Development of papaya chromosome-specific cytogenetic markers and cytogenetic map of papaya sex chromosomes

Abstract

Papaya (2n =2x =18) is a tropical and subtropical fruit tree grown worldwide. In recent years, the papaya genome has been sequenced and genetic maps have become available for analyzing genomic structure of the male-determining region of Y chromosome (MSY). However, research in the cytological aspect lags behind the model crops. One reason for slow cytological progress is because the papaya condensed chromosomes are small and similar in size, making it difficult to distinguish among them based on chromosomal morphology or staining pattern. By probing nine microsatellite marker-tagged BAC clones on papaya chromosome spread using fluorescence in situ hybridization (FISH) techniques, individual papaya metaphase chromosomes were distinguished and integrated with a genetic map. Then, a detailed cytogenetic map was constructed for the papaya sex chromosome (chromosome 1) by probing 15 microsatellite marker-tagged and 2 cytological-feature associated BAC clones on highly resolved papaya pachytene chromosomes. This cytogenetic map integrated the chromosomal features with genetic and physical data. Analysis of recombination rates along chromosome 1 revealed a small non-recombining region (12.2% of chromosome length) where the MSY is located, suggesting that papaya has a pair of young evolving homomorphic sex chromosomes. Sequence analysis of euchromatic and heterochromatic regions on the X chromosome showed an uneven distribution of genes and transposable elements. This cytological information enhances our understanding on the relationship between genome composition and chromosomal structure.