Re: Is there any relation between Chromosome length and Mutation accumulation?

In theory, increased amount of DNA should increase the absolute number of
mutations, but the rate of mutations per base pair should remain the same.
 Most mutations probably occur due to mispairing of bases during
replication; the probability of a given base pairing improperly (for
instance, because it happens to be in a rare tautomeric state during
replication) is constant.  Thus the "per gene" mutation rate shouldn't be
different because of chromosome size.   I suppose there could be
chromosome-bound DNA repair factors (or at least, ones that scan along DNA
more than they diffuse freely through the nucleoplasm), and if they were
allocated on a "per chromosome" basis, then the effective mutation rate
would be higher on large chromosomes than small ones -- but this is quite
speculative.  

In fact, it's not necessary to "imagine" a plant with large and small
chromosomes; the widely cultivated upland cotton, Gossypium hirsutum, is an
ancient allotetraploid, and it actually has two complete genomes.  The A
genome, originating in Old World wild progenitor species, is about twice as
large as the D genome, which originated in the New World.  The homeologous
chromosomes are proportionally larger in the A genome in all cases, due to
the presence of larger amounts of repetitive ("junk"?) DNA (Endrizzi et al.
1985).  In a tetraploid such as this species, a gene in one genome can be
silenced by mutation without phenotypic effect, becoming a pseudogene.  If
there were bias toward higher mutation rate in the genome with smaller
chromosomes, we'd expect more pseudogenes, and fewer expressed genes, in
the D genome of cotton.  Adams et al. (2003) studied 40 homoeologous gene
pairs in cotton.  Of these, 13 showed different expression for the A and D
homeologs; 5 from the A genome were expressed more, 2 from the D genome
were expressed more, and 6 varied in different plant tissues.  This was not
a significant bias toward either homolog, although the trend would be
toward expression of the gene from the larger A genome homolog.  

This experiment looked at expression, rather than actual mutation rates; I
don't know of a study that attempted to test exactly the hypothesis in your
question.  It could possibly be done by looking at divergence between A
genome genes in tetraploid cotton vs their A genome diploid wild relatives,
and the same divergence for D genome genes vs their wild diploid relatives.  

Basically, while it's possible to imagine ways that mutation rates could
differ in chromosomes of different sizes, I don't know of a direct test of
this, and what evidence I could find doesn't support the hypothesis.  

Adams K L, Cronn R, Percifield R, Wendel J F. Proc Natl Acad Sci USA.
2003;100:4649–4654.

Endrizzi, J.D., Turcotte, E.L., and Kohel, R.J. 1985. Genetics, cytology,
and evolution of Gossypium. Adv. Genet. 23: 271–375.