28 Papaya
The construction of the papaya hermaphrodite BAC library, made up of 39,168
clones with an average insert size of 132 kb and 13.7X genome coverage, allowed for
a new depth of exploration of the papaya sex chromosomes (Ming et al. 2001). The
HSY was mapped with 225 sex co-segregating AFLP markers on linkage Group 1,
showing severe suppressed recombination in this sex determining region. The SCAR
markers were developed from sex co-segregating AFLP markers, and were used to
screen the BAC library for physical mapping. Those BACs were extended by design-
ing probes from their BAC end sequences to scan the BAC library for overlapping
BACs. Through chromosome walking methods, a rudimentary physical map was
produced with two major and three minor contigs that spanned 2.5 Mb. These efforts
resulted in the discovery that severe suppression of recombination and degeneration
is occurring in 10% of these homologous chromosomes, leading to the conclusion
that these are in fact incipient sex chromosomes (Liu et al. 2004). Next, 50,661 BAC
ends from 26,017 BAC clones were sequenced, allowing for chromosome walk-
ing techniques to be implicated to identify additional BACs in this area of interest
(Lai et al. 2006). The completion of papaya whole genome sequence provided the
resources to expedite the physical map construction for the hermaphrodite HSY and
X-specific regions (Ming et al. 2010). The hermaphrodite BAC library clones were
finger printed and BACs associated with the 2.5 Mb physical maps were used to dis-
cover contigs in the whole genome physical map that could aid in expanding the HSY
through chromosome walking. Probes were designed from HSY BACS to detect
corresponding X and male Y BACs to produce male MSY and the corresponding
X-specific physical maps as well. Some of the BACs located on the HSY as well as
a selection of paired X- and Y-specific BACs were sequenced and investigated. The
HSY BACs showed a deficiency of genes, a large number of retro-elements, and
gene duplication events compared to the X (Yu et al. 2007). Using genes found on
both the HSY and X BACs, the divergence time of the X and Yh chromosomes was
estimated to be between 0.5 and 2.5 MYA, suggesting the sex chromosomes evolved
at the genus or species level (Yu et al. 2008a). The Y and Yh sequences were found
to be nearly identical and likely arose from the same ancestral chromosome, instead
of evolving separately. The divergence time between the Y and Yh chromosomes was
predicted to be 73,000 years (Yu et al. 2008b). In the male-specific regions of the
compared BACs, various chromosomal rearrangements have occurred such as inver-
sions, deletions, insertions, duplications and translocations. To date, the HSY and
corresponding X region of the hermaphrodite have been physically mapped. Each
physical map has only one remaining gap. The HSY physical map has a gap along
Border-A which has been filled on the X physical map. The corresponding X region
has a gap located towards the centre of the physical map between BACs 136D11 and
08K16, which is filled on the HSY physical map. The HSY spans ~8 Mb and the X
spans ~5 Mb.
Earlier hypotheses reported a single gene with three alleles, a group of closely
linked genes, genic balance of sex chromosome over autosomes, classical XY
chromosomes and regulatory elements of the flower development pathway. Recent
advancements in genomic technology make it possible to characterise the genomic
region involved in sex determination at the molecular level. High density linkage
mapping validated the hypothesis that predicted recombination suppression at the