Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae.

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere-telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere-telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere-telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.

Multilocus epistasis, linkage, and genetic variance in breeding populations with few parents.

In a previous study of maize (Zea mays L.) populations formed from few parents, we found that estimates of genetic variances were inconsistent with a simple additive genetic model. Our objective in the current study was to determine how multilocus epistasis and linkage affect the loss of genetic variance in populations created from a small number of parents (N). In simulation experiments, F(2) individuals from the same single cross were intermated to form progeny populations from N = 1, 2, 4, and 8 parents. Additive gene effects and metabolic flux epistasis due to L = 10, 50, and 100 loci were modeled. For additive, additive-with-linkage, epistatic, and epistasis-with-linkage models, we estimated the ratio between total genetic variance in the progeny population (V(N)) and base population (V(B) as well as the 95th (Delta(95%)) and 75th (Delta(75%)) percentile differences between the estimated V(N)/V(B) and the V(N)/V(B) expected for the additive model. The mean V(N)/V(B) ratio was lower under epistasis than under additivity, indicating that metabolic flux epistasis hastens the decline in genetic variance due to small N. In contrast, Delta(95%) was higher with epistasis than with additivity across the different levels of N and L. Linkage had little effect on the mean V(N)/V(B), whereas it increased Delta(95%) and Delta(75%) under both additivity and epistasis. Smaller N and L led to higher V(N)/V(B) particularly when epistasis was present. Overall, the results indicated that while metabolic flux epistasis led to a faster average decline in genetic variance, it also led to greater variability in this decline to the point that V(N)/V(B)was larger than expected in many populations.