SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes

Schneider K, Weisshaar B, Borschardt DC, Salamini F. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Molecular Breeding. 2001;8(1):63-74.Based on EST sequences, fragments of 37 genes have been amplified and sequenced in two inbred lines of sugar beet. The rate of single nucleotide polymorphisms (SNP) corresponded to 1 every 130 bp, with an average pgr (nucleotide diversity) value of 7.6×10^−3. When extrapolated to the whole sugar beet genome, randomly compared lines differ at 5.4×10^6 SNPs in the genetic pool considered. In a wider search for SNP-related polymorphisms, 96 fragments of expressed genes were scanned with SSCP (single-strand conformation polymorphism) and heteroduplex (HA) analyses in 8 inbred lines. One SSCP or HA polymorphism was found every 1,470 bp of amplified DNA, corresponding to 5×10^5 SSCP or HA loci in the whole genome. This frequency, 11 times lower than the SNP rate, was attributed to the high frequency of base pair substitution along the amplified fragment analysed electrophoretically. Therefore nucleotide variability was further studied by sequencing fragments of 10 genes in the same 8 lines. The results indicate that sugar beet alleles of expressed genes are very frequently organized as robust intragene haplotypes. In the 8 lines analysed, two haplotypes were identified for each of three gene fragments, three haplotypes for six gene fragments and four haplotypes for one gene fragment which is in good correspondence with the number of alleles detected by SSCP and HA analysis. In a cross between two lines, SSCP or HA alleles of expressed genes have 54% probability to be different