QTL-seq identifies an early flowering QTL located near flowering locus T in cucumber

Theoretical and Applied Genetics

Volumn 127, Issue 7, 2014, Pages 1491-1499

  Lu, Hongfeng ^a   Lin, Tao ^a   Klein, Joël ^a,b   Wang, Shenhao ^a   Qi, Jianjian ^a   Zhou, Qian ^a   Sun, Jinjing ^a   Zhang, Zhonghua ^a   Weng, Yiqun ^c   Huang, Sanwen ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGRONOMY; PLANTS (BOTANY);

EXPRESSION LEVELS; FLOWERING LOCUS T; MARKER-ASSISTED SELECTION; MICROSATELLITE MARKERS; MOLECULAR BREEDING; NEXT-GENERATION SEQUENCING; QUANTITATIVE RT-PCR; SEGREGATION ANALYSIS;

GENES;

ARABIDOPSIS; CUCUMIS SATIVUS;

GENETIC MARKER; MICROSATELLITE DNA;

AMINO ACID SEQUENCE; CHROMOSOME MAP; CUCUMBER; FLOWER; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; PHENOTYPE; PLANT CHROMOSOME; PLANT GENOME; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

AMINO ACID SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CUCUMIS SATIVUS; FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENETIC MARKERS; GENOME, PLANT; GENOTYPE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84925555084     PISSN: 00405752     EISSN: 14322242     Source Type: Journal    
DOI: 10.1007/s00122-014-2313-z     Document Type: Article

References (39)

1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M (2012) Genome sequencing reveals agronomically important loci in rice using Mut Map. Nature Biotech 30: 174-178
2. Chambers C, Shuai B (2009) Profiling micro RNA expression in Arabidopsis pollen using micro RNA array and real-time PCR. BMC Plant Biol 9(1): 87
3. Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316: 1030-1033
4. Dijkhuizen A, Staub JE (2002) QTL conditioning yield and fruit quality traits in cucumber (Cucumis sativus L.) effects of environment and genetic background. J New Seeds 4: 1-30
5. Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S et al (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464: 1039-1042
6. Fazio F, Staub JE, Stevens MR (2003) Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Theor Appl Genet 107: 864-874
7. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P (2009) The genome of the cucumber, Cucumis sativus L. Nature Genet 41: 1275-1281
8. Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D (1999) Activation tagging of the floral inducer FT. Science 286(5446): 1962-1965
9. Kong F, Liu B, Xia Z, Sato S, Kim B, Watanabe S, Yamada T, Tabata S, Kanazawa A, Harada K, Abe J (2010) Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol 154: 1220-1231
10. Koornneef M, Alonso-Blanco C, Peeters AJ, Soppe W (1998) Genetic control of flowering time in Arabidopsis. Annu Rev Plant Biol 49: 345-370
11. Lee R, Baldwin S, Kenel F, McCallum J, Macknight R (2013) FLOWERING LOCUS T genes control onion bulb formation and flowering. Nat Commun 4: 2884
12. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760
13. Li Z, Zhang ZH, Yan PC, Huang SW, Fei ZJ, Lin K (2011) RNAseq improves annotation of protein-coding genes in the cucumber genome. BMC Genom 12: 540
14. Li Q, Zhang C, Li J, Wang L, Ren Z (2012) Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus. PLo S One 7(10): e47576
15. Lifschitz E, Eviatar T, Rozman A, Shalit A, Goldshmidt A, Amsellem Z, Alvarez JP, Eshed Y (2006) The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proc Natl Acad Sci USA 103: 6398-6403
16. Lindhout P, Van Heusden S, Pet G, Van Ooijen JW, Sandbrink H, Verkerk R, Vrielink R, Zabel P (1994) Perspectives of molecular marker assisted breeding for earliness in tomato. Euphytica 79: 279-286
17. Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön C-C, Bauer E (2013) BSTA: a targeted approach combines bulked segregant analysis with nextgeneration sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genom 14: 628
18. Lv J, Qi J, Shi Q, Shen D, Zhang S, Shao G, Li H, Sun Z, Weng Y, Shang Y (2012) Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLo S One 7: e46919
19. Maheswaran M, Huang N, Sreerangasamy S, McCouch S (2000) Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa L.). Mol Breed 6: 145-155
20. Miao H, Gu XF, Zhang SP, Zhang ZH, Huang SW, Wang Y, Fang ZY (2012) Mapping QTLs for seedling-associated traits in cucumber. Acta Hort Sinica 39: 879-887
21. 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
22. Murray M, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4326
23. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721-726
24. Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45: 1510-1515
25. Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLo S One 4: e5795
26. Robbins MD, Staub JE (2009) Comparative analysis of markerassisted and phenotypic selection for yield components in cucumber. Theor Appl Genet 119: 621-634
27. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10: 297-304
28. Sato H, Heang D, Sassa H, Koba T (2009) Identification and characterization of FT/TFL1 gene family in cucumber. Breed Sci 59: 3-11
29. Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen J-E, Weigel D, Andersen SU (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6: 550-551
30. Swinnen S, Schaerlaekens K, Pais T, Claesen J, Hubmann G et al (2012) Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooledsegregant whole-genome sequence analysis. Genome Res 22: 975-984
31. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74: 174-183
32. Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K (2007) Hd3a protein is a mobile flowering signal in rice. Science 316: 1033-1036
33. Tanaka Y, Sano T, Tamaoki M, Nakajima N, Kondo N, Hasezawa S (2005) Ethylene inhibits abscisic acid-induced stomatal closure in Arabidopsis. Plant Physiol 138(4): 2337-2343
34. Taoka K, Ohki I, Tsuji H, Kojima C, Shimamoto K (2013) Structure and function of florigen and the receptor complex. Trends Plant Sci 18: 287-294
35. Tatlioglu T (1993) Cucumber Cucumis sativus L. Genetic improvement of vegetable crops. Pergamon Press, Tarrytown, pp 197-234
36. Van Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93(5): 343-349
37. Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C (2002) Map QTL4. 0, software for the calculation of QTL positions on genetic maps. Plant Research International, Wagenigen
38. Weng Y, Johnson S, Staub JE, Huang SW (2010) An extended microsatellite genetic map of cucumber, Cucumis sativus L. Hort Science 45: 880-886
39. Yang Z, Huang D, Tang W, Zheng Y, Liang K, Cutler AJ, Wu WR (2013) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. PLo S One 8(7): e68433