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Previous studies showed that the number of berries is a major component of the compactness level of the grapevine clusters. Variation in number of fruits is regulated by events occurring in the fruitset, but also before during the flower formation and pollination, through factors like the initial number of flowers or the gametic viability. Therefore, the identification of the genetic bases of this variation would provide an invaluable knowledge of the grapevine reproductive development and useful tools for managing yield and cluster compactness. We performed the phenotyping of four clones (two compact and two loose clones) of the Tempranillo cultivar with reproducible different levels of cluster compactness over seasons. Measures of reproductive performance included flower number per inflorescence, berry number per cluster, fruitset, coulure, and millerandage indices. Besides, their levels of several hormones during the inflorescence and flower development were determined, and their transcriptomes were evaluated at critical time points (just before the start and at the end of flowering). For some key reproductive traits, like number of berries per cluster and number of seeds per berry, clones bearing loose clusters showed differences with the compact clones and also differed from each other, indicating that each one follows different paths to produce loose clusters. Variation between clones was observed for abscisic acid and gibberellins levels at particular development stages, and differences in GAs could be related to phenotypic differences. Likewise, various changes between clones were found at the transcriptomic level, mostly just before the start of flowering. Several of the differentially expressed genes between one of the loose clones and the compact clones are known to be over-expressed in pollen, and many of them were related to cell wall modification processes or to the phenylpropanoids metabolism. We also found polymorphisms between clones in candidate genes that could be directly involved in the variation of the compactness level., This work was financially supported by the projects AGL2014- 59171R (co-funded by FEDER), AGL2010-15694, and the Ramón y Cajal (grant RYC-2011-07791), all from the Spanish MINECO.

Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r2-value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond., This work was supported by the Research Group A12 of Aragón (Spain) and the Marie Curie fellowship to AM.

To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in ‘Structure’ grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value. Published

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Lentil quantitative trait loci (QTL) related to plant structure (branches at first node, height of first node, total number of branches, plant height), growth habit (flowering time, pod dehiscence) and yield (number of seeds, seed weight, seed diameter) were located using a F2 population of 113 individuals derived from the intersubspecific cross of Lens culinaris ssp. culinaris and L. c. ssp. orientalis. Several traits were found to be significantly correlated. Using interval and composite interval mapping a total of 23 QTL for nine quantitative traits were located. No QTL was identified for the number of F3 seed produced. Six QTL were positioned respectively in linkage groups III and VI, and five QTL in linkage group I. Each remaining group included one or two QTL, except groups VII and IX where no QTL was found. The multiple QTL model explained more than 80% of the observed phenotypic variance with logarithm of the odds (LOD) scores above 10 for three of the quantitative traits analyzed (branches at first node, flowering time, and dehiscence). For the remaining traits the phenotypic variance explained was relatively low, between the 50% and 20%, and the LOD scores ranged between 4 and 8. The possible homology between some QTL and other previously described is discussed in relation to their chromosomal location., Se han cartografiado loci cuantitativos (QTL) de lenteja relacionados con la estructura de la planta (ramificaciones en el primer nudo, altura del primer nudo, número total de ramificaciones, altura de la planta), el ciclo de crecimiento (momento de floración, dehiscencia de vainas) y el rendimiento (número de semillas, peso de la semilla, diámetro de la semilla) utilizando una población F2 derivada del cruzamiento intersubespecífico de Lens culinaris ssp. culinaris por L. c. ssp. orientalis. Se encontraron varias características significativamente correlacionadas. Aplicando los métodos de los marcadores flanqueantes simple y compuesto, se localizó un total de 23 QTL para nueve características cuantitativas. No se identificó ningún QTL para el número de semillas F3 producidas. Se localizaron seis QTL respectivamente en los grupos de ligamiento III y VI, y cinco QTL en el grupo de ligamiento I. En cada uno de los restantes grupos de ligamiento se localizó uno o dos QTL, excepto en los grupos de ligamiento VII y IX, en los que no se hallaron QTL. El modelo múltiple de QTL explicó más de un 80% de la varianza fenotípica observada con valores del logaritmo decimal del cociente de verosimilitudes (LOD) por encima de 10 para tres de las características cuantitativas analizadas (ramificaciones en el primer nudo, momento de floración, dehiscencia de vainas). La varianza fenotípica explicada para el resto de las características fue relativamente baja, entre 50% y 20%, con valores LOD oscilando entre 4 y 8. Se discute la posible homología entre algunos QTL y otros previamente descritos en relación a su localización cromosómica.

Analysis of the ribosomal DNA (rDNA) intergenic spacers (IGS) (i.e., the IGS of 18S, 5.8S and 24S rDNA, and the NTS or non-transcribed spacer of 5S rDNA) of lentil cultivars and landraces (L. culinaris spp. culinaris) showed to have very low intraspecific length variability. PCR products of approximately 3200 bp were obtained from all cultivated materials; no significant electrophoretic differences were found between them. However, observable intraspecific polymorphism increased with the digestion of PCR-amplified IGSs by the restriction endonucleases BspHI, StuI and BstBI. This was also the case when specific PCR primers designed to amplify a particularly variable segment of the IGS were used. This segment includes two families of short, tandemly arranged, repeated sequences. Both methods revealed differences between some of the cultivated materials, yielding genetic markers that might be useful in further genetic mapping and breeding studies. Several NTS amplification products were observed in each plant, ranging from approximately 300 to 900 bp in the cultivated lentil. Differences between L. culinaris spp. culinaris and its related wild species (including the wild ancestor of the cultigen, L. culinaris spp. orientalis) were observed in the total length of their IGSs, the restriction patterns of the latter, and in their NTS variants., Los espaciadores intergénicos del DNA ribosomal (el IGS o espaciador intergénico del rDNA 18S, 5.8S, y 24S, y el NTS o espaciador no transcrito del rDNA 5S) de lenteja (L. culinaris spp. culinaris) mostraron muy poca variabilidad intraespecífica, tanto en cultivares como en variedades locales. De todos los materiales de esta especie se obtuvieron productos de amplificación por PCR con una longitud de unas 3200 pb, no observándose diferencias significativas mediante separación por electroforesis. Sin embargo, el polimorfismo intraespecífico aumentó mediante la digestión con endonucleasas de restricción (BspHI, StuI, y BstBI) de los IGS amplificados por PCR o por el uso de cebadores específicos que amplificaban segmentos particularmente variables del IGS. Estos segmentos incluyen dos familias de secuencias cortas agrupadas. Con ambos métodos se observaron diferencias entre materiales de lenteja, utilizables como posibles marcadores genéticos en posteriores trabajos de mejora o genética, como la confección de mapas genéticos. Se observaron varios productos de amplificación NTS en cada planta, cuyo tamaño osciló entre unas 300 y 900 pb en la lenteja cultivada, no observándose diferencias entre estos materiales. Sí se observaron diferencias entre L. culinaris spp. culinaris y las especies silvestres del género Lens (incluido el ancestro silvestre del cultigen, L. culinaris spp. orientalis), tanto en la longitud del IGS, como en su patrón de restricción, y en los conjuntos de NTS.

Analysis of the ribosomal DNA (rDNA) intergenic spacers (IGS) (i.e., the IGS of 18S, 5.8S and 24S rDNA, and the NTS or non-transcribed spacer of 5S rDNA) of lentil cultivars and landraces (L. culinaris spp. culinaris) showed to have very low intraspecific length variability. PCR products of approximately 3200 bp were obtained from all cultivated materials; no significant electrophoretic differences were found between them. However, observable intraspecific polymorphism increased with the digestion of PCR-amplified IGSs by the restriction endonucleases BspHI, StuI and BstBI. This was also the case when specific PCR primers designed to amplify a particularly variable segment of the IGS were used. This segment includes two families of short, tandemly arranged, repeated sequences. Both methods revealed differences between some of the cultivated materials, yielding genetic markers that might be useful in further genetic mapping and breeding studies. Several NTS amplification products were observed in each plant, ranging from approximately 300 to 900 bp in the cultivated lentil. Differences between L. culinaris spp. culinaris and its related wild species (including the wild ancestor of the cultigen, L. culinaris spp. orientalis) were observed in the total length of their IGSs, the restriction patterns of the latter, and in their NTS variants. Los espaciadores intergénicos del DNA ribosomal (el IGS o espaciador intergénico del rDNA 18S, 5.8S, y 24S, y el NTS o espaciador no transcrito del rDNA 5S) de lenteja (L. culinaris spp. culinaris) mostraron muy poca variabilidad intraespecífica, tanto en cultivares como en variedades locales. De todos los materiales de esta especie se obtuvieron productos de amplificación por PCR con una longitud de unas 3200 pb, no observándose diferencias significativas mediante separación por electroforesis. Sin embargo, el polimorfismo intraespecífico aumentó mediante la digestión con endonucleasas de restricción (BspHI, StuI, y BstBI) de los IGS amplificados por PCR o por el uso de cebadores específicos que amplificaban segmentos particularmente variables del IGS. Estos segmentos incluyen dos familias de secuencias cortas agrupadas. Con ambos métodos se observaron diferencias entre materiales de lenteja, utilizables como posibles marcadores genéticos en posteriores trabajos de mejora o genética, como la confección de mapas genéticos. Se observaron varios productos de amplificación NTS en cada planta, cuyo tamaño osciló entre unas 300 y 900 pb en la lenteja cultivada, no observándose diferencias entre estos materiales. Sí se observaron diferencias entre L. culinaris spp. culinaris y las especies silvestres del género Lens (incluido el ancestro silvestre del cultigen, L. culinaris spp. orientalis), tanto en la longitud del IGS, como en su patrón de restricción, y en los conjuntos de NTS.

Lentil quantitative trait loci (QTL) related to plant structure (branches at first node, height of first node, total number of branches, plant height), growth habit (flowering time, pod dehiscence) and yield (number of seeds, seed weight, seed diameter) were located using a F2 population of 113 individuals derived from the intersubspecific cross of Lens culinaris ssp. culinaris and L. c. ssp. orientalis. Several traits were found to be significantly correlated. Using interval and composite interval mapping a total of 23 QTL for nine quantitative traits were located. No QTL was identified for the number of F3 seed produced. Six QTL were positioned respectively in linkage groups III and VI, and five QTL in linkage group I. Each remaining group included one or two QTL, except groups VII and IX where no QTL was found. The multiple QTL model explained more than 80% of the observed phenotypic variance with logarithm of the odds (LOD) scores above 10 for three of the quantitative traits analyzed (branches at first node, flowering time, and dehiscence). For the remaining traits the phenotypic variance explained was relatively low, between the 50% and 20%, and the LOD scores ranged between 4 and 8. The possible homology between some QTL and other previously described is discussed in relation to their chromosomal location. Se han cartografiado loci cuantitativos (QTL) de lenteja relacionados con la estructura de la planta (ramificaciones en el primer nudo, altura del primer nudo, número total de ramificaciones, altura de la planta), el ciclo de crecimiento (momento de floración, dehiscencia de vainas) y el rendimiento (número de semillas, peso de la semilla, diámetro de la semilla) utilizando una población F2 derivada del cruzamiento intersubespecífico de Lens culinaris ssp. culinaris por L. c. ssp. orientalis. Se encontraron varias características significativamente correlacionadas. Aplicando los métodos de los marcadores flanqueantes simple y compuesto, se localizó un total de 23 QTL para nueve características cuantitativas. No se identificó ningún QTL para el número de semillas F3 producidas. Se localizaron seis QTL respectivamente en los grupos de ligamiento III y VI, y cinco QTL en el grupo de ligamiento I. En cada uno de los restantes grupos de ligamiento se localizó uno o dos QTL, excepto en los grupos de ligamiento VII y IX, en los que no se hallaron QTL. El modelo múltiple de QTL explicó más de un 80% de la varianza fenotípica observada con valores del logaritmo decimal del cociente de verosimilitudes (LOD) por encima de 10 para tres de las características cuantitativas analizadas (ramificaciones en el primer nudo, momento de floración, dehiscencia de vainas). La varianza fenotípica explicada para el resto de las características fue relativamente baja, entre 50% y 20%, con valores LOD oscilando entre 4 y 8. Se discute la posible homología entre algunos QTL y otros previamente descritos en relación a su localización cromosómica.