Homoeologous pairing and recombination in Solanum lycopersicoides monosomic addition and substitution lines of tomato

We compared meiotic pairing and recombination between tomato ( Lycopersicon esculentum) and homoeologous Solanum lycopersicoides chromosomes in monosomic additions (MAs) and substitution lines (SLs), each representing a single chromosome of the nightshade in a tomato background. Three configurations of each alien chromosome and its two tomato homoeologues were detected by genomic in situ hybridization in MA-7, -8, and -10 at diakinesis/metaphase-I: 1 trivalent (III), 1 bivalent + 1 univalent (II+I), and 3 univalents (3I). The II+I category was by far the most common, and the univalent was from S. lycopersicoides 91-99.5% of the time, indicating a high degree of preferential (homologous) pairing. In the corresponding substitution lines, association of homoeologous chromosomes was much higher (up to 90% of the cells), presumably due to the absence of homologous partners. However, SL-10 showed a surprisingly high frequency of univalents (about 73%). Genome-wide analysis of chromosome pairing revealed a decrease in the average chiasma frequency for both monosomic additions and substitution lines. Recombination between tomato and the nightshade was restricted in all cases, the reduction being more severe in each monosomic addition than in the corresponding substitution line. Recombination rates in the substitutions were less than those observed for the same chromosomes in the first backcross generation. Chromosomes 8 and 10 showed the highest and the lowest rates of homoeologous recombination, respectively. No recombination was detected between markers on the long arm of chromosome 10, presumably due to the presence of a paracentric inversion differentiating the two genomes in this region. The frequency of homoeologous pairing at diakinesis/metaphase-I was significantly higher than the rate of homoeologous recombination detected in the progeny, suggesting a strong selection against recombinant products in meiotic or post-meiotic stages.