Sequence variation and haplotype structure at the putative flowering-time locus COL1 of Brassica nigra

Motivated by a previous study indicating that polymorphism at an indel, Ind2, within the Brassica nigra COL1 gene is significantly associated with flowering time, we searched for evidence of selection in a sample of 41 complete sequences of B. nigra COL1. The within-gene population recombination rate is moderate, and all neutrality tests used in the present study failed to detect departure from the standard neutral model or evidence of selection. The haplotype structure of the 5'-half of the gene is primarily associated with the demographic history of the species and more specifically with the split between European and Ethiopian populations. whereas the structure of the 3'-half reflects the polymorphism at Ind2. This could be the result of selection or a combination of recombination and migration during the history of the sample of sequences. Without additional information on polymorphism in flanking areas, these two alternatives are difficult to tell apart. If selection acted on the gene, we suggest that if the indel itself is not the target of selection, among the polymorphic sites cosegregating with the polymorphism at Ind2, replacement polymorphisms around sites 890 and 1260 are the most likely quantitative trait nucleotides within the gene.