Using rice chromosome 1 pseudomolecule as a reference, a minimal tiling path for
the euchromatic arms of sorghum chromosome 3 was constructed, in which 23 contigs
contain an estimated 57.56 Mb of DNA. A total of 409 EST-STS markers and 255
genetic markers have been mapped onto the euchromatic arms providing excellent
integration of the genetic and physical maps. A total of 21 contigs containing 9 ESTSTS
and 35 genetic markers have been constructed across the heterochromatin block of
sorghum chromosome 3 which comprise 16.57 Mb of DNA.
Macrocolinearity between sorghum chromosome 3 and rice chromosome 1 was
examined based on the mapped EST-STS markers. Approximately 85% of the EST-STS
markers were colinear between these two homeologous chromosomes. Estimates of
recombination were also determined, which indicates the existence of recombination
cold and hot spots. Microcolinearity between sorghum chromosome 3 and rice chromosome 1 was
examined at two different levels. In one case, overlapping sorghum BAC pools
orthologous to a 5.1 Mb region of rice chromosome 1 were constructed and sequence
skimmed. Alignment of the sorghum skim sequences to the TIGR rice gene models
revealed ~62% colinearity between the two orthologous regions. In addition, colinearity
between sorghum chromosome 3 and rice chromosome 5 was detected within this region
which is likely due to the segmental homology between rice chromosome 1 and rice
chromosome 5. Microcolinearity between sorghum and rice was also examined by
comparing 2 fully sequenced sorghum chromosome 3 BAC clones to the orthologous
region of rice chromosome 1. In this analysis, ~65% colinearity was detected for
sorghum BAC 82G24 and ~59% colinearity was detected for sorghum BAC 181g10.
Microcolinearity was largely confined to gene coding regions and sequences of exons
displayed the highest percent identities. Small-scale gene rearrangements were also
detected.
Finally, RT-PCR analysis was carried out between a set of colinear and non-colinear
genes from sorghum and rice to determine whether the loss of colinearity between
orthologous genes resulted in a change in transcriptional regulation. No direct link
between loss of colinearity and expression pattern was detected in these experiments.
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/ETD-TAMU-1162 |
| Date | 15 May 2009 |
| Creators | Zhou, Bin |
| Contributors | Klein, Patricia |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | Book, Thesis, Electronic Dissertation, text |
| Format | electronic, application/pdf, born digital |
Page generated in 0.0021 seconds