A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection

Theoretical and Applied Genetics

Volumn 124, Issue 7, 2012, Pages 1229-1240

  Sargent, D J ^a,b   Passey, T ^a   Surbanovski N ^a   Lopez Girona, E ^a   Kuchta, P ^a,c   Davik, J ^d   Harrison, R ^a   Passey, A ^a   Whitehouse, A B ^a   Simpson, D W ^a  

^a EAST MALLING RESEARCH   (United Kingdom)

^b RESEARCH AND INNOVATION CENTRE   (Italy)

^c RESEARCH INSTITUTE OF HORTICULTURE   (Poland)

^d NORWEGIAN INSTITUTE OF BIOECONOMY RESEARCH   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; FRUITS; GENES; GENETIC ENGINEERING; MAPS;

GENE-SPECIFIC MARKERS; GENOME SEQUENCES; MAPPING POPULATIONS; MARKER-ASSISTED BREEDING; MOLECULAR MARKER; MORPHOLOGICAL CHARACTERS; NUMBER OF INVERSIONS; POLYPLOIDISATION;

CULTIVATION;

FRAGARIA; FRAGARIA VESCA; FRAGARIA X ANANASSA;

MICROSATELLITE DNA; PLANT DNA;

ARTICLE; BREEDING; CHROMOSOME MAP; FRAGARIA; GENETIC LINKAGE; GENETIC SELECTION; GENETICS; HOMOZYGOTE; PLANT CHROMOSOME; PLANT GENOME; POLYPLOIDY;

BREEDING; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; FRAGARIA; GENETIC LINKAGE; GENOME, PLANT; HOMOZYGOTE; MICROSATELLITE REPEATS; POLYPLOIDY; SELECTION, GENETIC;

EID: 84865593551     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-011-1782-6     Document Type: Article

References (40)

1. Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA, Miedaner T, Wurschum T (2011) Detection of segregation distortion loci in triticale (×Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genomics 12: 380.
2. Bringhurst RS (1990) Cytogenetics and evolution in American Fragaria. Hortscience 25: 879-881.
3. Chao SM, Zhang WJ, Akhunov E, Sherman J, Ma YQ, Luo MC, Dubcovsky J (2009) Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breed 23: 23-33.
4. Chen ZJ, Ni ZF (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays 28: 240-252.
5. Davis TM, DiMeglio LM, Yang RH, Styan SMN, Lewers KS (2006) Assessment of SSR marker transfer from the cultivated strawberry to diploid strawberry species: functionality, linkage group assignment, and use in diversity analysis. J Am Soc Hortic Sci 131: 506-512.
6. Dettori MT, Quarta R, Verde I (2001) A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 44: 783-790.
7. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101: 9891-9896.
8. Dirlewanger E, Cosson P, Boudehri K, Renaud C, Capdeville G, Tauzin Y, Laigret F, Moing A (2007) Development of a second-generation genetic linkage map for peach [Prunus persica (L.) Batsch] and characterization of morphological traits affecting flower and fruit. Tree Genet Genomes 3: 1-13.
9. Esselink GD, Nybom H, Vosman B (2004) Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method. Theor Appl Genet 109: 402-408.
10. Fedorova NJ (1946) Crossability and phylogenetic relations in the main European species of Fragaria. Compil Natl Acad Sci USSR 52: 545-547.
11. Fishman L, Kelly AJ, Morgan E, Willis JH (2001) A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 4: 1701-1716.
12. Hancock JF, Finn CE, Luby JJ, Dale A, Callow PW, Serce S (2010) Reconstruction of the Strawberry, Fragaria × ananassa, Using Genotypes of F. virginiana and F. chiloensis. Hortscience 45: 1006-1013.
13. Illa E, Sargent DJ, Lopez Girona E, Bushakra J, Cestaro A, Crowhurst R, Pindo M, Cabrera A, van der Knapp E, Iezzoni A, Gardiner S, Velasco R, Arus P, Chagné D, Troggio M (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 11: 9.
14. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (genome database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-D1040.
15. Kuras A, Korbin M (2010) PCo-A analysis of strawberry germplasm used in European breeding programs, based on evaluation of DNA polymorphism of investigated plants. J Fruit Ornam Plant Res 18: 7-16.
16. Lerceteau-Kohler E, Guerin G, Laigret F, Denoyes-Rothan B (2003) Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria × ananassa) using AFLP mapping. Theor Appl Genet 107: 619-628.
17. Lerceteau-Kohler E, Guerin G, Denoyes-Rothan B (2005) Identification of SCAR markers linked to Rca2 anthracnose resistance gene and their assessment in strawberry germplasm. Theor Appl Genet 111: 862-870.
18. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.
19. Nybom H, Esselink GD, Werlemark G, Vosman B (2004) Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L Sect. Caninae DC. Heredity 92: 139-150.
20. Parkin IAP, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171: 765-781.
21. Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L, Sargent DJ, Monfort A, Simpson D, Arus P, Guerin G, Denoyes-Rothan B (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behaviour of the cultivated octoploid strawberry. Genetics 179: 2045-2060.
22. Rousseau-Gueutin M, Gaston A, Ainouche A, Ainouche ML, Olbricht K, Staudt G, Richard L, Denoyes-Rothan B (2009) Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 51: 515-530.
23. Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14: 1163-1175.
24. Sargent DJ, Clarke J, Simpson DW, Tobutt KR, Arus P, Monfort A, Vilanova S, Denoyes-Rothan B, Rousseau M, Folta KM, Brassil NV, Battey NH (2006) An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 112: 1349-1359.
25. Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arús P, Simpson DW, Tobutt KR, Monfort A (2008) The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 51: 120-127.
26. Sargent DJ, Fernandéz-Fernandéz F, Ruiz-Roja JJ, Sutherland BG, Passey A, Whitehouse AB, Simpson DW (2009) A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map. Mol Breed 24: 293-303.
27. Sargent DJ, Kuchta P, Lopez Girona E, Zhang H, Davis TM, Celton JM, Marchese A, Korbin M, Folta KM, Shulaev V, Simpson DW (2011) Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence. Plant Genome 4: 1-13.
28. Senanayake YDA, Bringhurst RS (1967) Origin of Fragaria polyploids I. Cytological analysis. Am J Bot 54: 221-228.
29. Shulaev V, Sargent DJ, Crowhurst RN, Mockler RN, Veilleux RE, Folkerts O, Delcher AL, Jaiswal P, Liston A, Mane SP, Burns P, Mockaitis K, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJG, Williams K, Holt SH, Dickerman A, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Filichkin AAS, Velasco R, Troggio M, Viola R, Borodovsky M, Ashman TL, Aharoni A, Bennetzen J, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW, Fox SE, Givan SA, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Salzberg SL, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Folta KM (2011) Whole genome sequencing and analysis of diploid strawberry, Fragaria vesca, a compact and versatile perennial Rosaceous fruit. Nat Genet 43: 109-116.
30. Spigler RB, Lewers KS, Main DS, Ashman TL (2008) Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity 101: 507-517.
31. Spigler RB, Lewers KS, Johnson AL, Ashman TL (2010) Comparative mapping reveals autosomal origin of sex chromosome in octoploid Fragaria virginiana. J Hered 101: S107-S117.
32. Sugimoto T, Tamaki K, Matsumoto J, Yamamoto Y, Shiwaku K, Watanabe K (2005) Detection of RAPD markers linked to the everbearing gene in Japanese cultivated strawberry. Plant Breed 124: 498-501.
33. van Dijk T, Dubos T, Noordijk Y, Pikunova A, Yilmaz-Temel H, van de Weg E (2010) Increased effectiveness of mapping in octoploid strawberry through quantitative interpretation of SSR data. In: Plant and Animal Genomes XVIII conference Fruit and Nut Crops, San Diego, W257.
34. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42: 833-839.
35. Vera Ruiz EM, Soriano JM, Romero C, Zhebentyayeva T, Terol J, Zuriaga E, Llacer G, Abbott AG, Badenes ML (2011) Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region. Mol Plant Pathol 12: 535-547.
36. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
37. Wang YY, Sun XY, Zhao Y, Kong FM, Guo Y, Zhang GZ, Pu YY, Wu K, Li SS (2011) Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain. Plant Sci 181: 65-75.
38. Weebadde CK, Wang D, Finn CE, Lewers KS, Luby JJ, Bushakra J, Sjulin TM, Hancock JF (2008) Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry. Plant Breed 127: 94-101.
39. Zorrilla-Fontanesi Y, Cabeza A, Dominguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sanchez-Sevilla JF, Amaya I (2011a) Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). Theor Appl Genet 123: 755-778.
40. Zorrilla-Fontanesi Y, Cabeza A, Torres AM, Botella MA, Valpuesta V, Monfort A, Sanchez-Sevilla JF, Amaya I (2011b) Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily. Mol Breed 27: 137-156.