Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties (original) (raw)
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Genomic variation in recently collected maize landraces from Mexico
Genomics Data, 2016
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 (H E = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (H E = 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.
Genetic signals of origin, spread, and introgression in a large sample of maize landraces
Proceedings of the National Academy of Sciences, 2011
The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid-to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where ...
The Genomic Signature of Crop-Wild Introgression in Maize
PLoS Genetics, 2013
The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome--wide effects of these phenomena has only recently become possible. Crop--wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome--wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize--mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross--incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies. Author Summary Hybridization and introgression have been shown to play a critical role in the evolution of species. These processes can generate the diversity necessary for novel adaptations and continued diversification of taxa. Previous research has suggested that not all regions of a genome are equally permeable to introgression. We have conducted one of the first genome--wide assessments of patterns of reciprocal introgression in plant populations. We found evidence that suggests domesticated maize received adaptations to highland conditions from a wild relative, teosinte, during its spread to the high elevations of central Mexico. Gene flow appeared asymmetric, favoring teosinte introgression into maize, and was widespread across populations at putatively adaptive loci. In contrast, regions near known domestication and cross--incompatibility loci appeared particularly resistant to introgression in both directions of gene flow. Crop--wild study systems should play an important role in future studies of introgression due to their well--developed genomic resources and histories of reciprocal gene flow during crop expansion.
Crop Science, 2008
M aize (ZEA MAYS L.) was domesticated about 9000 yr ago in Mexico from tropical teosinte (Zea mays ssp. parviglumis) (Beadle, 1939; Doebley, 2004). Molecular analyses suggest a single domestication event (Matsuoka et al., 2002) that reduced the diversity present in maize compared to teosinte (Eyre-Walker et al., 1998; Vigouroux et al., 2002). Following domestication, mutation generated new alleles, while recombination created novel allele combinations. Furthermore, postdomestication gene fl ow from teosinte presumably increased the existing genetic base of maize (Doebley, 2004). The genetic variation of domesticated maize populations can be reduced or restructured by genetic drift
Wild Progenitor and Landraces Led Genetic Gain in the Modern-Day Maize (Zea mays L.)
Landraces - Traditional Variety and Natural Breed, 2021
Maize (Zea mays ssp. mays) originated from Mexico and Central America and grew worldwide for food, feed and industrial products components. It possesses ten chromosomes with a genome size of 2.3 gigabases. Teosinte (Z. mays ssp. parviglumis) is the probable progenitor of the modern-day maize. The maize domestication favored standing gain of function and regulatory variations acquired the convergent phenotypes. The genomic loci teosinte branched 1 (tb1) and teosinte glume architecture 1 (tga1) played a central role in transforming teosinte to modern-day maize. Under domestication and crop improvement, only 2% (~1200) genes were undergone selection, out of ~60000 genes. Around ~98% of the genes have not experienced selection; there is enormous variation present in the diverse inbred lines that can be potentially utilized to identify QTLs and crop improvement through plant breeding. The genomic resources of wild relatives and landraces harbor the unexplored genes/alleles for biotic/abi...
PloS one, 2017
This study describes the genetic diversity and population structure of 194 native maize populations from 23 countries of Latin America and the Caribbean. The germplasm, representing 131 distinct landraces, was genetically characterized as population bulks using 28 SSR markers. Three main groups of maize germplasm were identified. The first, the Mexico and Southern Andes group, highlights the Pre-Columbian and modern exchange of germplasm between North and South America. The second group, Mesoamerica lowland, supports the hypothesis that two separate human migration events could have contributed to Caribbean maize germplasm. The third, the Andean group, displayed early introduction of maize into the Andes, with little mixing since then, other than a regional interchange zone active in the past. Events and activities in the pre- and post-Columbian Americas including the development and expansion of pre-Columbian cultures and the arrival of Europeans to the Americas are discussed in re...
Annals of Applied Biology, 2012
The North of Argentina is one of the southernmost areas of maize landrace cultivation. Two distinct centres of diversity have been distinguished within this region: Northwestern Argentina (NWA), and Northeastern Argentina (NEA). Nowadays, maize landraces from this area are faced with two main risks. On the one hand, significant structural and functional changes have modified the rural environment with the boundaries of cropland areas experiencing a rapid expansion at the expense of northern natural forests and rangelands; and on the other, native gene pools are increasingly threatened by hybrids and commercial varieties which are more attractive relative to landraces. The first step towards any conservational action is the acquisition of an inclusive knowledge of the biological resources. For this purpose, our study assesses the genetic diversity and population dynamics of maize landraces from Northern Argentina using microsatellite markers. The Northeastern lowland region (NEA) was represented by 12 landraces (19 populations). In addition, six landraces (eight populations) from the Northwestern highland region (NWA) were used for comparison. For the NEA data set, a total of 126 alleles were found, with an average of 10.5 alleles per locus. Mean H o , H e and R s were 0.350, 0.467 and 2.72, respectively. Global fit to Hardy-Weinberg proportions was observed in 7 of 19 populations. Global estimates of F ST revealed significant differentiation among populations. Bayesian analyses of population structure allowed the recognition of two main gene pools (popcorns versus floury landraces). When NWA was added to the analysis, three clusters were distinguished: NEA popcorns, NEA flours and NWA racial complexes. Additional information on the relationships among these groups was retrieved from cluster analyses. This study shows that lowland landraces from Northern Argentina harbour considerable levels of genetic diversity, with contributions from different gene pools. Further studies encompassing a larger number of populations from the NEA region will certainly help to detect additional genetic variation, which may prove highly valuable in germplasm conservation and management. Future conservation efforts should focus on preserving NEA popcorns, NEA floury and NWA racial complexes as different management units.
Environmental Biosafety Research, 2005
There is much discussion of the probability of transgene flow from transgenic crop varieties to landraces and wild relatives in centers of origin or diversity, and its genetic, ecological, and social consequences. Without costly research on the variables determining gene flow, research on transgene frequencies in landrace (or wild relative) populations can be valuable for understanding transgene flow and its effects. Minimal research requirements include (1) understanding how farmer practices and seed systems affect landrace populations, (2) sampling to optimize N e /n (effective /census population size), (3) minimizing variance at all levels sampled, and (4) using N e to calculate binomial probabilities for transgene frequencies. A key case is maize in Mexico. Two peer-reviewed papers, based on landrace samples from the Sierra Juárez region of Oaxaca, Mexico, reached seemingly conflicting conclusions: transgenes are present (Quist and Chapela, 2001, Nature 414: 541-543; 2002, Nature 416: 602) or "detectable transgenes" are absent (Ortiz-García et al., 2005, Proc. Natl. Acad. Sci. USA 102: 12338-12343 and 18242). We analyzed these papers using information on Oaxacan maize seed systems and estimates of N e . We conclude that if Quist and Chapela's results showing presence are accepted, Ortiz-García et al.'s conclusions of no evidence of transgenes at detectable levels or for their introgression into maize landraces in the Sierra de Juárez of Oaxaca are not scientifically justified. This is because their samples are not representative, and their statistical analysis is inconclusive due to using n instead of N e . Using estimates of N e based on Ortiz-García et al.'s n, we estimate that transgenes could be present in maize landraces in the Sierra Juárez region at frequencies of ~1-4%, and are more likely to be present in the 90% of Oaxacan landrace area that is not mountainous. Thus, we have no scientific evidence of maize transgene presence or absence in recent years in Mexico, Oaxaca State, or the Sierra Juárez region. et al. 198 Environ. Biosafety Res. 4, 4 (2005) (Quist y Chapela, 2001, Nature 414: 541-543; 2002, Nature 416: 602) o no hay "transgénicos detectables" (Ortiz-García et al., 2005, Proc. Natl. Acad. Sci. USA 102: 12338-12343 y 18242). Nosotros hemos analizado estos artículos usando información de los sistemas de semilla de Oaxaca y cálculos de N e . Concluimos que si los resultados de Quist y Chapela mostrando la presencia de transgénicos son aceptados, las conclusiones de Ortiz-García et al. de que no existen transgénicos detectables en los maíces de la Sierra Juárez de Oaxaca no se justifican científicamente. Esto se debe a que los tamaños de muestra usados por Ortiz-García no son representativos y su análisis estadístico no es concluyente por que usaron n en lugar de N e . Usando estimadores de N e basado en el n de Ortiz-García et al., nosotros estimamos que transgénicos pueden ser presente en las razas de maíz de la región de Sierra Juárez en frecuencias de ~1-4%, además es posible que estén presentes en el 90% del área sembrado con maíz criollo que se encuentra en las zonas no montañosas de Oaxaca. Por lo tanto no hay evidencias científicas de la presencia o ausencia de maíz transgénico en años recientes en México, o en el estado de Oaxaca, o en la región de la Sierra Juárez.
bioRxiv (Cold Spring Harbor Laboratory), 2024
Maize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome-wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the Highland Northwestern maize (HNWA) and the Floury Northeastern maize (FNEA). Subsequently, we employed Essential Biodiversity Variables at the genetic level, as proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON), to evaluate the conservation status of these two groups. This assessment encompassed genetic diversity (Pi), inbreeding coefficient (F), and effective population size (Ne). FNEA showed low Ne values and high F values, while HNWA showed low Ne values and low Pi values, indicating that further genetic erosion is imminent for these landraces. Outlier detection methods allowed identification of putative adaptive genomic regions, consistent with previously reported flowering-time loci and chromosomal regions displaying introgression from the teosinte Zea mays ssp. mexicana. Finally, species distribution models were obtained for two future climate scenarios, showing a notable reduction in the potential planting area of HNWA and a shift in the cultivation areas of FNEA. Taken together, these results suggest that maize landraces from Northern Argentina may not be able to cope with climate change. Therefore, active conservation policies are advisable.