The phylogenetic history of Medicago was examined for 60 accessions from 56 species using two nuclear genes (CNGC5 and beta-cop) and one mitochondrial region (rpS14-cob). The results of several analyses revealed that extensive robustly supported incongruence exists among the nuclear genes, the cause of which we seek to explain. After rejecting several processes, hybridization and lineage sorting of ancestral polymorphisms remained as the most likely factors promoting incongruence. Using coalescence simulations, we rejected lineage sorting alone as an explanation of the differences among gene trees. The results indicate that hybridization has been common and ongoing among lineages since the origin of Medicago. Coalescence provides a good framework to test the causes of incongruence commonly seen among gene trees but requires knowledge of effective population sizes and generation times. We estimated the effective population size at 240,000 individuals and assumed a generation time of 1 year in Medicago (many are annual plants). A sensitivity analysis showed that our conclusions remain unchanged using a larger effective population size and/or longer generation time.

Mutations in the biosynthesis or signaling pathways of gibberellin (GA) can cause dwarfing phenotypes in plants, and the use of such mutations in plant breeding was a major factor in the success of the Green Revolution. DELLA proteins are GA signaling repressors whose functions are conserved in different plant species. Recent studies show that GA promotes stem growth by causing degradation of DELLA proteins via the ubiquitin-proteasome pathway. The most widely utilized dwarfing alleles in wheat (Triticum aestivum; e.g. Rht-B1b and Rht-D1b) encode GA-resistant forms of a DELLA protein that function as dominant and constitutively active repressors of stem growth. All of the previously identified dominant DELLA repressors from several plant species contain N-terminal mutations. Here we report on a novel dwarf mutant from Brassica rapa (Brrga1-d) that is caused by substitution of a conserved amino acid in the C-terminal domain of a DELLA protein. Brrga1-d, like N-terminal DELLA mutants, retains its repressor function and accumulates to high levels, even in the presence of GA. However, unlike wild-type and N-terminal DELLA mutants, Brrga1-d does not interact with a protein component required for degradation, suggesting that the mutated amino acid causes dwarfism by preventing an interaction needed for its degradation. This novel mutation confers nondeleterious dwarf phenotypes when transferred to Arabidopsis (Arabidopsis thaliana) and oilseed rape (Brassica napus), indicating its potential usefulness in other crop species.Dwarfism is a desirable characteristic for many agricultural plants. In grain crops, dwarfism can reduce lodging and increase harvest index, and the breeding of dwarf wheat (Triticum aestivum) and rice (Oryza sativa) cultivars was a major factor in the success of the Green Revolution (Khush, 2001). Dwarfism is often caused by mutations in genes controlling the biosynthesis or signaling pathway of the plant hormone GA (Peng et al., 1999;Hedden, 2003;Sun and Gubler, 2004). The most widely utilized semi-dwarf wheat cultivars in agriculture contain the Rht-B1b or Rht-D1b allele that encodes a mutant form of a DELLA protein, a GA signaling repressor (Peng et al., 1999;Hedden, 2003).DELLA proteins encoded by Rht and its orthologs in Arabidopsis (Arabidopsis thaliana; GAI, RGA, RGL1, and RGL2), maize (Zea mays; d8), grape (Vitis vinifera; VvGAI), barley (Hordeum vulgare; SLN1), and rice (SLR1) have conserved function as repressors of GA signaling (Sun and Gubler, 2004). Five DELLA protein genes (GAI, RGA, RGL1, RGL2, and RGL3) are present in Arabidopsis, and with the exception of RGL3, these genes have been shown to share partially overlapping roles in repressing GA-regulated plant growth and development . Genetic analysis indicates that RGA and GAI are the major repressors that modulate GA-mediated vegetative growth and floral induction; RGL2 is important in regulating seed germination; and RGL1 and RGL2, along with RGA, control flower development King et al., 2001;Lee et al., 2002;Cheng et al., 2004;Tyle...

BackgroundAlthough the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.ResultsFrom the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.ConclusionsThai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-19) contains supplementary material, which is available to authorized users.