Zhou, Bin (2006-12). Construction of a minimal tiling path across the euchromatic arms of sorghum chromosome 3 and comparative analysis with the rice chromosome 1 pseudomolecule. Doctoral Dissertation. Thesis uri icon

abstract

  • 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.
  • 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.

publication date

  • December 2006