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.

Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum.

Sorghum halepense L. (johnsongrass) is one of the world's most noxious weeds, and a paradigm for the potential dangers of crop-weed hybridization. Introduced into the southeastern United States about 200 years ago, S. halepense is a close relative of cultivated sorghum (Sorghum bicolor). Both artificial crossing and experimental field studies have demonstrated the potential for S. halepensex S. bicolor hybrid formation, but no prior study has addressed the long-term persistence of sorghum genes in johnsongrass populations. We surveyed 283 loci (on all 10 sorghum linkage groups) to identify 77 alleles at 69 loci that are found in US sorghum cultivars but are absent from a worldwide sampling of johnsongrass genotypes. These putatively cultivar-specific alleles were present in up to 32.3% of individuals in johnsongrass populations adjacent to long-term sorghum production fields in Texas and Nebraska. Lower frequencies of cultivar-specific alleles at smaller numbers of loci are found in johnsongrass populations from New Jersey and Georgia with no recent exposure to cultivated sorghum, suggesting that introgressed sorghum alleles may be dispersed across long distances. The number of cultivar-specific alleles and extensive multilocus patterns of cultivar-specific allelic composition observed at both linked and unlinked loci in the johnsongrass populations, are inconsistent with alternatives to introgression such as convergence, or joint retention of ancestral polymorphisms. Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated.

Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach.

G. Ledyard Stebbins suggested that self-fertilization (selfing) may be an evolutionary dead end because it may result in the loss of genetic diversity and consequently preclude adaptation to changing environments. While the basic premise of selfing as a dead end is widely accepted, there have been few rigorous evaluations of the hypothesis. We examine the foundations of the dead-end hypothesis by considering theoretical advances in the study of mating-system evolution. We discuss theories predicting the irreversibility of self-fertilization and the extinction of selfing lineages through the loss of adaptive potential and genetic degradation. In the second portion of the review, focusing on the irreversibility of selfing, we summarize the contribution of phylogenetic studies of mating-system evolution to determine if evolutionary history supports this well-established hypothesis. Most studies are in accord with the hypothesis; no single study unequivocally demonstrates the transition from highly selfing to outcrossing lineages. Finally, we discuss the problems encountered when phylogenetic studies rely on reconstruction of ancestral mating systems. To avoid some of these problems, we applied likelihood ratio tests of irreversibility of mating-system evolution to several data sets and found that current data sets are probably too small for this test.

Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation.

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a "grass genome model." Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. "Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis.

Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton).

Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from interspecific hybridization in nature. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3662 BC3F2 plants derived from 24 different BC1 individuals of a cross between Gossypium hirsutum and G. barbadense, large and widespread deficiencies of donor (G. barbadense) chromatin were found, and seven independent chromosomal regions were entirely absent. This skewed chromatin transmission is best accounted for by multilocus epistatic interactions affecting chromatin transmission. The observed frequencies of two-locus genotypes were significantly different from Mendelian expectations about 26 times more often than could be explained by chance (P < or = 0.01). For identical pairs of loci, different two-locus genotypes occurred in excess in different BC3 families, implying the existence of higher-order interlocus interactions beyond the resolution of these data. Some G. barbadense markers occurred more frequently than expected by chance, indicating that genomic interactions do not always favor host chromatin. A preponderance of interspecific allelic interactions involved one locus each in the two different subgenomes of (allotetraploid) Gossypium, thus supporting several other lines of evidence suggesting that intersubgenomic interactions contribute to unique features that distinguish tetraploid cotton from its diploid ancestors.