Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon

Theoretical and Applied Genetics

Volumn 126, Issue 2, 2013, Pages 349-358

  Sherman, Amir ^a   Eshed, Ravit ^a   Harel Beja, Rotem ^a   Tzuri, Galil ^a   Portnoy, Vitaly ^a   Cohen, Shahar ^a   Rubinstein, Mor ^a   Schaffer, Arthur A ^a   Burger, Joseph ^a   Katzir, Nurit ^a   Ophir, Ron ^a  

^a VOLCANI CENTER   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; MAPPING;

BULK SEGREGATION; GENETIC ANALYSIS; GENETIC VARIATION; GERMPLASM COLLECTIONS; MICROARRAY TECHNOLOGIES; SEQUENCE INFORMATIONS;

BIOASSAY;

CUCUMIS;

EID: 84873098084     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1983-7     Document Type: Article

References (63)

1. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1: e60.
2. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57: 289-300.
3. Bernardo A, Bradbury P, Ma H, Hu S, Bowden R, Buckler E, Bai G (2009) Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. BMC Genomics 10: 251.
4. Borevitz JO, Chory J (2004) Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol 7: 132-136.
5. Borevitz JO, Nordborg M (2003) The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol 132: 718-725.
6. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513-523.
7. Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, Sari MA, Collin F, Flowers JM, Pitrat M, Purugganan MD, Dogimont C, Bendahmane A (2008) A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321: 836-838.
8. Brauer MJ, Christianson CM, Pai DA, Dunham MJ (2006) Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics 173: 1813-1816.
9. Burger Y, Saar U, Katzir N, Paris HS, Yeselson Y, Levin I, Schaffer AA (2003) Development of sweet melon (Cucumis melo) genotypes combining high sucrose and organic acid content. J Am Soc Hortic Sci 128: 537-540.
10. Burger Y, Paris HS, Cohen R, Katzir N, Tadmor Y, Lewinsohn E, Schaffer AA (2009) Genetic diversity of Cucumis melo. Hortic Rev 36: 165-198.
11. Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P (2008) Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol 8: 97.
12. Chiang CW, Gajdos ZK, Korn JM, Kuruvilla FG, Butler JL, Hackett R, Guiducci C, Nguyen TT, Wilks R, Forrester T, Haiman CA, Henderson KD, Le Marchand L, Henderson BE, Palmert MR, McKenzie CA, Lyon HN, Cooper RS, Zhu X, Hirschhorn JN (2010) Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples. PLoS Genet 6: e1000866.
13. Danin-Poleg Y, Tadmor Y, Tzuri G, Reis N, Hirschberg J, Katzir N (2002) Construction of a genetic map of melon with molecular markers and horticultural traits, and localization of genes associated with ZYMV resistance. Euphytica 125: 373-384.
14. Das S, Bhat P, Sudhakar C, Ehlers J, Wanamaker S, Roberts P, Cui X, Close T (2008) Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array. BMC Genomics 9: 107.
15. DeCook R, Lall S, Nettleton D, Howell SH (2006) Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics 172: 1155-1164.
16. Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, Staub JE, Zalapa JE, Cuevas HE, Dace G, Oliver M, Boissot N, Dogimont C, Pitrat M, Hofstede R, van Koert P, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Schaffer A, Katzir N, Xu Y, Zhang H, Fukino N, Matsumoto S, Garcia-Mas J, Monforte AJ (2011) A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol 11: 111.
17. Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464: 1039-1042.
18. Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, Oeveren Jv, Peleman J, Buckler E, Eijk Mv (2007) Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Crop Sci 47: S135-S148.
19. 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.
20. Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101: 5-18.
21. Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, Dai N, Yeselson L, Meir A, Libhaber SE, Avisar E, Melame T, van Koert P, Verbakel H, Hofstede R, Volpin H, Oliver M, Fougedoire A, Stalh C, Fauve J, Copes B, Fei Z, Giovannoni J, Ori N, Lewinsohn E, Sherman A, Burger J, Tadmor Y, Schaffer AA, Katzir N (2010) A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theor Appl Genet 121: 511-533.
22. Harris KR, Ling KS, Wechter WP, Levi A (2009) Identification and utility of markers linked to the zucchini yellow mosaic virus resistance gene in watermelon. J Am Soc Hortic Sci 134: 529-534.
23. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan WuZ, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Fang L, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Li S, Zhang X, Wang J, Sun R, Zhang B, Jiang S, Du Y (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41: 1275-1281.
24. Joobeur T, King JJ, Nolin SJ, Thomas CE, Dean RA (2004) The Fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features. Plant J 39: 283-297.
25. Kaczorowski KA, Ki-Seung Kim KS, Diers BW, Hudson ME (2008) Microarray-based genetic mapping using soybean near-isogenic lines and generation of snp markers in the Rag1 aphid-resistance interval. Plant Genome 1: 89-98.
26. Kang ST, Mian MAR (2010) Genetic map of the powdery mildew resistance gene in soybean PI 243540. Genome 53: 400-405.
27. Kim S, Zhao K, Jiang R, Molitor J, Borevitz JO, Nordborg M, Marjoram P (2006) Association mapping with single-feature polymorphisms. Genetics 173: 1125-1133.
28. Kloosterman B, Oortwijn M, Uitdewilligen J, America T, de Vos R, Visser RG, Bachem CW (2010) From QTL to candidate gene: genetical genomics of simple and complex traits in potato using a pooling strategy. BMC Genomics 11: 158.
29. Kubicki B (1962) Inheritance of some characters in muskmelons (Cucumis melo). Genet Polonica 3: 265-274.
30. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT (2007) Single feature polymorphism discovery in rice. PLoS One 2: e284.
31. Luo MZ, Wang YH, Frisch D, Joobeur T, Wing RA, Dean RA (2001) Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome 44: 154-162.
32. Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9: 287.
33. Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A (2009) A transposon-induced epigenetic change leads to sex determination in melon. Nature 461: 1135-11388.
34. Marullo P, Aigle M, Bely M, Masneuf-Pomarede I, Durrens P, Dubourdieu D, Yvert G (2007) Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains. FEMS Yeast Res 7: 941-952.
35. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828-9832.
36. Nieto C, Morales M, Orjeda G, Clepet C, Monfort A, Sturbois B, Puigdomenech P, Pitrat M, Caboche M, Dogimont C, Garcia-Mas J, Aranda MA, Bendahmane A (2006) An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon. Plant J 48: 452-462.
37. Ophir R, Eshed R, Harel-Beja R, Tzuri G, Portnoy V, Burger Y, Uliel S, Katzir N, Sherman A (2010) High-throughput marker discovery in melon using a self-designed oligo microarray. BMC Genomics 11: 269.
38. Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2010) Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genomics 284: 121-136.
39. Pitrat M, Hanelt P, Hammer K (2000) Some comments on infraspecific classification of cultivars of melon. Acta Hortic 510: 29-36.
40. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
41. Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H, Xie B, Gu X, Wang X, Du Y, Jin W, Huang S (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4: e5795.
42. Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L (2005) Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res 15: 284-291.
43. Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R (2005) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 6: R54.
44. Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM (2009) Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics 10: 466.
45. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3.
46. Stepansky A, Kovalski I, Perl-Treves R (1999) Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Syst Evol 217: 313-332.
47. Sweeney JP, Chapman VJ, Hepner PA (1970) Sugar, acid, and flavor in fresh fruits. J Am Diet Assoc 57: 432-435.
48. van Ooijen JW, Voorrips RE (2001) JoinMap® 3. 0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen.
49. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC (2010) Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 107: 12629-12633.
50. Wang Y, Wyllie SG, Leach DN (1996) Chemical Changes during the Development and Ripening of the Fruit of Cucumis melo (Cv. Makdimon). J Agric Food Chem 44: 210-216.
51. Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58: 236-244.
52. Wenger JW, Schwartz K, Sherlock G (2010) Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet 6: e1000942.
53. Wernersson R, Juncker AS, Nielsen HB (2007) Probe selection for DNA microarrays using OligoWiz. Nat Protoc 2: 2677-2691.
54. West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW (2006) High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res 16: 787-795.
55. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW (1998) Direct allelic variation scanning of the yeast genome. Science 281: 1194-1197.
56. Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11: 182.
57. Wu Y, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet 4: e1000212.
58. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3: 579-588.
59. Yang YH, Thorne NP (2003) Normalization for two-color cDNA microarray data. Science and Statistics In: Goldstein DR (ed) A festschrift for terry speed-monograph series, Chapman and Hall/CRC press virginia beach, VA, USA, pp 403-418.
60. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15.
61. Yang SS, Xu WW, Tesfaye M, Lamb JFS, Jung H-JG, Samac DA, Vance CP, Gronwald JW (2009) Single-feature polymorphism discovery in the transcriptome of tetraploid alfalfa. Plant Genome 2: 224-232.
62. Zhang XM, Wu JA, Guo AG, Zhang H, Ma YA, Fang ZY, Wang XW (2010) Molecular mapping of MS-cd1 gene in Chinese kale. Afr J Biotechnol 9: 4550-4555.
63. Zhu T, Salmeron J (2007) High-definition genome profiling for genetic marker discovery. Trends Plant Sci 12: 196-202.