Genet 4(9):1681–1687
18. Gilmore BS, Bassil NV, Hummer KE (2011) DNA extraction protocols from dormant buds of twelve woody plant genera. J Am Pomol Soc 65:201–207
19. Guajardo V, Solis S, Sagredo B, Gainza F, Munoz C, Gasic K, Hinrichsen P (2015) Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 10(5):e0127750
20. Hackett CA, Luo ZW (2003) TetraploidMap: construction of a linkage map in autotetraploid species. J Hered 94:358–359
21. Hackett CA, Bradshaw JE, Meyer RC, McNicol JW, Milbourne D, Waugh R (1998) Linkage analysis in autotetraploid species: a simulation study. Genet Res Camp 71:143–154
22. Hackett CA, Bradshaw JE, McNicol JW (2001) Interval mapping of QTLs in autotetraploid species. Genetics 159:1819–1832
23. Hackett CA, Milne I, Bradshaw JE, Luo ZW (2007) TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species. J Hered 98:727–729
24. Hangun-Balkir Y, McKenney L (2012) Determination of antioxidant activities of berries and resveratrol. Green Chem Lett Rev 5(2):147–153
25. Johnson SA, Arjmandi BH (2013) Evidence for anti-cancer properties of blueberries: a mini review. Anticancer Agents Med Chem 13(8):1142–1148
26. Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C (2003) Construction of two genetic linkage maps in cultivated tetraploidalfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol 3:9
27. Kalt W, Joseph JA, Shukitt-Hale B (2007) Blueberries and human health. A review of the current research. J Am Pomol Soc 61:151–160
28. Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9(1):e1003215
29. Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2000) Predicting parental genotypes and gene segregation for tetrasomic inheritance. Theor Appl Genet 100:1067–1073
30. Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2001) Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157:1369–1385
31. McCormack D, McFadden D (2013) A review of Pterostilbene antioxidant activity and disease modification. Oxid med Cell Longev 2013:575482
32. Megalos BS, Ballington JR (1988) Unreduced pollen frequencies versus hybrid production in diploid- tetraploid Vaccinium crosses. Euphytica 39:271–278
33. Meyer RC, Milbourne D, Hackett CA, Bradshaw JE, McNicol JW, Waugh R (1998) Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans). Mol Gen Genet 259:150–160
34. Nielsen R, Paul JS, Alberechtsen A, Song YS (2011) Genotype and SNP calling from next generation sequencing data. Nat Rev Genet 12:443–451
35. Qu L, Hancock JF, Whallon JH (1998) Evolution in an autopolyploid group displaying predominantly bivalent pairing at meiosis: genomic similarity of diploid Vaccinium darrowii and autotetraploid Vaccinium corymbosum (Ericaceae). Am J Bot 85:698–703
36. Rimando AM, Kalt W, Magee JB, Dewey J, Ballington JR (2004) Resveratrol, pterostilbene, and piceatannol in Vaccinium berries. J Agric Food Chem 52(15):4713–4719
37. Rocher S, Jean M, Castonguay Belzile F (2015) Validation of genotyping by sequencing analysis in populations of tetraploid Alfalfa by 454 sequencing. PLoS ONE 10(6):e0131918
38. Rodriguez-Mateos A, Rendeiro C, Bergillos-Meca T, Tabatabaee S, George TW, Heiss C, Spencer JPE (2013) Intake and time dependence of blueberry flavonoid-induced improvements in vascular function: a randomized, controlled, double-blind, crossover intervention study with mechanistic insights into biological activity. Am J Clin Nutr 98:1179–1191
39. Rowland LJ, Mehra S, Dhanaraj AL, Ogden EL, Arora A (2003) Identification of molecular markers associated with cold tolerance in blueberry. Acta Hort 625:59–69
40. Rowland LJ, Dhanaraj AL, Naik D, Alkharouf N, Matthews B, Arora R (2008) Study of cold tolerance in blueberry using EST libraries, cDNA microarrays, and subtractive hybridization. HortSci 43:1975–1981
41. Rowland LJ, Bell D, Alkharouf N, Bassil N, Drummond F, Beers L, Buck E, Finn C, Graham J, McCallum S, Hancock J, Polashock J, Olmstead J, Main D (2012) Generating genomic tools for blueberry improvement. J Fruit Sci 12:276–287
42. Rowland LJ, Ogden EL, Bassil N, Buck EJ, McCallum S, Graham J, Brown A, Wiedow C, Campbell AM, Haynes KG, Vinyard BT (2014) Construction of a genetic linkage map of an interspecific diploid blueberry population and identification of QTL for chilling requirement and cold hardiness. Mol Breed 34:2033–2048
43. Russell J, Hackett C, Hedley P, Liu H, Milne L, Bayer M, Marshall D, Jorgensen L, Gordon S, Brennan R (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences. Mol Breed 33:835–849
44. Shuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Am Inc 18:233–234
45. Soltis DE, Soltis PS (1993) Molecular data and the dynamic nature of polyploidy. Crit Rev Plant Sci 12:243–273
46. Uitdewilligen J, Wolters AM, D’Hoop B, Borm T, Visser R, Eck H (2013) A next generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8(5):e62355
47. ® 4; Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen
48. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
49. Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA, Sargent DJ (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genom 14:2
50. Welch JE (1962) Linkage in autotetraploid maize. Genetics 47:367–396
51. Winter P, Kahl G (1995) Molecular marker technologies for plant improvement. World J Microbiol Biotechnol 11:438–448
52. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanskley SD (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83:294–300
53. Wu R, Gallo-Meager M, Littell RC, Zeng ZB (2001) A general polyploidy model for analyzing gene segregation in outcrossing tetraploid species. Genetics 159:869–882