Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China

Tree Genetics and Genomes

Volumn 8, Issue 5, 2012, Pages 975-990

  Cao, Ke ^a   Wang, Lirong ^a   Zhu, Gengrui ^a   Fang, Weichao ^a   Chen, Changwen ^a   Luo, Jing ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Association mapping; Genetic diversity; Linkage disequilibrium; Peach landrace

Indexed keywords

PRUNUS PERSICA;

EID: 84866731814     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-012-0477-8     Document Type: Article

References (60)

1. Abbott AG, Rajapakse S, Sosinski B, Lu ZX, Sossey-Alaoui K, Gannavarapu M, Reighard G, Ballard RE, Baird WV, Scorza R, Callahan A (1997) Construction of saturated linkage maps of peach crosses segregating for characters controlling fruit quality, tree architecture and pest resistance. Acta Horticult 465: 41-49.
2. Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Salakhutdinov IB, Buriev ZT, Saha S, Scheffler BE, Jenkins JN, Abdukarim A (2008) Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92: 478-487.
3. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19: 341-356.
4. Aranzana MJ, Abbassi EK, Howad W, Arus P (2010) Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. Genetics 11: 69.
5. Bailey JS, French AP (1932) The inheritance of certain characters in the peach. Proc Am Soc Hortic Sci 29: 127-130.
6. Barnaud A, Lacombe T, Doligez A (2006) Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theor Appl Genet 112: 708-716.
7. Brummell DA (2006) Cell wall disassembly in ripening fruit. Funct Plant Biol 33(2): 103-119.
8. Cao K, Wang LR, Zhu GR, Fang WC, Cheng CW, Zhao P (2011) Construction of a linkage map and identification of a resistance gene analog markers for root-knot nematode in wild peach, Prunus kansuensis. J Am Soc Hortic Sci 136: 190-197.
9. Celia M, Gogorcena CY, Moreno MA (2010) Phenotypic diversity and relationships of fruit quality traits in peach and nectarine [Prunus persica (L.) Batsch] breeding progenies. Euphytica 171: 211-226.
10. Cheng ZP, Huang HW (2009) SSR fingerprinting Chinese peach cultivars and landraces (Prunus persica) and analysis of their genetic relationships. Sci Hortic-Amsterdam 120: 188-193.
11. Dirlewanger E, Moing A, Rothan C, Svanella L, Pronier V, Guye A, Plomion C, Monet R (1999) Mapping QTL controlling fruit quality in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 98: 18-31.
12. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howard W, Arus P (2004a) Comparative mapping and marker assisted selection in Rosaceae fruit crops. PNAS 101: 9891-9896.
13. Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N, Claverie M, Voisin R, Poizat C, Lafargue B, Baron O, Laigret F, Kleinhentz M, Arus P, Esmenjaud D (2004b) Microsatellite genetic linkage maps of myrobalan plum and an almond-peach hybrid location of root-knot nematode resistance genes. Theor Appl Genet 109(4): 827-838.
14. Esbroeck GA, Bowman DT, May OL, Calhoun DS (1999) Genetic similarity indices for ancestral cotton cultivars and their impact on genetic diversity estimates of modern cultivars. Crop Sci 39(2): 323-328.
15. Etienne C, Rothan C, Moing A, Plomion C, Bodenes C, Dumas LS, Cosson P, Pronier V, Monet R, Dirlewanger E (2002) Candidate genes and QTL for sugar and organic acid content in peach (Prunus persica (L.) Batsch). Theor Appl Genet 105: 145-159.
16. Evanno G, Regaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
17. Fan SH, Bielenberg DG, Zhebentyayeva TN, Reighard GL, Okie WR, Holland D, Abbott AG (2010) Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica). New Phytol 185: 917-930.
18. Faust M, Timon B (1995) Origin and dissemination of peach. Hortic Rev 17: 331-379.
19. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
20. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
21. Hancock JF (2008) Temperate fruit crop breeding: germplasm to genomics. Springer, Heidelberg.
22. Ibrokhim YA, Abdusattor A (2008) Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics 2008: 1-18.
23. Illa E, Eduardo I, Marc Audergon J, Barale F, Dirlewanger E, Li XW, Moing A, Lambert P, Dantec LL, Gao ZS, Poëssel JL, Pozzi C, Rossini L, Vecchietti A, Aruś P, Howad W (2010) Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality. Mol Breed 28(4): 667-682.
24. Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao JS (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121: 475-487.
25. Joobeur T (1998) Construccíon de un mapa de marcadores moleculares y análisis genético de caracteres agronónicos en Prunus. PhD thesis, Universtat de Lleida, Spain.
26. Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118: 979-992.
27. Layne DR, Bassi D (2008) The peach: botany, production and uses. CAB, Cambridge.
28. Lester DR, Sherman WB, Atwell BJ (1996) Endopolygalacturonase and the melting flesh (M) locus in peach. J Am Soc Hortic Sci 121: 231-235.
29. Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
30. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15: 271-289.
31. Mariette S, Tavaud M, Arunyawat U, Capdeville G, Millan M, Salin F (2010) Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. Genetics 11: 77.
32. Mather DE, Hyes PM, Chalmers KJ, Eglinton J, Matus I, Richardson K, Von Zitzewitz J, Marquez-Cedillo L, Hearnden P, Pal N (2004) Use of SSR marker data to study linkage disequilibrium and population structure in Hordeum vulgare: prospects for association mapping in barley. In: International barley genetics symposium, Brno, Czech Republic, pp 302-307.
33. Morgutti S, Negrini N, Nocito FF, Ghiani A, Bassi D, Cocucci M (2006) Changes in endopolygalacturonase levels and characterization of a putative endo-PG gene during fruit softening in peach genotypes with nonmelting and melting flesh fruit phenotypes. New Phytol 171: 315-328.
34. Murayama H, Arikawa M, Sasaki Y, Cin VD, Mitsuhashi W, Toyomasu T (2009) Effect of ethylene treatment on expression of polyuronide-modifying genes and solubilization of polyuronides during ripening in two peach cultivars having different softening characteristics. Postharvest Biol Tec 52(2): 196-201.
35. Nei M, Tajima FA, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19: 153-170.
36. Newell MA, Cook D, Tinker NA, Jannink JL (2011) Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies. Theor Appl Genet 122: 623-632.
37. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30: 190-193.
38. Ogundiwin EA, Peace CP, Gradziel TM, Parfitt DE, Bliss FA, Crisosto CH (2009) A fruit quality gene map of Prunus. BMC Genomics 10: 587.
39. Peace CP, Crisosto CH, Gradziel TM (2005) Endopolygalacturonase: a candidate gene for Freestone and Melting flesh in peach. Mol Breed 16: 21-31.
40. Pritchard JK, Wen W (2004) Documentation for STRUCTURE software. The University of Chicago Press, Chicago.
41. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
42. Pushpendra KG, Sachin R, Pawan LK (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
43. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479-11484.
44. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273: 1516-1517.
45. Rodriguez AJ, Sherman WB, Scorza R, Wisniewski M, Okie WR (1994) "Evergreen" peach, its inheritance and dormant behavior. J Am Soc Hortic Sci 119: 789-792.
46. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
47. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). PNAS 98: 9161-9166.
48. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ESIV (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286-289.
49. Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115: 697-708.
50. Vavilov NI (1951) The origin variation immunity and breeding of cultivated plants. Chron Bot Ronald, New York (translation by K Star Chester).
51. Verde I, Quarta R, Cerdrola C, Dettori MT (2002) QTL analysis of agronomic traits in a BC1 peach population. Acta Horticult 592: 291-297.
52. Wang ZH, Zhuang EJ (2001) Fruit monograph for peach in China. China Forest Press, Beijing.
53. Wang Y, Georgi LL, Reighard GL, Scorza R, Abbott AG (2002) Genetic mapping of the evergrowing gene in peach [Prunus persica (L.) Batsch]. J Hered 93: 352-358.
54. Wang KL, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie TK, Espley RV, Hellens RP, Allan AC (2010) An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol 10: 50.
55. Washington State University (2010) Marker search. Department of Horticulture and Landscape Architecture. Pullman. Washington. US. 10 June 2010. http://www. rosaceae. org/bio/content/?title=&url=/cgi-bin/gdr/gdr_marker_search. cgi&style=width: 950px; height: 1024px.
56. Xie RJ, Li XW, Chai ML, Song LJ, Jia HJ, Wu DJ, Chen MJ, Chen KM, Aranzana MJ, Gao ZS (2010) Evaluation of the genetic diversity of Asian peach accessions using a selected set of SSR markers. Sci Hortic-Amsterdam 125: 622-629.
57. Yamamoto T, Shimada T, Imai T, Yaegaki H, Haji T, Matsuta N, Yamaguchi M, Hayashi T (2001) Characterization of morphological traits based on a genetic linkage map in peach. Breed Sci 51: 271-278.
58. Yeh FC, Yang RC, Boyle T (1999) POPGENE Microsoft windows-based software for population genetic analysis. A joint project development by Fancis C. Yeh and Rong-Cai Yang, University of Alberta and Tim Boyle, Center for International Forestry Research, Bogor, Indonesia.
59. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155-160.
60. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.