Symposium II: Maize Biology
S024: The Codifying Genome of the Palomero Mexican landrace.
Vielle-Calzada, Jean-Philippe Contact Presenter||Authors||Vielle-Calzada, Jean-Philippe (A) Martinez de la Vega, Octavio (A) Vega-Arrenguin, Julio (A) Hernandez-Guzman, Gustavo (A) Ibarra-Laclette, Enrique (A) Jimenez-Moraila, Beatriz (A) Corona-Armenta, Guilermo (A) Alvarez-Mejia, Cesar (A) Fernandez-Cortes, Araceli (A) de la Riva, Gustavo (A) Herrera-Estrella, Alfredo (A) Herrera-Estrella, Luis (A) |
(A): National Laboratory of Genomics for Biodiversity - Cinvestav Mexico|
Large-scale sequencing efforts concentrated in B73 will not be sufficient to fully understand maize genome organization and identify all functional units available in the domesticated gene pool. To complement the large-scale B73 sequencing initiative and explore landrace genomic diversity, we undertook the structural and functional characterization of the Palomero genome after estimating its genome to be 22% smaller than B73. Palomero is an ancient popcorn landrace and a member of the Central and Northern Highlands Group that produce short individuals (140-180 cm) and grow at elevations above 2000 meters. A total of 1.2 million Sanger reads (10% HCot; 90% enzyme-based methyl-filtration) and 213 pyrosequencing runs (50% methyl-filtered, 50% whole genome sequencing) were sequenced for a 3.2X coverage. A total of 337.6 Mb have been assembled in close to 400,000 gene-enriched contigs averaging 0.91 kb in size. This effort has been complemented by an in-depth pyrosequence-based global transcriptional analysis of the same genotype. As expected, a significant percentage of codifying transcripts are not reported in public databases, suggesting that a large portion of the molecular and functional diversity contained in landraces remains unexplored. We have identified a collection of ultraconserved genomic regions lacking polymorphisms between Palomero and the inbred line B73. Our results represent an initial landmark to explore the functional diversity of Mexican landraces in the context of maize domestication and enhancement.