Article
Sequencing cucumber (Cucumis sativus L.) chloroplast genomes identifies differences between chilling-tolerant and -susceptible cucumber lines
aUSDA/ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr., University of Wisconsin, Madison, WI 53706, USA.
bDepartment of Life Science, Dongguk University, Seoul, 100-715, Korea.
cDepartment of Horticulture, 1575 Linden Dr, University of Wisconsin, Madison, WI 53706, USA.
Corresponding editor: L. Bonen
Published on the web 12 April 2007.
Genome, 2007, 50:(2) 215-225, 10.1139/G07-003
Abstract
Chilling injury in cucumber (Cucumis sativus L.) is conditioned by maternal factors, and the sequencing of its chloroplast genome could lead to the identification of economically important candidate genes. Complete sequencing of cucumber chloroplast (cp)DNA was facilitated by the development of 414 consensus chloroplast sequencing primers (CCSPs) from conserved cpDNA sequences of Arabidopsis (Arabidopsis thaliana L.), spinach (Spinacia oleracea L.), and tobacco (Nicotiana tabacum L.) cpDNAs, using degenerative primer technologies. Genomic sequence analysis led to the construction of 301 CCSPs and 72 cucumber chloroplast-specific sequencing primers (CSSPs), which were used for the complete sequencing of cpDNA of Gy14 (155 525 bp) and ‘Chipper’ (155 524 bp) cucumber lines, which are, respectively, susceptible and tolerant to chilling injury (4 °C for 5.5 h) in the first leaf stage. Comparative cpDNA sequence analyses revealed that 1 sequence span (located between genes trnK and rps16) and 2 nucleotides (located in genes atpB and ycf1) differed between chilling-susceptible and -tolerant lines. These sequence differences correspond to previously reported maternally inherited differences in chilling response between reciprocal F1 progeny derived from these lines. Sequence differences at these 3 cpDNA sites were also detected in a genetically diverse array of cucumber germplasm with different chilling responses. These and previously reported results suggest that 1 or several of these sequences could be responsible for the observed response to chilling injury in cucumber. The comprehensive sequencing of cpDNA of cucumber by CCSPs and CSSPs indicates that these primers have immediate applications in the analysis of cpDNAs from other dicotyledonous species and the investigation of evolutionary relationships.
Keywords: consensus primer, low temperature, maternal inheritance, abiotic stress
References
- Chaw, S.-M., Chang, C.-C., Chen, H.-L., and Li, W.-H.. 2004. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol. Evol. 58: 424–441.
- Chung S-M, Decker-Walters DS, Staub JE. 2003. Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses. Can. J. Bot. 81: 814-832 a Abstract.
- Chung S-M, Staub JE, Fazio G. 2003. Inheritance of chilling injury: a maternally inherited trait in cucumber. J. Am. Soc. Hortic. Sci. 128: 526-530 b ISI.
- Demesure B, Comps B, Thiebaut B, Barriere G, Letouzey J. 1995. A genetic study of Fagus sylvatica L. var. tortuosa Pepin. Ann. Sci. For. (Paris) 52: 103-115 .
- Drescher, A., Ruf, S., Calsa, T., Jr., Carrer, H., and Bock, R. 2000. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 22: 97–104.
- Grivet D, Heinze B, Vendramin GG, Petit RJ. 2001. Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Mol. Ecol. Notes 1: 345-349 .
- Havey MJ. 1997. Predominant paternal transmission of the mitochondrial genome in cucumber. J. Hered. 88: 232-235 ISI.
- Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, et al.. 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217: 185-194 CrossRef, Medline.
- Maier RM, Neckermann K, Igloi GL, Kossel H. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614-628 Medline.
- Maniatis, T., Fritsch, E.F., and Sambrook, J. 1982. Molecular cloning: A laboratory manual. Cold Spring Harbor publisher, Cold Spring Harbor, N.Y.
- Schmitz-Linneweber C, Maier RM, Alcaraz J-P, Cottet A, Herrmann RG, Mache R. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45: 307-315 Medline.
- Staub JE, Serquen FC, Gupta M. 1996. Genetic markers, map construction, and their application in plant breeding. HortScience 31: 729-740 ISI.
- Sthapit BR, Witcombe JR. 1998. Inheritance of tolerance to chilling stress in rice during germination and plumule greening. Crop Sci. 38: 660-665 ISI.
- Vallejos CE, Tanksley SD. 1983. Segregation of isozyme markers and cold tolerance in an interspecific backcross of tomato (Lycopersicon esculentum, Lycopersicon hirsutum). Theor. Appl. Genet. 66: 241-247 ISI.
