Cross-amplification of EST-derived markers among 16 grass species

The availability of a large number of expressed sequence tags (ESTs) has facilitated the development of molecular markers in members of the grass family. As these markers are derived from coding sequences, cross-species amplification and transferability is higher than for markers designed from genomic DNA sequences. In this study, 919 EST-based primers developed from seven grass species were assessed for their amplification across a diverse panel of 16 grass species including cereal, turf and forage crops. Out of the 919 primers tested, 89 successfully amplified DNA from one or more species and 340 primers generated PCR amplicons from at least half of the species in the panel. Only 5.2% of the primers tested produced clear amplicons in all 16 species. The majority of the primers (66.9%) were developed from tall fescue and rice and these two species showed amplification rate of 41.6% and 19.0% across the panel, respectively. The highest amplification rate was found for conserved-intron scanning primers (CISP) developed from pearl millet (91%) and sorghum (75%) EST sequences that aligned to rice sequences. The primers with successful amplification identified in this study showed promise in other grass species as demonstrated in differentiating a set of 13 clones of reed canary grass, a species for which very little genomic research has been done. Sequences from the amplified PCR fragments indicated the potential for the transferable CISP markers for comparative mapping purposes. These primer sets can be immediately used for within and across species mapping and will be especially useful for minor grass species with few or no available molecular markers

Molecular cytogenetics (FISH, GISH) of Coccinia grandis: A ca. 3 myr-old species of Cucurbitaceae with the largest Y/autosome divergence in flowering plants

The independent evolution of heteromorphic sex chromosomes in 19 species from 4 families of flowering plants permits studying X/Y divergence after the initial recombination suppression. Here, we document autosome/Y divergence in the tropical Cucurbitaceae Coccinia grandis, which is ca. 3 myr old. Karyotyping and C-value measurements show that the C. grandis Y chromosome has twice the size of any of the other chromosomes, with a male/female C-value difference of 0.094 pg or 10% of the total genome. FISH staining revealed 5S and 45S rDNA sites on autosomes but not on the Y chromosome, making it unlikely that rDNA contributed to the elongation of the Y chromosome; recent end-to-end fusion also seems unlikely given the lack of interstitial telomeric signals. GISH with different concentrations of female blocking DNA detected a possible pseudo-autosomal region on the Y chromosome, and C-banding suggests that the entire Y chromosome in C. grandis is heterochromatic. During meiosis, there is an end-to-end connection between the X and the Y chromosome, but the X does not otherwise differ from the remaining chromosomes. These findings and a review of plants with heteromorphic sex chromosomes reveal no relationship between species age and degree of sex chromosome dimorphism. Its relatively small genome size (0.943 pg/2C in males), large Y chromosome, and phylogenetic proximity to the fully sequenced Cucumis sativus make C. grandis a promising model to study sex chromosome evolution. Copyright © 2012 S. Karger AG, Base

CGIAR Operations under the Plant Treaty Framework

The history of CGIAR and the development and implementation of the International Treaty on Plant Genetic Resources for Food and Agriculture (“Plant Treaty”) are closely intertwined. In accordance with the agreements that 11 CGIAR centers signed with the Plant Treaty’s Governing Body under Article 15 of the treaty, >730,000 accessions of crop, tree, and forage germplasm conserved in CGIAR genebanks are made available under the terms and conditions of the multilateral system of access and benefit sharing, and the CGIAR centers have transferred almost 4 million samples of plant genetic resources under the system. Many activities of CGIAR centers and their genebanks (e.g., crop enhancement, improved agronomic methods, seed system strengthening, and capacity building) are influenced by, and promote, the Plant Treaty’s objectives. The continued existence and optimal functioning of the Plant Treaty’s multilateral system of access and benefit sharing is critically important to CGIAR in the pursuit of its mission. However, the multilateral system has encountered some challenges since the Plant Treaty came into force. The successful conclusion of the ongoing process for enhancing the functioning of the multilateral system could increase monetary benefit sharing and incentives for exchanging more germplasm. In the meantime, increased efforts are necessary to promote nonmonetary benefit sharing through partnerships, technology transfer, information exchange, and capacity building. These efforts should be integrated into countries’ and organizations’ work to implement the Plant Treaty’s provisions on conservation and sustainable use of plant genetic resources, and farmers’ rights

Adaptive Traits Are Maintained on Steep Selective Gradients despite Gene Flow and Hybridization in the Intertidal Zone

Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain the 3 distinct genetic and morphological taxa within their preferred vertical distribution ranges. On the strength of distributional, genetic, physiological and morphological differences, we propose elevation of F. spiralis var. platycarpus from variety to species level, as F. guiryi

'Junk' DNA and long-term phenotypic evolution in <em>Silene</em> section <em>Elisanthe</em> (Caryophyllaceae)

Nuclear DNA content variation over orders of magnitude across species has been attributed to 'junk' repetitive DNA with limited adaptive significance. By contrast, our previous work on Silene latifolia showed that DNA content is negatively correlated with flower size, a character of clear adaptive relevance. The present paper explores this relationship in a broader phylogenetic context to investigate the long-term evolutionary impacts of DNA content variation. The relationship between nuclear DNA content and phenotype variation was determined for four closely related species of Silene section Elisanthe (Caryophyllaceae). In addition to a consistent sexual dimorphism in DNA content across all of the species, we found DNA content variation among populations within, as well as among, species. We also found a general trend towards a negative correlation between DNA content and flower and leaf size over all four species, within males and females as well as overall. These results indicate that repetitive DNA may play a role in long-term phenotypic evolution.</p

GENETIC-VARIATION IN ECBALLIUM-ELATERIUM (CUCURBITACEAE) - BREEDING SYSTEM AND GEOGRAPHIC-DISTRIBUTION

Dioecy, the separation of sexes, has arisen independently many times in the course of angiosperm evolution. Avoidance of inbreeding is clearly involved in the evolution of dioecy, and as a consequence we predict that dioecious populations should maintain higher levels of genetic variation than closely related nondioecious populations. We tested that prediction by comparing allozymic variation in two closely related taxa, the monoecious and dioecious subspecies of the Mediterranean cucurbit, Ecballium elaterium. Thirteen polymorphic loci were screened for seeds sampled from 10 monoecious and 13 dioecious populations spanning the geographic ranges of the subspecies in Spain. The dioecious subspecies showed strikingly greater allelic diversity and heterozygosity than the monoecious subspecies. A hierarchical F-statistic analysis clearly demonstrated considerable genetic variation within populations for the dioecious populations, whereas for the monoecious populations almost all genetic variation resulted from differences among populations. The general pattern of homozygosity within monoecious populations suggests that they are highly inbred. In order to assess historical influences on current patterns of genetic variation, we conducted a genetic-distance analysis. The observed relationship between genetic distance and geographic distance between populations supports the hypothesis that the subspecies' current allopatric distributions on the Iberian Peninsula are the result of separate waves of colonization from the north (monoecious) and south (dioecious).</p

`Junk' DNA and phenotypic evolution in Silene section Siphonomorpha

One of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size in Silene latifolia has been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species in Silene sect. Elisanthe. Given the presence of sex chromosomes in dioecious Silene species, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioecious Silene is a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species of Silene sect. Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect. Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect. Siphonomorpha for petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect. Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect. Elisanthe, and particularly in S. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa

'Junk' DNA and long-term phenotypic evolution in <em>Silene</em> section <em>Elisanthe</em> (Caryophyllaceae)

Nuclear DNA content variation over orders of magnitude across species has been attributed to 'junk' repetitive DNA with limited adaptive significance. By contrast, our previous work on Silene latifolia showed that DNA content is negatively correlated with flower size, a character of clear adaptive relevance. The present paper explores this relationship in a broader phylogenetic context to investigate the long-term evolutionary impacts of DNA content variation. The relationship between nuclear DNA content and phenotype variation was determined for four closely related species of Silene section Elisanthe (Caryophyllaceae). In addition to a consistent sexual dimorphism in DNA content across all of the species, we found DNA content variation among populations within, as well as among, species. We also found a general trend towards a negative correlation between DNA content and flower and leaf size over all four species, within males and females as well as overall. These results indicate that repetitive DNA may play a role in long-term phenotypic evolution.</p