In search of new genomic regions involved in maize domestication.

1. 24 kb 26 kb A In search of new genomic regions involved in maize domestication. Alvarez-Mejia, Cesar, Martinez de la Vega Octavio, Herrera-Estrella Luis, Herrera-Estrella Alfredo, and Vielle-Calzada Jean-Philippe. Laboratorio Nacional de Genómica para la Biodiversdad; Langebio Cinvestav Irapuato. Km. 9.6, Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato Guanajuato México. Introduction Classification and distribution of NIdSRs. Maize was domesticated from Teosinte (Zea mays ssp parviglumis) in Mexico, ~9000 years ago, presumably in a region of the Balsas river drainage, at the intersection of Michoacán and Guerrero and México States1,3. Although some genes such as TB1 and TGA1 were shown to have been affected by artificial selection related to domestication2,4,, their function is not sufficient to explain the drastic morphological differences that distinguish teosinte and maize, suggesting that an important portion of genomic regions that contributed to maize domestication remains to be explored. We have initiated a genomic comparative procedure to find new genomic regions containing gene candidates that were influenced by maize domestication. The distribution of NIdSRs in the ZmB73 genome shows some particularities: (1) Zones highest content of NIdSR’s correspond to regions with chloroplast and mitochondria identity; (2) Zones with lowest content of NIdSR correspond to regions with high nucleotide variability, often related to redundant or repeated sequences, or neutral genes. For further investigation, we selected classes where genomic segments containing tb1 and tga1 are classified. The selection of these classes takes also into consideration a frequency of recombination of at least 1 Cm/Mb, a parwaise length representation of at least 1 Kb, and ZmB73 gene annotation. Close to 200 genes were analyzed and 7 were selected in a pilot screen to study nucleotide variability and test for neutrality. Distribution of Teosinte in Mexico. Adapted from Matzuoka et al 2005 Methodology and Results B. Initial studies of nucleotide variability in gene target regions. Comparative Genomic Analysis ZmB73-Palomero - ≥ 95% of identity. - ≥ 200 pb 100% identical - Non redundant at the genome level. -Selection of Nearly Identical Sequence Region. (NIdSR) From a 200 genes list, we selected 7 genes to analyse nucleotide variability in 16 native landraces and 16 local Balsas teosinte populations. We also plan to pursue our analysis of previously identified regions containing heavy meal response affected by domestication8. Identification and comparison of these genes with their genomic sequence in Mo17 inbred line confirmed a drastic reduction in nucleotide variability. - Length ≥ 1 Kb - Gene Annotation - High concentration of NidSR/150 Kb - Frequency of recombination ≥ 1 Cm/Mb Gene Target -Selection of 10 candidates genes. - Selection and annotation of 100 Kb around the NidSR selected. - Polymorphic analysis of three regions contained within 100 Kb. Polymorphic analysis determination A. Genomic comparison of Zea mays ssp mays B73 inbred line6,7 (ZmB73) and Zea mays ssp mays Palomero landrace8 (ZmPal) and identification of Nearly Identical Sequences Regions (NIdSRs) C. Selection of widely diverse regions for analysis of nucleotide variability. Taking the position of the target gene as a reference, we will analyse nucleotide variability in a region encompassing 100 kb around the coding sequence. This procedure could offer hints on possible events of selection sweep. Distribution of NIdSRs in continous 150 Kb genomic segments Example of genomic structure and annotation of 100 kb around a target gene (A). Blue: ZmB73 genome linear trend. Red: location of Palomero sequences with at least 95% shared identity. Regions for nucleotide polymorphic analysis are marked in green. Summary. a) Genomic sequence comparisons between a maize landrace and an inbred line are useful to find new genomic regions involved in domestication. b) Regions containing a high number of NIdSRs can often represent organellar genome insertions. c) A pilot analysis of nucleotide variability is underway for new widely distributed regions showing low polymorphism in B73, Palomero, and Mo17. Acknowledgements. We thank Patrick Schnable for frequency recombination data and maizegdb and maizesequence for the B73 genome data. This work was supported by grant ZEA-2006 from SAGARPA, CONACyT, and the Howard Hughes Medical Institute International Scholars Program. Red Line. Distribution of NIdSRs in segments of 150 Kb each. Blue Line, Frequency of recombination (in Cm/Mb5) Grey Lines, Syntenic analysis of 150 Kb regions containg highest number of NIdSRs. References Moeller, D. A., Tenaillon, M. I., Tiffin, P. , Genetics. 176, 1799-809 (2007). Clark, R. M., Wagler, T. N., Quijada, P., Doebley, J. , Nature Genetics. 38, 594-7 (2006). Matsuoka, Y. , Breeding Science. 55, 383-390 (2005). Doebley, J., Gaut, B., Smith, B. , Cell. 127, 1309-1321 (2006). Liu S., Yeh, C.-T., Ji, T., K. Ying, Wu, H., Tang, H. M., Fu, Y., Nettleton,D., and Schnable,P. S., PLoS Genetics5:e1000733 (2009). http://www.maizegdb.org http://www.maizesequence.org 8. Vielle-Calzada J.-P., Martinez De La Vega, O., Hernandez-Guzman, G., et al. Science. 326:1078-1078 (2009). The NIdSR distribution in the genome of zmB73 was grouped in arbitrary classes depending on their NidSR content per 150 Kb segments. Whereas classes containing the highest number NIdSRs (class 17 to 26)are related to chloroplast and mitochondria genomic insertions, classes with lowest number of NIdSRs are related to neutral genes (Class 1 to 5).