Veronica A. Vallejo

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.

Detection of DNA changes in somaclonal mutants of rice using SSR markers and transposon display

Somaclonal variation detected in plant tissues grown in vitro can be heritable, and thus provides an opportunity for plant breeders and geneticists to generate novel variants. However, incidence of somaclonal variation is problematic for plant transformation efforts and for micropropagation of true-to-type clones. The origin of somaclonal variation is still not well understood. In this study, 120 SSR markers, distributed across all 12 chromosomes of rice, have been used to analyze eight somaclonal mutants derived from seven different cultivars. Of these, 13 SSRs have detected polymorphisms between the bacterial blight resistant mutant HX-3 and its wild-type Minghui 63. While, ten SSRs have revealed differences between a purple sheath mutant, Z418, and the wild-type C418. None of the SSRs have been able to distinguish between tall and dwarf mutants, 02428h and A418, and their wild-type counterparts, respectively. Interestingly, six SSRs have identified differences in at least three mutant lines and their corresponding wild-type genotypes. These results have suggested that some SSR markers in the rice genome may detect higher numbers of polymorphisms than others. In addition, a transposon display (TD) of five active rice transposons, Tos17, Karma, mPing, nDart and dTok, has been conducted to evaluate DNA changes of eight mutants. Some mutant lines, such as HX-3 and Z418, have exhibited differences from their corresponding wild-type genotypes in TDs with two transposons. This has indicated that new insertions of transposons are involved in somaclonal variation derived from tissue culture. Taken together, these results suggest that multiple molecular mechanisms are responsible for somaclonal variation detected in tissue culture of rice.

New insights into the anthracnose resistance of common bean landrace G 2333.

The common bean landrace G 2333 carries a three gene pyramid for anthracnose resistance: Co-4 2 , Co-5 and Co-7. The Co-4 2 gene is well characterized but less information is available on Co-5 and Co-7. The objectives of this study were to determine if a new allele of Co-5 is present in G 2333; to characterize the spectrum of resistance condi- tioned by the Co-7 gene by deriving lines which only possess the Co-7 gene; and to test the MSU7 lines for allelism to Co-3. We propose that G 2333 carries a second allele at the Co-5 gene, different from that possessed by TU, and that the allele in G 2333 (SEL 1360) be designated Co-5 2 . With the exception of breeding line MSU7-1, the other derived MSU7 lines do not carry the Co-7 gene and are not allelic to Co-3 suggesting that G 2333 carries more than three genes for an- thracnose resistance.

Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

BackgroundPetunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper.ResultsHere we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate.ConclusionsThe high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest.