Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales

Abstract

A high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F 2 plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 markers, including 706 microsatellite loci and the morphological marker fruit flesh color, were mapped into nine major and three minor linkage groups. The resulting map spanned 1069.9 cM with an average distance of 1.5 cM between adjacent markers. This sequence-based microsatellite map resolved the very large linkage group 2 (LG 2) of the previous high-density map using amplified fragment length polymorphism markers. The nine major LGs of our map represent papaya's haploid nine chromosomes with LG 1 of the sex chromosome being the largest. This map validates the suppression of recombination at the male-specific region of the Y chromosome (MSY) mapped on LG 1 and at potential centromeric regions of other LGs. Segregation distortion was detected in a large region on LG 1 surrounding the MSY region due to the abortion of the YY genotype and in a region of LG6 due to an unknown cause. This high-density sequencetagged genetic map is being used to integrate genetic and physical maps and to assign genome sequence scaffolds to papaya chromosomes. It provides a framework for comparative structural and evolutional genomic research in the order Brassicales. Papaya is a perennial plant species that flowers as early as 3 months and produces fruit in 9 months; it is trioecious with an intriguing sex determination system with three basic sex types: male, female, and hermaphrodite. A high-density genetic map of papaya, constructed using 1498 AFLP and three morphological markers revealed severe suppression of recombination at the sex determination locus with 225 cosegregating markers accounting for 66% of the markers on linkage group 1 (LG 1) and 15% of the markers genomewide . This AFLP map provided a critical piece of evidence for defining the primitive Y chromosome in papaya . Sequence comparison of Y-specific fragments from males and hermaphrodites confirmed that 1

Comparative Genetic Mapping Points to Different Sex Chromosomes in Sibling Species of Wild Strawberry (Fragaria)

“…Furthermore, sex chromosomes have diverged within one section of the genus, with species Silene diclinis possessing neo-sex chromosomes, while two sister species (S. latifolia and S. dioica) have only the ancestral state (Howell et al 2009). Despite the wide phylogenetic distribution of dioecy and sex chromosomes in flowering plants (Charlesworth 2002), only a handful have been the subject of genetic mapping studies (grape: Telgmann-Rauber et al 2007; papaya: Sondur et al 1996;Ma et al 2004;Chen et al 2007; kiwifruit: Testolin et al 2001), and even fewer have been the subject of comparative analyses that can inform on other evolutionary dynamics (e.g., Rumex: Navajas- Perez et al 2005;Cunado et al 2007; Silene: Howell et al 2009;papaya: Yu et al 2008a;Wu et al 2010).…”

Genetic-molecular characterization of backcross generations for sexual conversion in papaya (Carica papaya L.)

“…Eighty-four genomic regions containing microsatellite sequences were analyzed, of which only 20 showed well-defined differentiation between the parents. These regions were accessed from SSR primers developed by Eustice et al (2008), whose genomic locations were determined by genetic mapping performed by Chen et al (2007).…”

“…The characteristics of the primers and their disposition among the linkage groups (LG) as described by Chen et al (2007) are summarized in Table 1. Of the 20 regions accessed by the primers, 4 were genic regions located in LG3 (1), LG5 (1), and LG7 (2).…”

“…Additionally, their genomic distribution, evolutionary dynamics, biological function, and practical utility have been examined in several studies (Guichoux et al, 2011). In the papaya tree, hundreds of microsatellites have already been identified and characterized (Eustice et al, 2008;Oliveira et al, 2010), and the genomic location of many microsatellites has been determined by genetic mapping (Chen et al, 2007).…”

Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing

“…A total of 114 primers were analyzed, of which only 20 provided a well-defined distinction between the parents. Such SSR markers have been developed by Eustice et al (2008) from the genetic mapping performed by Chen et al (2007).…”