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Bu araştırmada hücre çekirdeğinde bulunan ve havuçta sitoplazmik genetik erkek kısırlığı kontrol eden Restorers of fertility (Rf) genlerinin genetik haritasının AFLP (amplified fragment length polymorphism - çoğaltılmış parça uzunluğu farklılığı) markırları kullanılarak çıkarılması amaçlanmıştır. Araştırma kapsamında iki haritalama popülasyonu kullanılmıştır. Popülasyonların çiçek yapıları incelenmiş ve taze yaprak örneklerinden DNA izolasyonu yapılmıştır. Birinci haritalama popülasyonundan 96 havuç bitkisinin çiçek yapısı incelenmiş ve bunlardan 37 bitkinin erkek kısır 59 bitkinin ise erkek fertil olduğu belirlenmiştir. Bu verilerle yapılan Ki-kare testine göre hücre çekirdeğinde bulunan erkek kısırlık genlerinin açılım oranının 9:7 olduğu tespit edilmiştir (p = 0,30). F2 popülasyonundaki bu açılım oranı, havuçta petaliod tipi sitoplazmik genetik erkek kısırlığının iki genle kontrol edildiğini göstermektedir. İkinci haritalama popülasyonundan 160 havuç bitkisinin çiçek yapısı incelenmiştir. 124 bitkinin erkek fertil ve 36 bitkinin ise erkek kısır olduğu tespit edilmiştir. Ki-Kare testine göre hücre çekirdeğinde bulunan erkek kısırlık geni 3:1 oranında açılım göstermektedir (p = 0.47). Bu sonuca göre HP2 popülasyonunda hücre çekirdeğinde bulunan erkek kısırlık genlerinden sadece birinin açılım gösterdiği belirlenmiştir. Yapılan AFLP analizlerinde HP1 popülasyonundan 8 adet erkek kısır ile 8 adet erkek fertil bitki ve HP2 popülasyonundan ise yine 8 adet erkek kısır ile 8 adet erkek fertil bitki seçilmiştir. 16 adet erkek kısır ve 16 adet erkek fertil bitki kullanılarak 225 AFLP primer kombinasyonun analizi tamamlanmıştır. Her iki popülasyonda da sadece erkek fertil bitkilerde çoğalan 2 AFLP bandı 2 primer kombinasyonu belirlenmiştir. Bunlardan birincisi Markır-1 olarak adlandırılmış ve EACT-MCAT primer kombinasyonunda tespit edilmiştir. Markır-1 erkek kısır bitkilerin sadece birinde çoğalmış ve erkek fertil bitkilerin ikisinde çoğalmamıştır. Diğer AFLP markırı ise Markır-2 olarak adlandırılmış ve EATA-MCTG primer kombinasyonunda belirlenmiştir The purpose of this research was to map carrot nuclear Rf genes using AFLP (amplified fragment length polymorphism) markers. In this study, two segregating carrot populations were used. Their flower structure was determined and the DNA samples were isolated from fresh leaves of each plant. In the first F2 carrot population segregating for male sterility was composed of 96 plants and 37 of those plants were male sterile while 59 plants were male fertile. According to chi-square test results fit to 9:7 Mendelian segregation ratio (p value=0,30) (male fertile: male sterile) indicated that two genes were segregating and male fertility is dominant. In second population, 160 carrot plants were segregating for male sterility. 124 plants were male fertile while 36 plants were male sterile. According to chi-square test, this result fits 3:1 Mendelian segregation ratio (p value=0,47) (male fertile: male sterile) suggesting that only single gene was segregating and male fertility is dominant. Eight male sterile and eight male fertile plants from first population and eight male sterile and eight male fertile plans from second population were chosen for the AFLP analysis. 225 AFLP primer combination were analyzed by using 16 male sterile and 16 male fertile plants. In two primer combination, two AFLP bands amlified only in male fertile plants but were not amplified in male sterile plants indicating possible association with male sterility in carrot. First AFLP amplified DNA fragment was called Markır-1 and it was amplified with EACT-MCAT primer combination. While these AFLP amplified DNA fragment was present only in one male sterile plant, it did not amplified in two of male fertile plants. Other AFLP amplified DNA fragment was called Markır-2 and it was amplified by primer combination of EATA-MCTG TOVAG

Background\ud During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.\ud \ud Methodology/Principal findings\ud Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM), and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection.\ud \ud Matsam identified four loci possibly under natural selection – also confirmed by FST-outlier methods – and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation.\ud \ud Conclusions/Significance\ud These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

The cultivated potato (Solanum tuberosum ssp. tuberosum) has more than 200 related wild species distributed along the Andes, adapted to a wide range of geographical and ecological areas. Since the last century, several collection expeditions were carried out to incorporate genetic variability into the potato germplasm around the world. However, little is known about the reproductive ecology and genetic population structure of natural potato population from field studies. The aim of this work is to study, in the field, the genetic variability and reproductive strategies of populations of one of the most widely distributed potato species in Argentina, Solanum kurtzianum, growing in Mendoza province. AFLP markers showed that the genetic variability is mainly present among plants within populations, indicating that in the sampled populations, sexual reproduction is more relevant than clonal multiplication (by tubers). Additional evidence was obtained evaluating the genetic diversity in populations with a distribution in patches, where several genotypes were always detected. From a field study performed in the Villavicencio Natural Reserve, we found that the average number of plump seeds per fruit was 94.3, identified and calculated the foraging distance of four insect pollinators, and demonstrated the seed dispersal by storm water channels. We argue that the breeding system, the two modes of reproduction and the ecological interaction described here may have a prominent role in determining the genetic structure of S. kurtzianum populations, and discuss the importance of field studies on population genetics, reproductive biology and ecology to design collections and conservation strategies. Fil: Marfil, Carlos Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina Fil: Masuelli, Ricardo Williams. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-san Juan; Argentina

Delimiting the spatial extension of a hybrid zone is essential to understand its historical origin and to identify the geographical and/or environmental factors which delimit it. Rhinella atacamensis and R. arunco are two sister species which together inhabit Chile between 25° and 38° S. Their distribution limits coincide at about 32° S, where recently it was reported that they hybridize in a small watershed (Pupío creek). Although the genetic evidence suggests that these two species form a hybrid swarm, they are not mixed homogeneously in the entire watershed, but rather are spatially segregated: R. arunco is found in the lower part of the creek and R. atacamensis in the higher part. An extensive exploration north and south of 32° S revealed other instances of hybridization, with the same pattern of spatial segregation within other watersheds. This study describes the hybrid zone combining mitochondrial sequences and nuclear AFLP markers. In the northern part, the hybrid zone is a narrow strip which crosses several watersheds and extends more than 130 km from NW-SE, so that R. atacamensis is found at higher altitudes towards the south. However, two points south of this strip show that the hybrid zone is more extensive and complex, and probably extends along the entire border of the mountain chains which form the watershed of the Aconcagua River (32°30' - 33° S). We propose an explanation for the origin of this hybrid zone considering paleoclimatic and orographic information, and briefly discuss the taxonomic implications of these results. Definir la extensión espacial de una zona de hibridación es esencial para entender su origen histórico e identificar los factores geográficos y/o ambientales que la delimitan. Rhinella atacamensis y R. arunco son dos especies hermanas que en conjunto habitan entre los 25 y 38° S a lo largo de Chile. Sus límites de distribución coinciden aproximadamente a los 32° S, donde recientemente se reportó que hibridan en una pequeña cuenca hidrográfica (estero Pupío). Aunque la evidencia genética sugiere que estas especies forman un enjambre híbrido, no se mezclan homogéneamente a lo largo de la cuenca sino que se segregan espacialmente: R. arunco se encuentra en la parte baja del estero, mientras que R. atacamensis se ubica en la parte alta. Una extensa exploración al norte y sur de los 32° S reveló otras instancias de hibridación donde se mantiene el mismo patrón de segregación espacial dentro de otras cuencas. En este estudio se describe esta zona de hibridación combinando secuencias mitocondriales y marcadores nucleares AFLP. En su parte norte, la zona conforma una estrecha franja que atraviesa varias cuencas extendiéndose más de 130 km en dirección noroeste-sureste, de manera que R. atacamensis se encuentra cada vez a mayor altura a medida que se avanza hacia el sur. Sin embargo, dos puntos ubicados el sur de esta franja muestran que la zona de hibridación es más extensa y compleja, y que probablemente se extiende por todo el borde de las cadenas de cerros que conforman la cuenca hidrográfica del río Aconcagua (32°30' - 33° S). Se plantea una explicación para el origen de esta zona de hibridación considerando antecedentes paleoclimáticos y orográficos y se discuten brevemente las implicancias taxonómicas de estos resultados.

Aims: The objective of this work was to design an amplified fragment length polymorphism (AFLP)-derived specific primer for the detection of Fusarium solani aetiological agent of peanut brown root rot (PBRR) in plant material and soil. Methods and Results: Specific primers for the detection of the pathogen were designed based on an amplified region using AFLPs. The banding patterns by AFLPs showed that isolates from diseased roots were clearly distinguishable from others members of the F. solani species complex. Many bands were specific to F. solani PBRR, one of these fragments was selected and sequenced. Sequence obtained was used to develop specific PCR primers for the identification of pathogen in pure culture and in plant material and soil. Primer pair FS1/FS2 amplified a single DNA product of 175 bp. Other fungal isolates occurring in soil, included F. solani non-PBRR, were not detected by these specific primers. The assay was effective for the detection of pathogen from diseased root and infected soils. Conclusions: The designed primers for F. solani causing PBRR can be used in a PCR diagnostic protocol to rapidly and reliably detect and identify this pathogen. Significance and Impact of the Study: These diagnostic PCR primers will aid the detection of F. solani causing PBRR in diseased root and natural infected soils. The method developed could be a helpful tool for epidemiological studies and to avoid the spread of this serious disease in new areas. Fil: Casasnovas, F.. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina Fil: Fantini, Emanuel Nicolás. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Palazzini, Juan Manuel. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Giaj Merlera, Guillermo. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Chulze, Sofia Noemi. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Reynoso, Maria Marta. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Torres, Adriana Mabel. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

Approximately 80% of sowed grassland is installed with multi-species of grass - legume, leading to complex interactions between species and induced the phenomenon of competition what may affect the production, species abundance, and thus the agronomic value. The plant breeding of forage results in the creation of so-called synthetic varieties, but this selection is conventionally performed in a single-species context. It is therefore necessary to achieve greater efficiency of plant breeding, taking into account the interactions due to the presence of other species to improve the creation of a variety used in mixtures. In order to obtain the necessary knowledge to selection for mixtures, it is necessary to conduct experiments. But the distinction between varieties in a plot can be difficult, morphological characters often not sufficient to distinguish these varieties. It is therefore necessary to develop a molecular tool, such as differential genotyping using molecular markers to be able to follow in time and study the varietal diversity. The objective of this work was to develop a molecular differential genotyping tool on white clover, which will discriminate different varieties in the mixtures studied. Using this tool, it will be possible to determine the implantation rate T0 and follow the proportion of each variety in the trial conducted over time.; Environ 80% des prairies semées sont installées en mélange plurispécifique d’associations graminées – légumineuses, induisant des interactions complexes entre espèces, avec notamment le phénomène de compétition qui peut avoir des conséquences sur la production, l’abondance des espèces, et donc sur la valeur agronomique. La sélection des plantes fourragères permet la création de variétés dites synthétiques, mais cette sélection s’effectue classiquement dans un cadre monospécifique. Il est donc nécessaire, pour arriver à une plus grande efficacité de la création variétale, de prendre en compte les interactions dues à la présence d’autres espèces dans la création d’une variété destinée à être utilisée en mélange. Afin d’obtenir les connaissances nécessaires à la sélection fourragère pour les mélanges, il est donc nécessaire de conduire des expérimentations. Mais la a distinction de variétés dans une parcelle expérimentale peut être compliquée, les caractères morphologiques ne suffisent souvent pas à discriminer les variétés présentes. Il est donc nécessaire de mettre au point un outil moléculaire, comme le génotypage différentiel des variétés à l’aide de marqueurs moléculaires pour pouvoir suivre dans le temps et étudier la diversité variétale en présence. L’objectif de ce stage a été mettre au point un outil moléculaire sur le trèfle blanc, qui permettra de discriminer les différentes variétés dans les mélanges étudiés. A l’aide de cet outil, il sera alors possible de déterminer le taux d’implantation à T0 et de suivre la proportion de chaque variété dans l’essai conduit au cours du temps.

Genetic marker studies can assist restoration practice through selection of seed sources that conserve historical levels of gene diversity and population genetic differentiation. We examined genetic variation and structure within and among mainland and island populations of Elymus glaucus, a perennial bunchgrass species native to western North American grasslands that is targeted for grassland restoration. Island populations of E. glaucus represent sensitive sites and potentially distinctive seed sources for reintroduction, and little is known of their genetic composition. Genetic diversity and structure were estimated using amplified fragment length polymorphism markers for 21 populations and 416 individuals distributed across two coastal California mainland locations and three California Channel Islands. Eight primer combinations resulted in 166 markers, of which 165 (99.4 %) were polymorphic. The number of polymorphic bands was significantly greater among mainland populations relative to island sites, and locally common alleles were present for each sampled island and mainland location. Population structure was high (62.9 %), with most variation (55.8 %) distributed among populations, 7.1 % between mainland and island locations, and the remainder (37.1 %) within populations. Isolation by distance was only apparent among islands. Using marker data to recommend appropriate seed sources for restoration, E. glaucus seeds are best derived within islands with collections representing a large number of individuals from matching environments. Given the limited gene flow and prior evidence of adaptive divergence among populations of this species, regional collections are recommended in all cases to maintain diversity and to avoid long-distance introductions of highly differentiated plant material. © 2014 Published by Oxford University Press on behalf of the Annals of Botany Company.

International audience; High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

In this study, we examine the population structure and inbreeding level of the Italian Lipizzan horse breed by means of AFLP fingerprinting and SSR genotyping. A total of 245 AFLP marker alleles were scored across all horses (n=140) living in the Italian Lipizzan stud in 2007, and microsatellite analysis was performed on all mares (n=42) and stallions (n=7) by genotyping at 30 SSR marker loci. A total of 53 (21.6%) AFLP marker alleles were scored as polymorphic among the animals, with a mean frequency of 0.722. Based on this subset of markers, 123 animals were assigned to three distinct subgroups of 44, 41 and 38 animals, respectively, each one showing a within-subgroup mean Dice's genetic similarity around 86% (standard error

El Perú ha sido reconocido como uno de los más importantes centros de diversidad del cultivo de maní y de acuerdo a la evidencia arqueológica, pudo haber sido el centro de origen para dicho cultivo. Para incrementar el conocimiento de la diversidad genética del maní en el Perú, se evaluaron 65 accesiones de maní, correspon-dientes a 21 variedades locales, de las cuencas de los ríos San Alejandro, Ucayali y Aguaytía, de la Región Ucayali. Las accesiones fueron proporcionadas por el proyecto “Modelos de diversidad y de erosión genética en cultivos tradicionales: Asesoría rápida y detección temprana de riesgos usando herramientas SIG”, ejecutado en el Instituto Nacional de Innovación Agraria. Se utilizó la técnica AFLP para estimar la variabilidad genética del cultivo, así como para identificar áreas con la mayor riqueza genética. Se obtuvo un total de 157 bandas polimórficas (45,6%), a partir de 10 combinaciones de iniciadores AFLP en nuestras 65 entradas de maní. Se consideraron sólo 135 bandas polimórficas, en base a su contenido de información polimórfica (0,1, Peru has been recognized as one of the most important centers of diversity of the peanut crop and according to archaeological evidence, may have been the center of origin for it. Due to poor knowledge of the current levels of genetic diversity of peanut in Peru, they were evaluated 65 peanut accessions, corresponding to 21 local varieties from the basins of the rivers San Alejandro, Ucayali and Aguaytia, in the Ucayali region; kindly provided by the project "Models of diversity and genetic erosion of traditional crops: Rapid advice and early detection of risks using GIS tools", performed at the “Instituto Nacional de Innovacion Agraria”. AFLP technique was used to estimate the genetic variability of the crop in the region and to identify areas with the greatest genetic wealth. There were a total of 157 polymorphic bands (45.6%), from 10 AFLP primer combinations in our 65 entries of peanuts. We considered only 135 polymorphic bands, based on their polymorphic information content (0.1

Peru has been recognized as one of the most important centers of diversity of the peanut crop and according to archaeological evidence, may have been the center of origin for it. Due to poor knowledge of the current levels of genetic diversity of peanut in Peru, they were evaluated 65 peanut accessions, corresponding to 21 local varieties from the basins of the rivers San Alejandro, Ucayali and Aguaytia, in the Ucayali region; kindly provided by the project "Models of diversity and genetic erosion of traditional crops: Rapid advice and early detection of risks using GIS tools", performed at the “Instituto Nacional de Innovacion Agraria”. AFLP technique was used to estimate the genetic variability of the crop in the region and to identify areas with the greatest genetic wealth. There were a total of 157 polymorphic bands (45.6%), from 10 AFLP primer combinations in our 65 entries of peanuts. We considered only 135 polymorphic bands, based on their polymorphic information content (0.1 El Perú ha sido reconocido como uno de los más importantes centros de diversidad del cultivo de maní y de acuerdo a la evidencia arqueológica, pudo haber sido el centro de origen para dicho cultivo. Para incrementar el conocimiento de la diversidad genética del maní en el Perú, se evaluaron 65 accesiones de maní, correspon-dientes a 21 variedades locales, de las cuencas de los ríos San Alejandro, Ucayali y Aguaytía, de la Región Ucayali. Las accesiones fueron proporcionadas por el proyecto “Modelos de diversidad y de erosión genética en cultivos tradicionales: Asesoría rápida y detección temprana de riesgos usando herramientas SIG”, ejecutado en el Instituto Nacional de Innovación Agraria. Se utilizó la técnica AFLP para estimar la variabilidad genética del cultivo, así como para identificar áreas con la mayor riqueza genética. Se obtuvo un total de 157 bandas polimórficas (45,6%), a partir de 10 combinaciones de iniciadores AFLP en nuestras 65 entradas de maní. Se consideraron sólo 135 bandas polimórficas, en base a su contenido de información polimórfica (0,1

Resistance of eggplant against Ralstonia solanacearum phylotype I strains was assessed in a F6 population of recombinant inbred lines (RILs) derived from a intra-specific cross between S. melongena MM738 (susceptible) and AG91-25 (resistant). Resistance traits were determined as disease score, percentage of wilted plants, and stem-based bacterial colonization index, as assessed in greenhouse experiments conducted in Réunion Island, France. The AG91-25 resistance was highly efficient toward strains CMR134, PSS366 and GMI1000, but only partial toward the highly virulent strain PSS4. The partial resistance found against PSS4 was overcome under high inoculation pressure, with heritability estimates from 0. 28 to 0. 53, depending on the traits and season. A genetic map was built with 119 AFLP, SSR and SRAP markers positioned on 18 linkage groups (LG), for a total length of 884 cM, and used for quantitative trait loci (QTL) analysis. A major dominant gene, named ERs1, controlled the resistance to strains CMR134, PSS366, and GMI1000. Against strain PSS4, this gene was not detected, but a significant QTL involved in delay of disease progress was detected on another LG. The possible use of the major resistance gene ERs1 in marker-assisted selection and the prospects offered for academic studies of a possible gene for gene system controlling resistance to bacterial wilt in solanaceous plants are discussed., De Ruiter Seeds; Enza Zaden; Gautier Semences; Nunhems; Rijk Zwaan; Vilmorin Cie; European Regional Development Funds (FEDER) of the European Union; Conseil Regional de la Reunion

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; In order to optimize the management of genetic resources, in most cases a representative sample of the germplasm collections needs to be developed. The establishment of a core collection is thus of major importance either to minimize the cost associated with the management of the associated germplasm or to apply analysis onto representative bases. In order to select a representative core collection among the Tunisian apricot germplasm of 110 accessions large, the Maximization strategy algorithm was used. This algorithm was shown to be the most convenient when using both morphological traits and molecular markers. Three core collections based on morphological characters, molecular markers or the combined data were compared. Our data indicate that both the molecular and the morphological markers have to be considered to obtain a core collection that represents the global diversity of the 110 accessions. Using this method, a subset of 34 selected accessions was found to represent accurately the 110 accessions present in the whole collection (75 to 100% for the morphological characters and 97% of the molecular markers). These results show that the combination of molecular and morphological markers is an efficient way to characterize the apricot core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License., [Background]: Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). [Results]: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. [Conclusion]: Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties., This research was funded by the INIA projects RTA2008-00035-C02-01/02 and RTA2011-00044-C02-1/2 of the Spanish Instituto Nacional de Investigación y Tecnología Agraria and FEDER funds (EU). The NVD grant was supported by the Programa de Formación del Personal Técnico e Investigador from IFAPA, co-financed with European Social Funds.

Cocoon related characteristics are economically important traits in the silkworm, Bombyx mori L. (Lepidoptera: Bombycidae). In this study a genetic linkage map was developed that identified QTL controlling the cocoon weight, cocoon shell weight, and cocoon shell percentage using 161 amplified fragment length polymorphism (AFLP) markers. Twenty PstI/TaqI primer combinations were employed to genotype 78 F(2) progenies derived from a cross between P107 Japanese inbred line and Khorasan Lemon Iranian native strain. Among polymorphic markers, 159 AFLP markers were assigned to 24 linkage groups at the LOD threshold of 2.5 that varied in length from 4 to 299 cM. The total length of the linkage map was 2747 cM, giving an average marker resolution of 19.31 cM. A total of 21 AFLP markers were identified that were distributed over the ten linkage groups linked to the three studied traits using the composite interval mapping method. The explained variation rate by QTL controlling cocoon weight, cocoon shell weight, and cocoon shell percentage ranged from 0.02% to 64.85%, 0.2% to 49.11%, and 0.04% to 84.20%, respectively. These QTL controlled by different actions as well as under dominance, additive, partial dominance, dominance, and over dominance.

International audience; We have constructed the first integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597 markers, 206 of which are sequence-based, distributed over a length of 530 cM on seven LGs. By using a larger effective population size and therefore higher marker density, the marker order in the ICM is more reliable than in the single population maps. This is supported by a more even marker distribution and a decrease in gap sizes in the consensus map as compared to the single population maps. This unified map establishes a standard nomenclature for rose LGs, and presents the location of important ornamental traits, such as self-incompatibility, black spot resistance (Rdr1), scent production and recurrent blooming. In total, the consensus map includes locations for 10 phenotypic single loci, QTLs for 7 different traits and 51 ESTs or gene-based molecular markers. This consensus map combines for the first time the information for traits with high relevance for rose variety development. It will serve as a tool for selective breeding and marker assisted selection. It will benefit future efforts of the rose community to sequence the whole rose genome and will be useful for synteny studies in the Rosaceae family and especially in the section Rosoideae.

•DNA methylation can cause heritable phenotypic modifications in the absence of changes in DNA sequence. Environmental stresses can trigger methylation changes and this may have evolutionary consequences, even in the absence of sequence variation. However, it remains largely unknown to what extent environmentally induced methylation changes are transmitted to offspring, and whether observed methylation variation is truly independent or a downstream consequence of genetic variation between individuals.•Genetically identical apomictic dandelion (Taraxacum officinale) plants were exposed to different ecological stresses, and apomictic offspring were raised in a common unstressed environment. We used methylation-sensitive amplified fragment length polymorphism markers to screen genome-wide methylation alterations triggered by stress treatments and to assess the heritability of induced changes.•Various stresses, most notably chemical induction of herbivore and pathogen defenses, triggered considerable methylation variation throughout the genome. Many modifications were faithfully transmitted to offspring. Stresses caused some epigenetic divergence between treatment and controls, but also increased epigenetic variation among plants within treatments.•These results show the following. First, stress-induced methylation changes are common and are mostly heritable. Second, sequence-independent, autonomous methylation variation is readily generated. This highlights the potential of epigenetic inheritance to play an independent role in evolutionary processes, which is superimposed on the system of genetic inheritance

To reduce the level of redundancy in a collection of cultivated lettuce, data from 160 amplified fragment length polymorphism (AFLP) fragments and 10 polymorphic microsatellites were used in combination with passport data and morphological data, the latter obtained from an experimental field trial performed for verification purposes. Based on the observed distribution of the number of marker differences between and within accessions, a minimum of three AFLP differences and two microsatellite differences were regarded as levels warranting distinction between accessions in the redundancy analysis. The strategy followed in the redundancy analysis was mainly based on the confirmation of duplication by each of two independently generated data sources. The molecular data were used for the validation as well as the identification of potential duplicates, revealing a total number of 198 redundancies, corresponding to 12.9% of the total collection. Trueness to type, number of characterization and evaluation data, and collection management considerations, such as available seed quantities and germination percentages, were used as primary, secondary and tertiary criteria to decide which accession from duplication groups to maintain in the collection. Removal of accessions showed negligible effects on total collection diversity, as quantified for AFLPs and microsatellites, characterization and evaluation traits and resistance profiles against downy mildew pathotypes, indicating that the applied strategy was effective.

Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species., BMC Plant Biology, 10, ISSN:1471-2229

Blackberry cultivation has increased its popularity in Turkey due to the use of more blackberries in Turkish cuisine. To provide farmers with well adapted blackberry cultivars, some blackberry cultivars including a Boysenberry genotype from North America has been planted to various geographical regions in Turkey. In this study, genetic diversity among these blackberry cultivars and their genetic relationship with Boysenberry and raspberry were analyzed using AFLP markers. Our results indicated that Blackberry cultivars from North America had narrow genetic background which can pose a problem for future breeding programs. Blackberry genotypes selected from Bursa province of Turkey shared all AFLP markers with the cultivar Chester, which suggests that they were not unique genotypes. Although genetic similarity between Boysenberry and blackberry was low, Boysenberry was genetically related to common blackberry cultivars. On the other hand, AFLP analysis was unable to detect any genetic relationship between Boysenberry and common raspberry cultivars from North America in this study.

Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop.

Despite some data on tall fescue diversity using molecular markers, mainly from United States accessions, there is a lack of knowledge on the global diversity all over the world for this species. The objectives of this study were to evaluate the sub-structure of tall fescue world wide variability and to place French cultivars into this sub-structure using AFLP markers. One plant per accession from 32 ecotypes and 40 plants from six French cultivars were used. A total of 116 polymorphic fragments were scored from two primers combinations. Clustering analysis on 32 ecotypes of tall fescue from all over the world showed two distinct clusters: European and Mediterranean types. In the Mediterranean type two clusters could be distinguished probably illustrating different colonization origins. The analysis of six French cultivars representing the French seed market showed six genetically distinct subsets which were included in the European type.

Despite the efforts of breeders and the extensive use of fungicide control measures, late blight still remains a major threat to potato cultivation worldwide. The introduction of genetic resistance into cultivated potato is considered a valuable method to achieve durable resistance to late blight. Here, we report the identification and cloning of Rpi-vnt1.1, a previously uncharacterized late-blight resistance gene from Solanum venturii. The gene was identified by a classical genetic and physical mapping approach and encodes a coiled-coil nucleotide-binding leucine-rich repeat protein with high similarity to Tm-22 from S. lycopersicum which confers resistance against Tomato mosaic virus. Transgenic potato and tomato plants carrying Rpi-vnt1.1 were shown to be resistant to Phytophthora infestans. Of 11 P. infestans isolates tested, only isolate EC1 from Ecuador was able to overcome Rpi-vnt1.1 and cause disease on the inoculated plants. Alleles of Rpi-vnt1.1 (Rpi-vnt1.2 and Rpi-vnt1.3) that differed by only a few nucleotides were found in other late-blight-resistant accessions of S. venturii. The late blight resistance gene Rpi-phu1 from S. phureja is shown here to be identical to Rpi-vnt1.1, suggesting either that this strong resistance gene has been maintained since a common ancestor, due to selection pressure for blight resistance, or that genetic exchange between S. venturii and S. phureja has occurred at some time.

A cytogenetic map has been developed for diploid potato (Solanum tuberosum), in which the arms of the 12 potato bivalents can be identified in pachytene complements using multicolor fluorescence in situ hybridization (FISH) with a set of 60 genetically anchored bacterial artificial chromosome (BAC) clones from the RHPOTKEY BAC library. This diagnostic set of selected BACs (five per chromosome) hybridizes to euchromatic regions and corresponds to well-defined loci in the ultradense genetic map, and with these probes a new detailed and reliable pachytene karyotype could be established. Chromosome size has been estimated both from microscopic length measurements and from 4',6-diamidino-2-phenylindole fluorescence-based DNA content measurements. In both approaches, chromosome 1 is the largest (100-115 Mb) and chromosome 11 the smallest (49-53 Mb). Detailed measurements of mega-base-pair to micrometer ratios have been obtained for chromosome 5, with average values of 1.07 Mb/mum for euchromatin and 3.67 Mb/mum for heterochromatin. In addition, our FISH results helped to solve two discrepancies in the potato genetic map related to chromosomes 8 and 12. Finally, we discuss the significance of the potato cytogenetic map for extended FISH studies in potato and related Solanaceae, which will be especially beneficial for the potato genome-sequencing project.

"The objective of this study was to determine the genetic structure of populations of the mexican fruit fly Anastrepha ludens (Loew) in NE citrus growing regions of Mexico. The work was conducted during 2005 at the Center of Genomic Biotechnology in Reynosa, Tamaulipas, Mexico. AFLP markers using four different pairs of initiators were used on specimens collected from the native, ancestral host, yellow chapote (Casimiroa greggii S. Wats) and the exotic host, citrus (Citrus sinensis (L.) Osbeck cv Valencia). The four combinations of initiators amplified an average of 95 AFLP fragments. A total of 382 products were obtained and 259 (67%) of them were polymorphous. The overall index of genetic diversity was 28%, with 3% difference between the genotypes collected from yellow chapote as compared to the genotypes collected from sweet orange. Cluster analysis and principal components showed a close genetic relation among A. ludens specimens regardless of the origin. Although, the dendrogram showed two main groups, the genetic distance varied from 0.0 to 10%, suggesting that despite the reproductive isolation, host groups are not evolving. These results are discussed in the context of evolution and conclude on practical implications of the ongoing eradication program through sterile insect technique and the geographical origin of this species."

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars. Scientific and Technical Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [105 O 586] This research was supported by the Scientific and Technical Research Council of Turkey under the project code TUBITAK TOVAG: 105 O 586.

Amplified fragment length polymorphism (AFLP) using six marker combinations were applied to detect genetic variation and phylo genetic relationships among 12 indigenous Chinese chicken breeds and a Recessive White chicken breed introduced from France. The DNA was pooled for each group. Polymorphic bands, breed-specific bands and genetic similarity coefficients of 13 chicken breeds were derived from the AFLP data. A total of 280 polymorphic bands was generated from which nine specific bands were observed for the Shouguang and the Dongxiang Dark chicken. One specific band was observed in the pooled DNA of the Jiuyuan Dark chicken, the Xingyi Bantam chicken and the Recessive White chicken. The genetic similarity coefficients among the 12 indigenous Chinese chicken breeds varied between 0.635 - 0.860, and 0.188 - 0.360 between the Recessive White and the indigenous Chinese chicken breeds. The UPGMA based tree yielded two clusters for the 13 chicken breeds, with the Recessive White chickens forming a distinct cluster. In summary, the genetic similarity coefficients and the UPGMA tree of the 13 chicken breeds were consistent with their breeding history and geographical distribution. These results provide useful data with regard to the genetic diversity, genetic relationships and identification of chicken breeds in China. Keywords: Indigenous chicken breeds, AFLP markers, genetic variation, genetic relationshipsSouth African Journal of Animal Science Vol. 38 (3) 2008: pp. 193-200

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.

Fruit flavour of traditional tomato ecotypes differs from that of modern varieties, the latter being often blamed for lack of flavour. To respond to consumer complaints breeders should know the range of genetic variability available in tomato resources, including local ecotypes, for improving flavour. For this purpose, multitrait characterization, including biochemical, sensorial and molecular analyses, was performed on 12 Italian tomato ecotypes that belong to different types (San Marzano, Sorrento, and Vesuvio). The ecotypes showed a significant variation both in glucose and citric acid content. As for amino acid determination, lysine, aspartic acid and serine showed significant variation among the three types analyzed. Sensory analysis clearly evidenced differences among genotypes: the San Marzano ecotypes revealed sensory profiles that differ from the control processing variety in perception of sweetness and sourness, whereas the Sorrento and Vesuvio ecotype profiles were similar to the fresh market control. In particular, Vesuvio genotypes exhibited a good intensity of tomato aroma and sweetness and an intermediate level of acidity. Finally, molecular characterization performed through AFLP markers provided evidence for a very high level of polymorphism: an ecotype-specific AFLP pattern was identified for at least 11 genotypes, thus defining their molecular fingerprints.

International audience; Powdery mildew (Blumeria graminis f. sp. tritici) is one of the major diseases of wheat (Triticum aestivum). The objective of the present study was to describe the quantitative resistance to powdery mildew of the winter wheat line RE714 at the seedling stage and to identify microsatellite markers tightly linked to the RE714 resistance QTL, which could be used in marker-assisted selection. A population of 160 recombinant inbred lines obtained from the cross between RE714 (resistant) and Hardi (susceptible) was genotyped with microsatellite and AFLP markers. Fifteen powdery mildew isolates were used to test the resistance of these lines at the seedling stage. QTL analysis enabled us to identify three major QTLs controlling powdery mildew resistance in RE714: a QTL located on chromosome 2A, corresponding to the Pm4b gene, explaining 76-93% of the phenotypic variance for resistance to six isolates; two QTLs located on chromosomes 5D and 6A, each explaining 20-67%of the phenotypic variance for resistance tofive isolates.AminorQTLfor resistance to four of the six isolates revealing Pm4b was detected in the same region as the 5D QTL. Other minor QTLs were detected on chromosomes 2A and 6B, explaining, respectively, 10.9 and 11.5% of the phenotypic variance for resistance to isolate 96-27. The maps around the three major QTLs were enriched with microsatellite markers that could be used in marker-assisted selection of these QTLs.

Recent advances in the fields of computational biology and molecular biology techniques have led to the emerging discipline of population genomics, whose main objective is the study of the spatial structure of genetic diversity. This structure is determined by both neutral forces, like migration and drift, and adaptive forces, like natural selection, and has important applications in many fields like medical genetics or conservation biology. Here, we develop new statistical methods to evaluate the role of natural selection and environment in this spatial structure. All these methods are based on the Bayesian Dirichlet-multinomial model of genetic differentiation. First, we propose to include environmental variables in the estimation process, in order to identify the biotic and abiotic factors that determine the genetic structure. Then, we study the possibility of extending the Dirichlet-multinomial model to dominant markers, which have become very popular in the last few years, but which are affected by various ascertainment biases. Finally, we try to separate neutral effects from adaptive effects on the genetic structure, in order to identify regions of the genome influenced by natural selection. Three databases have been analyzed as illustrations of the use of these new methods: human data, data of argan tree in Morocco, and data of periwinkle. Finally, we developed three softwares implementing these various models; Les récents progrès, dans les domaines de la biologie computationnelle et des techniques de biologie moléculaire, ont conduit à l'émergence d'une nouvelle discipline appelée génomique des populations, et dont l'un des objectifs principaux est l'étude de la structure spatiale de la diversité génétique. Cette structure est déterminée à la fois par des forces neutres, comme la migration et la dérive, et des forces adaptatives comme la sélection naturelle, et trouve des applications importantes dans de nombreux domaines comme la génétique médicale ou la biologie de la conservation. Nous développons ici de nouvelles méthodes statistiques pour évaluer le rôle de la sélection naturelle et de l'environnement dans cette structure spatiale. Le modèle bayésien Dirichlet-multinomial de différenciation génétique est utilisé comme base à ces différentes méthodes. Dans un premier temps, nous proposons d'inclure des variables environnementales dans l'estimation de la structure génétique afin d'identifier les facteurs biotiques et abiotiques qui la déterminent. Ensuite, nous étudions la possibilité d'étendre le modèle Dirichlet-multinomial aux marqueurs dominants, devenus très populaires ces dernières années, mais affectés par différents biais de recrutement. Enfin, nous cherchons à séparer les effets neutres des effets de la sélection naturelle, afin, en particulier, d'identifier les régions du génome qui y sont soumis. Trois bases de données ont été analysées pour illustrer l'utilisation de ces nouvelles méthodes : des données humaines, des données de l'arganier du Maroc et des données de littorine. Finalement, nous avons développé trois logiciels implémentant ces différents modèles.

An integrated map for lettuce comprising of 2,744 markers was developed from seven intra- and inter-specific mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-specific crosses. In the two L. saligna x L. sativa inter-specific crosses, a total of 155 and 116 markers in 13 regions exhibited significant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identification, and studies of genome evolution in the Compositae.

Recent advances in the fields of computational biology and molecular biology techniques have led to the emerging discipline of population genomics, whose main objective is the study of the spatial structure of genetic diversity. This structure is determined by both neutral forces, like migration and drift, and adaptive forces, like natural selection, and has important applications in many fields like medical genetics or conservation biology. Here, we develop new statistical methods to evaluate the role of natural selection and environment in this spatial structure. All these methods are based on the Bayesian Dirichlet-multinomial model of genetic differentiation. First, we propose to include environmental variables in the estimation process, in order to identify the biotic and abiotic factors that determine the genetic structure. Then, we study the possibility of extending the Dirichlet-multinomial model to dominant markers, which have become very popular in the last few years, but which are affected by various ascertainment biases. Finally, we try to separate neutral effects from adaptive effects on the genetic structure, in order to identify regions of the genome influenced by natural selection. Three databases have been analyzed as illustrations of the use of these new methods: human data, data of argan tree in Morocco, and data of periwinkle. Finally, we developed three softwares implementing these various models, Les récents progrès, dans les domaines de la biologie computationnelle et des techniques de biologie moléculaire, ont conduit à l'émergence d'une nouvelle discipline appelée génomique des populations, et dont l'un des objectifs principaux est l'étude de la structure spatiale de la diversité génétique. Cette structure est déterminée à la fois par des forces neutres, comme la migration et la dérive, et des forces adaptatives comme la sélection naturelle, et trouve des applications importantes dans de nombreux domaines comme la génétique médicale ou la biologie de la conservation. Nous développons ici de nouvelles méthodes statistiques pour évaluer le rôle de la sélection naturelle et de l'environnement dans cette structure spatiale. Le modèle bayésien Dirichlet-multinomial de différenciation génétique est utilisé comme base à ces différentes méthodes. Dans un premier temps, nous proposons d'inclure des variables environnementales dans l'estimation de la structure génétique afin d'identifier les facteurs biotiques et abiotiques qui la déterminent. Ensuite, nous étudions la possibilité d'étendre le modèle Dirichlet-multinomial aux marqueurs dominants, devenus très populaires ces dernières années, mais affectés par différents biais de recrutement. Enfin, nous cherchons à séparer les effets neutres des effets de la sélection naturelle, afin, en particulier, d'identifier les régions du génome qui y sont soumis. Trois bases de données ont été analysées pour illustrer l'utilisation de ces nouvelles méthodes : des données humaines, des données de l'arganier du Maroc et des données de littorine. Finalement, nous avons développé trois logiciels implémentant ces différents modèles.

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMapA (R) 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity.

Times Cited: 24; International audience; Today, with the rapid development of population genomics, the genetic basis of adaptation can be unraveled directly at the genome level, without any prerequisites about the selectively advantageous genes or traits. For nonmodel species, it is now possible to screen many markers randomly scattered across the genome and to distinguish between the neutral genetic background and outlier loci displaying an atypical behavior (e.g., a higher differentiation between populations). This study investigated the genetic frame of adaptation to a gradient of altitude in the common frog (Rana temporaria) by means of a genome scan based on 392 amplified fragment length polymorphism markers. Using two outlier detection methods never applied to dominant data so far, we sought for loci with a genetic differentiation diverging from neutral expectations when comparing populations from different altitudes. All the detected loci were sorted out according to their most probable cause for outlier behavior and classified as false positives, outliers due to local effects, or outliers associated with altitude. Altogether, eight good candidate loci were identified as potentially involved in adaptation to altitude because they were picked out in several independent interaltitude comparisons. This result illustrated the potential of genome-wide surveys to reveal selection signatures along selection gradients, where the association between environmental variables and fitness-related traits may be complex and/or cryptic. In this article, we also underlined the need for confirmation of the selection footprints for the outlier loci. Finally, we provided some preliminary insights into the genetic basis of adaptation along an altitudinal cline in the common frog.

• Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. • A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. • Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. • Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL. © The Authors (2005).

V f is the most widely used resistance gene in the breeding for scab resistant apple cultivars. Distorted segregation ratios for V f -resistance have frequently been reported. Here we revealed that sub-lethal genes caused the distorted segregation. The inheritance of V f was examined in six progenies by testing linked molecular markers. Three progenies showed distorted segregations that could be explained by three sub-lethal genes (sl1, sl2 and sl3), of which sl1, sl2 were closely linked to V f . The s11 gene was located at about 14 cM from V f and expressed itself only in the presence of another independently segregating sub-lethal gene sl3. Only the double homozygous recessive genotypes (sl1sl1 sl3sl3) were lethal, which occurred at first as dwarf and poor vigour plants during the first three months after germination. The sl2 gene was also linked to V f and its lethality was expressed prior to seed germination and also required the homozygous recessive presence of sl3. The map position of sl3 has not yet been identified. The linkage of V f to sub-lethal genes usually results in a shortage of V f -resistant progenies. But in some exceptional crosses, it will lead to abundance of resistant seedling.