Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado \u2018Hass\u2019 draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan 7 Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community

Random Amplified Polymorphic DNA Analysis of Olive (Olea europaea L.) Cultivars

J. AM. SOC. HORT. SCI

Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics

Well-resolved phylogenetic trees are essential for us to understand evolutionary processes at the level of species. The degree of species-level resolution in the plant phylogenetic literature is poor, however, largely due to the dearth of sufficiently variable molecular markers. Unlike the common genic approach to marker development, we generated DNA sequences of monomorphic nuclear microsatellite flanking regions in a phylogenetic study of Annona species (Annonaceae). The resulting data showed no evidence of paralogy or allelic diversity that would confound attempts to reconstruct the species tree. Microsatellite flanking regions are short, making them practical to use, yet have astounding proportions of variable characters. They have 3.5- to 10-fold higher substitution rates compared to two commonly used chloroplast markers, have no rate heterogeneity among nucleotide positions, evolve in a clock-like fashion, and show no evidence of saturation. These advantages are offset by the short length of the flanking regions, resulting in similar numbers of parsimony informative characters to the chloroplast markers. The neutral evolution and high variability of flanking regions, together with the wide availability of monomorphic microsatellite loci in angiosperms, are useful qualities for species-level phylogenetics. The general methodology we present here facilitates to find phylogenetic markers in groups where microsatellites have been develope

Las regiones flanqueantes de loci de microsatélites monomórficos proporcionan una nueva fuente de datos para la filogenia a nivel de especie vegetal

Los árboles filogenéticos bien resueltos son esenciales para que comprendamos los procesos evolutivos a nivel de especies. Sin embargo, el grado de resolución a nivel de especie en la literatura filogenética vegetal es pobre, en gran parte debido a la escasez de marcadores moleculares suficientemente variables. A diferencia del enfoque genético común para el desarrollo de marcadores, generamos secuencias de ADN de regiones flanqueantes de microsatélites nucleares monomórficos en un estudio filogenético de Annonaespecies (Annonaceae). Los datos resultantes no mostraron evidencia de paralogía o diversidad alélica que confundiría los intentos de reconstruir el árbol de la especie. Las regiones flanqueantes de microsatélites son cortas, lo que las hace prácticas de usar, pero tienen proporciones asombrosas de caracteres variables. Tienen tasas de sustitución de 3,5 a 10 veces más altas en comparación con dos marcadores de cloroplasto comúnmente utilizados, no tienen heterogeneidad de tasas entre las posiciones de los nucleótidos, evolucionan en forma de reloj y no muestran evidencia de saturación. Estas ventajas se compensan con la corta longitud de las regiones flanqueantes, lo que da como resultado un número similar de caracteres informativos de parsimonia a los marcadores de cloroplasto. La evolución neutra y la alta variabilidad de las regiones flanqueantes, junto con la amplia disponibilidad de loci de microsatélites monomórficos en las angiospermas, son cualidades útiles para la filogenia a nivel de especie. La metodología general que presentamos aquí facilita la búsqueda de marcadores filogenéticos en grupos donde se han desarrollado microsatélites.Well-resolved phylogenetic trees are essential for us to understand evolutionary processes at the level of species. The degree of species-level resolution in the plant phylogenetic literature is poor, however, largely due to the dearth of sufficiently variable molecular markers. Unlike the common genic approach to marker development, we generated DNA sequences of monomorphic nuclear microsatellite flanking regions in a phylogenetic study of Annona species (Annonaceae). The resulting data showed no evidence of paralogy or allelic diversity that would confound attempts to reconstruct the species tree. Microsatellite flanking regions are short, making them practical to use, yet have astounding proportions of variable characters. They have 3.5- to 10-fold higher substitution rates compared to two commonly used chloroplast markers, have no rate heterogeneity among nucleotide positions, evolve in a clock-like fashion, and show no evidence of saturation. These advantages are offset by the short length of the flanking regions, resulting in similar numbers of parsimony informative characters to the chloroplast markers. The neutral evolution and high variability of flanking regions, together with the wide availability of monomorphic microsatellite loci in angiosperms, are useful qualities for species-level phylogenetics. The general methodology we present here facilitates to find phylogenetic markers in groups where microsatellites have been developed

Human diets drive range expansion of megafauna-dispersed fruit species

Peer Revie