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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 ...
Proceedings of the National Academy of Sciences, 2016
Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens dating at a similar age of 5,300–4,970 calibrated y B.P. On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, we show herein that the earliest maize from San Marcos cave was a partial domesticate diverging from the landraces and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci, such as teosinte branched1 (tb1) and brittle endosperm2 (bt2), had already lost most of the nucleotide variability present in Balsas teosinte, others, such as teosinte glume architecture1 (tga1) and sugary1 (su1), conserved partial levels of nucleotide v...
The relevance of gene flow with wild relatives in understanding the domestication process
Royal Society Open Science, 2020
The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the many aspects of domestication process depends on having an adequate representation of wild relatives. Cultivated maize ( Zea mays ssp. mays ) is one of the most important crops in the world, with a long and a relatively well-documented history of domestication. The current consensus points towards a single domestication event from teosinte Zea mays ssp. parviglumis from the Balsas Basin in Southwestern Mexico. However, the underlying diversity of teosintes from Z. mays ssp . parviglumis and Zea mays ssp. mexicana was not taken into account in early studies. We used 32 739 single nucleotide polymorphisms (SNPs) obtained from 29 teosinte populations and 43 maize landraces to explore the re...
Proceedings of the National Academy of Sciences
Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index (FST) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a result ...
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...
Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs
Frontiers in genetics, 2017
In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into "landraces." Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples. In order to investigate the genomic foundation of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina MaizeSNP50 BeadChip) obtained from 50 samples representing five maize landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico), and searched for markers suitable for landrace assignment. Landrace clusters could not be identified taking all the genomic information, but they become manifest taking only a subset of SNPs with high FST am...