Molecular markers for seed colour in Brassica juncea

A detailed RFLP map was used to map QTLs associated with seed colour in Brassica juncea using a doubled-haploid population derived from a cross between a black/brown-seeded cultivar and a yellow-seeded breeding line. Segregation analysis suggested that seed colour was under control of 2 unlinked loci with duplicate gene action. However, QTL analysis revealed 3 QTLs, SC-B4, SC-A10 and SC-A6, affecting seed colour. The QTLs were consistent across environments, and individually explained 43%, 31%, and 16%, respectively, and collectively 62% of the phenotypic variation in the population. Digenic interaction analysis showed that closest flanking locus of QTL SC-B4, wg7b6cNM, had strong epistasis with the locus wg5a1a, which is tightly linked to QTL SC-A6. The interaction of these 2 loci explained 27% of the phenotypic variation in the population, while the whole model explained 84%. In a multiple regression model, the effects of QTL SC-A10, as well as its interaction with other loci, were non-significant, whereas the effects of loci wg7b6cNM and wg5a1a and their interaction were significant. Ninety-eight percent of the DH lines carried the expected alleles of loci wg7b6cNM and wg5a1a for seed colour, confirming that only these 2 loci were linked to seed colour in B. juncea. Four additional digenic interactions significantly affected seed colour, and all 5 digenic interactions were consistent across environments.Key words: epistasis, Brassica juncea, seed colour, quantitative trait loci, molecular mapping.

EST derived PCR-based markers for functional gene homologues in cotton

We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for developing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs amplified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the corresponding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis.Key words: Gossypium arboreum, cotton, expressed sequence tag, PCR, known-function genes.