Abstract
Little is known about the extent of allelic diversity of genes in the complex polyploid, sugarcane. Using sucrose phosphate synthase (SPS) Gene (SPS) Family III as an example, we have amplified and sequenced a 400 nt region from this gene from two sugarcane lines that are parents of a mapping population. Ten single nucleotide polymorphisms (SNPs) were identified within the 400 nt region of which seven were present in both lines. In the elite commercial cultivar Q165A, 10 sequence haplotypes were identified, with four haplotypes recovered at 9% or greater frequency. Based on SNP presence, two clusters of haplotypes were observed. In IJ76-514, a Saccharum officinarum accession, 8 haplotypes were identified with 4 haplotypes recovered at 13% or greater frequency. Again, two clusters of haplotypes were observed. The results suggest that there may be two SPS Gene Family III genes per genome in sugarcane, each with different numbers of different alleles. This suggestion is supported by sequencing results in an elite parental sorghum line, 403463-2-1, in which 4 haplotypes, corresponding to two broad types, were also identified. Primers were designed to the sugarcane SNPs and screened over bulked DNA from high and low Sucrose-containing progeny from a cross between Q165A and IJ76-514. The SNP frequency did not vary in the two bulked DNA samples, suggesting that these SNPs from this SPS gene family are not associated with variation in sucrose content. Using an ecotilling approach, two of the SPS Gene Family III haplotypes were mapped to two different linkage groups in homology group 1 in Q165A. Both haplotypes mapped near QTLs for increased sucrose content but were not themselves associated with any sugar-related trait.
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References
Aitken K, Jackson PA, McIntyre CL (2005) Construction of a genetic linkage map of a sugarcane cultivar (Saccharum spp.) using AFLP and SSR markers. Theor Appl Genet 110:789–801
Aitken KS, Jackson PA, McIntyre CL (2006) QTL identified for sugar related traits in a sugarcane (Saccharum spp.) cultivar × S. officinarum population. Theor Appl Genet 112:1306–1317
Bertin P, Gallais A (2001) Genetic variation for nitrogen use efficiency in a set of recombinant inbred lines II␣– QTL detection and coincidences. Maydica 46:53–68
Bureau of Sugar Experiment Stations (1984) The standard laboratory manual for Australian sugar milling. Vol 1. Principles and practices. BSES, Brisbane Australia
Bull TA, Glasziou KT (1963) The evolutionary significance of sugar accumulation in Saccharum. Aust J Biol Sci 16:737–742
Castledon CK, Aoki N, Gillespie VJ, MacRae E, Quick WP, Buchner P, Foyer CH, Furbank RT, Lunn JE (2004) Evolution and function of the sucrose-phosphate synthase gene families in wheat and other grasses. Plant Physiol 135:1753–1764
Causse M, Rocher J-P, Pelleschi S, Barriere Y, de Vienne D, Prioul J-L (1995) Sucrose-phosphate synthase: an enzyme with heterotic activity correlated with maize growth. Crop Sci 35:995–1001
Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786
Cordeiro GM, Eliott F, McIntyre CL, Casu RE, Henry RJ (2006) Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theor App Genet (in press)
Cronn R, Cedroni M, Hasselkorn T, Grover C, Wendel JF (2002) PCR-mediated recombination in amplification products derived from polyploid cotton. Theor App Genet 104:482–489
Dȁ9Hont A, Grivet L, Feldmann P, Rao S, Berding N, Glaszmann J-C (1996) Characterization of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 250:45–413
Dufour P, Deu M, Grivet L, Dȁ9Hont A, Paulet F, Bouet A, Lanaud C, Glaszmann J-C, Hamon P (1996) Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid. Theor Appl Genet 94:409–418
Grivet L, Dȁ9Hont A, Dufour P, Hamon P, Roques D, Glaszmann J-C (1994) Comparative genome mapping of sugar cane with other species within the Andropogoneae Tribe. Heredity 73:500–508
Grivet L, Dȁ9Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC (1996) RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid. Genetics 142:987–1000
Grivet L, Glaszmann JC, Arruda P (2001) Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phophogluconate dehydrogenase genes. Genetics and Mol Biol 24:161–167
Grivet L, Glaszmann JC, Vincentz M, da Silva F, Arruda P (2003) ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes. Theor Appl Genet 106:190–197
Hoisington DA (1992) Laboratory protocols. CIMMYT Applied molecular genetics laboratory. Mexico, D.F. CIMMYT
Ishimaru K, Ono K, Kashiwagi T (2004) Identification of a new gene controlling plant height in rice using the candiate-gene approach. Planta 218:399–395
Leloir LF, Cardini CE (1955) The biosynthesis of sucrose phosphate. J Biol Chem 214:157–165
Ming R, Liu SC, Bowers JE, Moore PH, Irvine JE et al (2002) Construction of a Saccharum consensus genetic␣map from two interspecific crosses. Crop Sci 42:570–583
Oleykowski CA, Mullins CRB, Godwin AK, Yeung AT (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597–4602
Panje RR, Babu CN (1960) Studies in Saccharum spontaneum. Distribution and geographical association of chromosome numbers. Cytologia 25:152–172
Rocher JP, Prioul JL, Lecharny A, Reyss A, Joussaume M (1989) Genetic variability in carbon fixation, sucrose-P-synthase and ADP glucose pyrophosphorylase in maize plants of differeing growth rate. Plant Physiol 89:416–420
Rossi M, Arujo P, Paulet F, Garsmeur O, Dias V, Hui C, Van Sluys MA, Dȁ9Hont A (2003) Genome distribution and characterization of EST derived sugarcane resistance gene analogs. Mol Gen Genom 269:406–419
Sarquis JI, Gonzalez H, Sanchez de Jimenez E, Dunlap JR (1998) Physiological traits associated with mass selection for improved yield in a maize population. Field Crops Res 56:239–246
Seneweerra SP, Basra AS, Barlow EW, Conroy JP (1995) Diurnal regulation of leaf blade elongation in rice by CO2. Plant Physiol 108:1471–1477
Shailaja K, Rathore M, Puri N, Yadav D, Singh NK (2002) PCR amplification of the hypervariable region of wheat triticin genes. J Cereal Sci 35:129–134
Sobral BWS, Braga DPV, LaHood ES, Keim P (1994) Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. Subtribe of the Andropoganeae Dumort. Tribe Theor Appl Genet 87:843–853
Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L, Henikoff S (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4(12):28 July 2004
Walsh PS, Erlich HA, Higuchi R (1992) Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl 1:241–250
Wang DM, Shen B, Liu CJ (2006) False positives – a persistent problem in screening bacterial artificial chromosome library based on PCR amplification in hexaploid wheat (Triticum aestivum L.). Genome (in press)
Worrall AC, Bruneau JM, Summerfelt K, Boersig M, Voelker TA (1991) Expression of maize sucrose phosphate synthase in tomato alters leaf carbohydrate partitioning. Plant Cell 3:1121–1130
Zhu YJ, Komor E, Moore PH (1997) Sucrose accumulation in the sugarcane stem is regulated by the difference between the activities of soluble acid invertase and sucrose phosphate synthase. Plant Physiol 115:609–616
Acknowledgements
This research was undertaken with partial funding from the Cooperative Research Centre for Sugar Industry Innovation Through Biotechnology. We also thank BSES Ltd and CSR Technical Field Department for sugarcane plant material and the Queensland Department of Primary Industries and Fisheries for sorghum plant material.
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McIntyre, C., Jackson, M., Cordeiro, G. et al. The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane. Mol Breeding 18, 39–50 (2006). https://doi.org/10.1007/s11032-006-9012-7
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DOI: https://doi.org/10.1007/s11032-006-9012-7