Phenology, pollen synchronization and fruit characteristics of european hazelnut (Corylus avellana L.) cv. tonda de Giffoni in three sites of central Chile

Phenology, pollen synchronization and fruit characteristics were studied during the season 2011-2012 for European hazelnut (Corylus avellana L.) cv. "Tonda di Giffoni" and three of its pollinizers ("Tonda Romana", "Tonda Gentile delle Langhe" and "Barcelona") in three agro-ecological conditions of central Chile. Male and female blooms occurred from June through August, with a flowering span ranging between two to two and a half months depending on the cultivar, pollinizer and study sites. "Tonda di Giffoni" male flowering onset occurred during the first week of June, up to two weeks earlier than female flowers (271 to 417 chilling hours) showing a marked protandrus dichogamy. "Tonda Gentile delle Langhe" and "Barcelona" pollinizers completely covered the female flowering period of "Tonda di Giffoni", while "Tonda Romana" fail to cover the first flowering week. In general, starting dates for the different phenological stages were directly and significantly (P<0.05) correlated with chilling hour accumulation and growing degree days. Fruit set (34.1%) and maximum fruit diameter (16.6 mm) were significantly lower in the case of "Tonda Gentile delle Langhe" compared to "Tonda Romana" (82.2%, 17.3 mm) and "Barcelona" (74.7%, 17.4 mm).Phenology, pollen synchronization and fruit characteristics were studied during the season 2011-2012 for European hazelnut (Corylus avellana L.) cv. "Tonda di Giffoni" and three of its pollinizers ("Tonda Romana", "Tonda Gentile delle Langhe" and "Barcelona") in three agro-ecological conditions of central Chile. Male and female blooms occurred from June through August, with a flowering span ranging between two to two and a half months depending on the cultivar, pollinizer and study sites. "Tonda di Giffoni" male flowering onset occurred during the first week of June, up to two weeks earlier than female flowers (271 to 417 chilling hours) showing a marked protandrus dichogamy. "Tonda Gentile delle Langhe" and "Barcelona" pollinizers completely covered the female flowering period of "Tonda di Giffoni", while "Tonda Romana" fail to cover the first flowering week. In general, starting dates for the different phenological stages were directly and significantly (P<0.05) correlated with chilling hour accumulation and growing degree days. Fruit set (34.1%) and maximum fruit diameter (16.6 mm) were significantly lower in the case of "Tonda Gentile delle Langhe" compared to "Tonda Romana" (82.2%, 17.3 mm) and "Barcelona" (74.7%, 17.4 mm)

Development and characterization of InDel markers for Lupinus luteus L. (Fabaceae) and cross-species amplification in other Lupin species

Background: Strong artificial selection and/or natural bottle necks may limit genetic variation in domesticated species. Lupinus luteus, an orphan temperate crop, has suffered diversity reductions during its bitter/sweet alkaloid domestication history, limiting breeding efforts and making molecular marker development a difficult task. The main goal of this research was to generate new polymorphic insertion\u2013deletion (InDel) markers to aid yellow lupin genetics and breeding. By combining genomic reduction libraries and next generation sequencing, several polymorphic InDel markers were developed for L. luteus L. Results: A total of 118 InDel in silico polymorphic markers were identified. Eighteen InDel primer sets were evaluated in a diverse L. luteus core collection, where amplified between 2\u20133 alleles per locus. Observed heterozygosity (HO; 0.0648 to 0.5564) and polymorphic information content (PIC; 0.06 to 0.48) estimations revealed a moderate level of genetic variation across L. luteus accessions. In addition, ten and nine InDel loci amplified successfully Lupinus hispanicus Boiss & Reut, and Lupinus mutabilis Sweet, respectively, two L. luteus close relatives. PCA analysis identified two L. luteus clusters, most likely explained by the domestication species history. Conclusion: The development of InDel markers will facilitate the study of genetic diversity across L. luteus populations, as well as among closely related species

Amplification, contraction and genomic spread of a satellite DNA family (E180) in Medicago (Fabaceae) and allied genera

Background and AimsSatellite DNA is a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNA is an important element in genome organization and evolution in plants. Here we assess the presence and physical distribution of the repetitive DNA E180 family in Medicago and allied genera. Our goals were to gain insight into the karyotype evolution of Medicago using satellite DNA markers, and to evaluate the taxonomic and phylogenetic signal of a satellite DNA family in a genus hypothesized to have a complex evolutionary history.MethodsSeventy accessions from Medicago, Trigonella, Melilotus and Trifolium were analysed by PCR to assess the presence of the repetitive E180 family, and fluorescence in situ hybridization (FISH) was used for physical mapping in somatic chromosomes.Key ResultsThe E180 repeat unit was PCR-amplified in 37 of 40 taxa in Medicago, eight of 12 species of Trigonella, six of seven species of Melilotus and in two of 11 Trifolium species. Examination of the mitotic chromosomes revealed that only 13 Medicago and two Trigonella species showed FISH signals using the E180 probe. Stronger hybridization signals were observed in subtelomeric and interstitial loci than in the pericentromeric loci, suggesting this satellite family has a preferential genomic location. Not all 13 Medicago species that showed FISH localization of the E180 repeat were phylogenetically related. However, nine of these species belong to the phylogenetically derived clade including the M. sativa and M. arborea complexes.ConclusionsThe use of the E180 family as a phylogenetic marker in Medicago should be viewed with caution. Its amplification appears to have been produced through recurrent and independent evolutionary episodes in both annual and perennial Medicago species as well as in basal and derived clades

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora

Development and characterization of InDel markers for Lupinus luteus L. (Fabaceae) and cross-species amplification in other Lupin species

Background: Strong artificial selection and/or natural bottle necks may limit genetic variation in domesticated species. Lupinus luteus, an orphan temperate crop, has suffered diversity reductions during its bitter/sweet alkaloid domestication history, limiting breeding efforts and making molecular marker development a difficult task. The main goal of this research was to generate new polymorphic insertion–deletion (InDel) markers to aid yellow lupin genetics and breeding. By combining genomic reduction libraries and next generation sequencing, several polymorphic InDel markers were developed for L. luteus L. Results: A total of 118 InDel in silico polymorphic markers were identified. Eighteen InDel primer sets were evaluated in a diverse L. luteus core collection, where amplified between 2–3 alleles per locus. Observed heterozygosity (HO; 0.0648 to 0.5564) and polymorphic information content (PIC; 0.06 to 0.48) estimations revealed a moderate level of genetic variation across L. luteus accessions. In addition, ten and nine InDel loci amplified successfully Lupinus hispanicus Boiss & Reut, and Lupinus mutabilis Sweet, respectively, two L. luteus close relatives. PCA analysis identified two L. luteus clusters, most likely explained by the domestication species history. Conclusion: The development of InDel markers will facilitate the study of genetic diversity across L. luteus populations, as well as among closely related species

Root variability among yellow lupin (Lupinus luteus L.) accessions grown at low temperatures in an undisturbed substrate

Abstract Root variation has become an important target for geneticists, ecologists, and breeders, given its direct influence on plant adaptation, resilience to climate change, and biomass and seed yields. However, the underground nature of roots has limited the assessment of root variability in plant species. In this study, we evaluated several root traits in a sample of distinct yellow lupin accessions grown under cold conditions and at three time points. Analyses of variance showed a highly significant accession (genotype) effect on primary root length (PRL), primary root area (PRA), and total root area (TRA), indicating that at least part of the root variation was explained by a genetic component. Significant accession*time interactions for PRL and PRA suggested that root growth rates (assessed using these traits) may change over time across genotypes; however, a more extensive study including a larger number of accessions and growing times must be conducted to confirm this finding. Differences among L. luteus accessions in PRL, PRA and TRA suggest the existence of favorable variation in plantlet root traits and the possibility of breeding stronger and better-established yellow lupin plants when grown under cold conditions.Resumen La variación fenotípica de las raíces se ha convertido en un objetivo importante para genetistas, ecólogos y mejoradores, dada su influencia directa sobre la adaptación de las plantas, la resistencia al cambio climático, biomasa y el rendimiento de las semillas. Sin embargo, su naturaleza subterránea ha limitado la evaluación de la variabilidad contenida en las especies vegetales. En este estudio se evaluaron caracteres de la raíz en una muestra de accesiones diversas de lupino amarillo, cultivadas bajo condiciones de frío y durante tres puntos de su desarrollo. Análisis de varianza mostraron que la longitud de raíz primaria (LRP), el área de raíz primaria (ARP) y el área de raíz total (ART) fueron altamente significativas para el efecto accesión (genotipo), señalando que al menos parte de la variación observada se explicaría por un componente genético. Las interacciones significativas de accesión*tiempo, para LR y ARP, sugirieron que las tasas de crecimiento de raíz para los distintos genotipos pueden cambiar con el tiempo; sin embargo, más estudios, incluyendo un mayor número de accesiones y tiempos de crecimiento, deben realizarse para confirmar este hallazgo. Diferencias entre las accesiones de L. luteus para LR, ARP y ART sugieren la existencia de variación favorable para los caracteres de raíz y la posibilidad de mejorar plantas de lupino amarillo más robustas y mejor establecidas cuando se cultiven bajo condiciones frías

Image correlation method for DNA sequence alignment.

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment

A six nuclear gene phylogeny of Citrus (Rutaceae) taking into account hybridization and lineage sorting.

BACKGROUND: Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4-12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. METHODOLOGY AND PRINCIPAL FINDINGS: (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. CONCLUSIONS: We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches-gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus

Identification of a low digestibility δ-Conglutin in yellow lupin (Lupinus luteus L.) seed meal for atlantic salmon (Salmo salar L.) by coupling 2D-PAGE and mass spectrometry.

The need of quality protein in the aquaculture sector has forced the incorporation of alternative plant proteins into feeding diets. However, most plant proteins show lower digestibility levels than fish meal proteins, especially in carnivorous fishes. Manipulation of protein content by plant breeding can improve the digestibility rate of plant proteins in fish, but the identification of low digestibility proteins is essential. A reduction of low digestibility proteins will not only increase feed efficiency, but also reduce water pollution. Little is known about specific digestible protein profiles and/or molecular identification of more bioavailable plant proteins in fish diets. In this study, we identified low digestibility L. luteus seed proteins using Atlantic salmon (Salmo salar) crude digestive enzymes in an in vitro assay. Low digestibility proteins were identified by comparing SDS-PAGE banding profiles of digested and non-digested lupin seed proteins. Gel image analysis detected a major 12 kDa protein band in both lupin meal and protein isolate digested products. The 12 kDa was confirmed by 2D-PAGE gels and the extracted protein was analyzed with an ion trap mass spectrometer in tandem mass mode. The MS/MS data showed that the 12 kDa low digestibility protein was a large chain δconglutin, a common seed storage protein of yellow lupin. Comparison of the protein band profiles between lupin meal and protein isolates showed that the isolatation process did not affect the low digestibility of the 12 kDa protein

Peak and sequence length relationship

<p>. The amplitude of the peak in the correlation plane increases when the sequence length increases; however their relationship is not lineal.</p