The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane
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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.
KeywordsSugarcane SNP Sucrose phosphate synthase Ecotilling Sugar Sorghum
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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.
- 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 112:1306–1317Google Scholar
- Bertin P, Gallais A (2001) Genetic variation for nitrogen use efficiency in a set of recombinant inbred lines II␣– QTL detection and coincidences. Maydica 46:53–68Google Scholar
- Bureau of Sugar Experiment Stations (1984) The standard laboratory manual for Australian sugar milling. Vol 1. Principles and practices. BSES, Brisbane AustraliaGoogle Scholar
- Bull TA, Glasziou KT (1963) The evolutionary significance of sugar accumulation in Saccharum. Aust J Biol Sci 16:737–742Google Scholar
- Cordeiro GM, Eliott F, McIntyre CL, Casu RE, Henry RJ (2006) Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theor App Genet (in press)Google Scholar
- 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 250:45–413Google Scholar
- 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 24:161–167Google Scholar
- Hoisington DA (1992) Laboratory protocols. CIMMYT Applied molecular genetics laboratory. Mexico, D.F. CIMMYTGoogle Scholar
- Panje RR, Babu CN (1960) Studies in Saccharum spontaneum. Distribution and geographical association of chromosome numbers. Cytologia 25:152–172Google Scholar
- Seneweerra SP, Basra AS, Barlow EW, Conroy JP (1995) Diurnal regulation of leaf blade elongation in rice by CO2. Plant Physiol 108:1471–1477Google Scholar
- 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 87:843–853Google Scholar
- 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 2004Google Scholar
- 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)Google Scholar