Genomic variation in recently collected maize landraces from Mexico

AbstractThe present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE=0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE=0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law

DIVERSIDAD GENÉTICA DE ESPECIES SILVESTRES DEL GÉNERO Nicotiana II: CARACTERIZACIÓN MOLECULAR MEDIANTE MARCADORES RAPD

Las especies silvestres del género Nicotiana son reservorios de genes de resistencia a plagas, así como para rasgos cualitativos y fitoquímicos importantes, los cuales no están presentes en las variedades cultivadas. El objetivo de trabajo fue caracterizar la variabilidad genética de 10 especies silvestres del género Nicotiana mediante el uso de marcadores RAPD (Fragmentos Polimórficos de ADN Amplificados al Azar). De los diez cebadores usados en el ensayo RAPD, cuatrode ellos produjeron productos de amplificación que resultaron apenas visibles para ser evaluados o no fueron consistentemente reproducibles y seis cebadores produjeron un total de 117 bandas, 100% polimórficas. Todas las bandas se evaluaron para la comparación de la amplificación, para un promedio de 19,5 bandas por cebador. El mayor nivel de polimorfismo entre las especies se observó en Nicotianavelutina Wheelen y Nicotiana glutinosa L. con 35,89% y 32,47% respectivamente, ambas del subgénero Petunioides. En contraste, el menor porcentaje de polimorfismo se observó en la especie Nicotiana knightiana Goodsp (18,80%), perteneciente al subgénero Rustica. El patrón obtenido en el dendrograma coincide con la clasificación tradicional de las especies del género Nicotiana. En nueve, de las 10 especies silvestres del género Nicotiana evaluadas, todos los cebadores generaron al menos dos bandas específicas. El total de los 32 marcadores específicos de cada especie encontrados en elpresente estudio podría resultar de gran utilidad en los programas de mejoramiento genético

Admixture output

Contains the log, .Q, .P and se files of the admixture analyses. For command line used and code for plotting see the Scripts section of this repo

Data from: Genomic variation in recently collected maize landraces from Mexico

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. Parviglumis and ssp. Mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a following up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law

Genetic variation and dispersal patterns in three varieties of Pinus caribaea (Pinaceae) in the Caribbean Basin

Background – Pinus caribaea Morelet comprises three varieties of tropical pines distributed in the Caribbean Basin: P. caribaea var. hondurensis, var. caribaea, and var. bahamensis. The insular and continental distribution of these varieties, as well as the geological processes in the region, have been important factors for analysing evolutionary processes implicated in the diversification of these lineages. In this study, we evaluate the genetic and geographic structure within and between these three varieties in order to infer the possible origin and dispersal routes of these taxa.Methods – We used six polymorphic nuclear microsatellites (nSSR) in fifteen representative populations of the three pine varieties, sampled throughout their natural range in Central America, Cuba and the Bahamas islands.Results – The varieties contain similar levels of genetic variation (mean He = 0.571), with several populations out of Hardy-Weinberg equilibrium, and significant levels of inbreeding (0.097–0.184, P ≤ 0.05). A slight but significant genetic differentiation was found between the varieties (RST = 0.088) and populations (RST= 0.082), and genetic differentiation increased with geographic distance (r2 = 0.263). Distance and Bayesian BAPS analyses generated seven groups; two represented by the two island varieties and the remainder by the Central American populations of var. hondurensis. Migration rate estimates between pairs of groups ranged from M = 0.47 to M = 20.16. Estimates were generally higher from the continent to islands, with the highest migration rate estimated from a continental genetic group to the Cuba island group of var. hondurensis (M = 20.16).Conclusions – This study supports the hypothesis of a recent origin of these pine taxa through the migration of an ancestor from Central America, where the historical demography is associated with events of colonization, expansion and contraction of populations. The genetic variation and differentiation suggest that the three varieties are divergent lineages that currently share allelic variants, indicating that their speciation has not yet completed

Genetic variation and dispersal patterns in three varieties of Pinus caribaea (Pinaceae) in the Caribbean Basin

Background – Pinus caribaea Morelet comprises three varieties of tropical pines distributed in the Caribbean Basin: P. caribaea var. hondurensis, var. caribaea, and var. bahamensis. The insular and continental distribution of these varieties, as well as the geological processes in the region, have been important factors for analysing evolutionary processes implicated in the diversification of these lineages. In this study, we evaluate the genetic and geographic structure within and between these three varieties in order to infer the possible origin and dispersal routes of these taxa.Methods – We used six polymorphic nuclear microsatellites (nSSR) in fifteen representative populations of the three pine varieties, sampled throughout their natural range in Central America, Cuba and the Bahamas islands.Results – The varieties contain similar levels of genetic variation (mean He = 0.571), with several populations out of Hardy-Weinberg equilibrium, and significant levels of inbreeding (0.097–0.184, P ≤ 0.05). A slight but significant genetic differentiation was found between the varieties (RST = 0.088) and populations (RST= 0.082), and genetic differentiation increased with geographic distance (r2 = 0.263). Distance and Bayesian BAPS analyses generated seven groups; two represented by the two island varieties and the remainder by the Central American populations of var. hondurensis. Migration rate estimates between pairs of groups ranged from M = 0.47 to M = 20.16. Estimates were generally higher from the continent to islands, with the highest migration rate estimated from a continental genetic group to the Cuba island group of var. hondurensis (M = 20.16).Conclusions – This study supports the hypothesis of a recent origin of these pine taxa through the migration of an ancestor from Central America, where the historical demography is associated with events of colonization, expansion and contraction of populations. The genetic variation and differentiation suggest that the three varieties are divergent lineages that currently share allelic variants, indicating that their speciation has not yet completed

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene

Scripts for analyses and plots

Content: 'admixtureplot.R' to plot admixture analyses, 'maices_estimatingpopgenstats_wrapall.R' R code for estimating He, Ho, and Fst, 'maices_PCAs_plots.html' and 'maices_PCAs_plots.Rmd' show a Rmarkdown document used to plot the PCA, NJ trees and maps. 'runadmixture.sh' code used to run admixture. These scripts need the data and metada available at the DataandMetadata.zip section of this repositor

Data and Meta

'data/SNPs' contains SNP data provided in plink and gds format along with a README of how each file was produced. 'data/spatial' contains the shapefiles used for the maps. Please uncompress each one before use. 'meta/maizteocintle_SNP50k_meta_extended.txt' is a text file containing sampling locality, lat, long, and other metadata of each of the samples. Columns correspond to the data collected as part of the Global Maize Proyect and are further detailed at http://www.biodiversidad.gob.mx/genes/pdf/proyecto/Anexo13_Base %20de%20datos/Contenido%20y%20observaciones%20de%20la%20BdeD.pd