Genetic signals of origin, spread, and introgression in a large sample of maize landraces

Abstract

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 subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.T he geography of origins and diversification of agricultural species has important implications for unraveling the ecological context of Neolithic societies and for understanding current patterns of diversity in domesticated plants and animals. Traditionally the realm of archeology and botany (1, 2), the study of plant domestication has seen important contributions from genetics during the last two decades (3). Genetic data often provide evidence that is hard to obtain by other means, making it an invaluable complement to other lines of inquiry.As a case in point, molecular markers were instrumental in establishing the single domestication of maize (Zea mays subspecies mays) from an extant wild relative (4, 5). Maize was shown to originate from annual teosinte (Zea mays subspecies parviglumis, hereafter parviglumis) around 9,000 y B.P., placing domestication in the mid-to lowland regions of southwest Mexico where parviglumis grows endemically. As predicted by this result (6), excavations in the heart of parviglumis' distribution have produced the earliest (8,700 y B.P.) phytolith evidence for maize cultivation (7). Other finds from Tabasco (7,300 y B.P.) (8) and Panama (7,400 y B.P.) (9) also support an early presence of maize throughout the Meso-American lowlands.Although different types of evidence seemingly concur, questions nonetheless remain about the interpretation of the genetic data. While unequivocal with respect to maize's wild ancestor, marker evidence suggests that maize from the Mexican highlands, rather than from the lowlands, is most closely related to parviglumis and appears to have given rise to all cultivars currently grown throug...

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

“…Recently, phylogeographic studies have added substantially to the understanding of crop history (Van Heerwaarden et al, 2011;Oliveira et al, 2012;Roullier et al, 2013). However, if a study is performed on a finer geographical scale, more power in terms of genetic markers and number of individuals is needed.…”

“…Phylogeographic studies of landrace crops have often been restricted to single individuals (for example, Saisho and Purugganan, 2007;Isaac et al, 2010;Van Heerwaarden et al, 2011) or aggregate samples from accessions, using pooling schemes (for example, Hunt et al, 2011;Jones et al, 2011;Oliveira et al, 2012). This allows a much higher number of accessions to be studied, but comes at the cost of ignoring within-accession genetic diversity.…”

“…Geographic patterns in the distribution of genetic diversity can give information about the geographic origin of lineages or the effects of migration routes (Avise, 2009) and have, among other species, been applied to crop plants (for example, Olsson and Schaal, 1999;Londo et al, 2006;Saisho and Purugganan, 2007). Insights into the genetic structure of crop species provide not only a better understanding of their evolutionary history but can also increase the knowledge about cultural exchange in agrarian communities (Van Heerwaarden et al, 2011;Oliveira et al, 2012;Roullier et al, 2013).…”

Genetic Architecture of Domestication-Related Traits in Maize

“…genetic diversification from selection for adaptation to new environments and distinct crop uses in different populations (Darwin 1868;van Heerwaarden et al 2011;Hufford et al 2012;Meyer and Purugganan 2013). Integrating information about the genetic architecture of domestication traits with population genetics data can help refine the understanding of the contribution of sequence variation to domestication and postdomestication developmental and morphological changes in crops.…”

Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

“…In addition, mapping populations of inter-mated B73xMo17 recombinant inbred lines and doubled haploids have been generated to facilitate genetic analyses 9,10 . Numerous comparative genomics studies of other maize cultivars and wild ancestors have examined the origin of maize as well as events of adaptation and artificial selection [11][12][13][14][15][16][17] . However, the studies are limited to comparisons of non-repetitive and low-repetitive sequences.…”