A study of allelic diversity underlying flowering-time adaptation in maize landraces

Abstract

Landraces (traditional varieties) of domesticated species preserve useful genetic variation, yet they remain untapped due to the genetic linkage between the few useful alleles and hundreds of undesirable alleles. We integrated two approaches to characterize the diversity of 4,471 maize landraces. First, we mapped genomic regions controlling latitudinal and altitudinal adaptation and identified 1,498 genes. Second, we used F-one association mapping (FOAM) to map the genes that control flowering time, across 22 environments, and identified 1,005 genes. In total, we found that 61.4% of the single-nucleotide polymorphisms (SNPs) associated with altitude were also associated with flowering time. More than half of the SNPs associated with altitude were within large structural variants (inversions, centromeres and pericentromeric regions). The combined mapping results indicate that although floral regulatory network genes contribute substantially to field variation, over 90% of the contributing genes probably have indirect effects. Our dual strategy can be used to harness the landrace diversity of plants and animals.

Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs

“…We identified 14 landrace-informative SNPs that are independent from altitude. Even though our altitude analysis does not account for all the environmental factors, previous studies establish altitude as the principal factor shaping maize genomic variation (van Heerwaarden et al, 2011; Breña Ochoa, 2013; Arteaga et al, 2015; Romero Navarro et al, 2017), thus making it a valid approximation of environmentally driven natural selection.…”

“…Recent studies on Mexican maize genomic diversity have found that the distribution of genetic variation is better explained by environmental variables governed by altitude and latitude than by landrace identity (van Heerwaarden et al, 2011; Breña Ochoa, 2013; Arteaga et al, 2015; Romero Navarro et al, 2017). Maize is grown throughout Mexico along an altitude gradient spanning 0–2,700 masl.…”

“…Maize is grown throughout Mexico along an altitude gradient spanning 0–2,700 masl. This wide range in altitude correlates with a substantial range in temperature and moisture gradients, which are associated with local adaptation of maize populations growing at different altitudes (Pressoir and Berthaud, 2004; Mercer et al, 2008; Ruiz-Corral et al, 2008; Romero Navarro et al, 2017). Agronomically, local adaptation implies high levels of genotype-by-environment interactions, making it difficult to grow landraces in altitudes different from their original ones (Perales et al, 2003; Mercer et al, 2008; Lorant et al, 2017).…”

“…parviglumis growing in lowlands. Highland maize populations' genomic constitution is notably influenced by teosinte mexicana growing sympatrically, as there are high levels of gene flow among them (van Heerwaarden et al, 2011; Hufford et al, 2013; Lorant et al, 2017; Romero Navarro et al, 2017). Taken together, these facts account for the correlation between genetic variation and altitude.…”

The C4 Model Grass Setaria Is a Short Day Plant with Secondary Long Day Genetic Regulation

“…Breeding for insensitivity was an early step in the improvement of maize, with selection first occurring in pre-historic times by early farmers as they took maize north and south from its site of domestication in central Mexico (Romero Navarro et al, 2017). Similar efforts were made by sorghum breeders in the last century as they moved African tropical germplasm to temperate latitudes in the United States, Australia and Europe (Stephens et al, 1967).…”