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United States Department of Agriculture

Agricultural Research Service


Location: Plant Science Research

2012 Annual Report

1a.Objectives (from AD-416):
Objectives are to (1) identify genes and genome regions controlling key traits in diverse maize germplasm using multiple populations and novel genetic mapping methods; (2) identify and characterize new sources of resistance to southern leaf blight (SLB), gray leaf spot (GLS), northern leaf blight (NLB), and Fusarium ear rot by developing new near-isogenic line sets, identifying QTL conferring resistance to multiple foliar diseases, and evaluating the known genetic diversity among public maize inbreds; and (3) incorporate favorable alleles from exotic maize into adapted maize lines, with particular emphasis on improvement of resistance to Fusarium ear rot and fumonisin contamination.

1b.Approach (from AD-416):
Develop genetic mapping populations appropriate for identification of favorable alleles in exotic maize by identifying genome regions and specific genes controlling the response to photoperiod in multiple tropical maize inbreds. Develop interconnected multiple populations and novel statistical methods to map specific genes controlling quantitative trait variation in diverse maize. Fine-map QTL for SLB, NLB, GLS, Fusarium ear rot and fumonisin contamination resistance. Characterize specific disease resistance QTL using near-isogenic line pairs. Identify QTL conferring resistance to multiple foliar diseases. Complete multiple environment screening of a 302-line population encompassing the known genetic diversity among public maize inbreds for resistance to SLB, NLB and GLS. Identify new sources of resistance to SLB, Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Develop new lines with elite agronomic performance and enhanced resistance to Fusarium ear rot by backcrossing. Test if selection for resistance to Fusarium ear rot results in improved resistance to contamination by the associated mycotoxin fumonisin.

3.Progress Report:
Millions of DNA variants were tested to identify 50 - 100 associated with the flowering response of maize to long daylengths. Several of these associated variants are in or adjacent to genes that have been shown to control daylength responses in other crops. A combination of high resolution genetic mapping in multiple populations, association analysis, and gene expression assays confirmed the identity of a gene called ZmCCT as the most important photoperiod response gene in maize.

Superior backcross-derived lines combining resistance to Fusarium ear rot and hybrid yield potential were identified and advanced to 2nd year yield trials. 50 advanced lines from the USDA Germplasm Enhancement of Maize (GEM) project and the North Carolina State University maize inbred development programs were tested for resistance to Fusarium ear rot and fumonisin contamination resistance. 100 GEM lines were tested for resistance to southern leaf blight.

Several loci associated with the maize hypersensitive defense response have been identified with extremely high precision using association mapping in a population of 300 diverse lines each of which was genotyped by our collaborators at ~50,000 SNP loci.

We created two maize chromosome segment substitution line populations of 300 lines each, designed specifically for the identification of disease resistance loci. Each line within a population shares a common genetic background that is susceptible to multiple diseases, carries a different genomic segment bred in from a more resistant variety. This will allow us to test the effect of small genomic substitutions on multiple disease resistance, as a way to locate resistance genes.

We have used RNA-seq technology to define a set of 8000 genes that are significantly up or down-regulated during the maize hypersensitive response.

Previously we identified several loci from teosinte, the wild progenitor of maize, which were associated with resistance to southern leaf blight and gray leaf spot. We have now produced populations segregating for these loci and using these populations in two cases have successfully verified their effects.

1. Identification of genes associated with plant disease response. A genome wide association study was performed to detect loci modulating the hypersensitive defense response associated with a maize mutant gene Rp1-D21, which causes plants to react as if they were infected by a pathogen even in the absence of the pathogen. The population analyzed was based on genetic crosses of 279 diverse maize inbreds with a line carrying Rp1-D21. The population was evaluated for visible signs of the defense response in the field over 2 years (2009 and 2010) across two locations, IN and NC. More than 50,000 DNA sequence variants were tested for association with the hypersensitive response. The known hrm1 QTL was detected in this analysis but with a much higher precision than previously. Five genes associated with the defense response were mapped with extremely high precision. Four of these genes are known to be involved with programmed cell death pathways. These genes are being further analyzed.

Review Publications
Hung, H., Browne, C.J., Guill, K.E., Coles, N., Eller, M., Garcia, A., Lepak, N.K., Melia-Hancock, S., Oropeza-Rosas, M., Salvo, S., Upadyayula, N., Buckler IV, E.S., Flint Garcia, S.A., Mcmullen, M.D., Rocheford, T., Holland, J.B. 2012. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity. 108:490-499.

Holland, J.B., Coles, N.D. 2011. QTL controlling masculinization of ear tips in a maize (Zea mays L.) intraspecific cross. Genes, Genomes, and Genomics. 1:337-341.

Hung, H., Shannon, L.M., Tian, F., Bradbury, P., Chen, C., Flint Garcia, S.A., McMullen, M.D., Ware, D., Buckler IV, E.S., Doebley, J.F., Holland, J.B. 2012. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proceedings of the National Academy of Sciences. 109:E1913–E1921.

Avendano-Lopez, A., Sanchez-Gonzales, J., Ruiz-Corral, J., De La Cruz-Larios, L., Santacruz-Rubalcava, F., Sanchez Hernandez, C., Holland, J.B. 2011. Seed dormancy in Mexican teosinte. Crop Science. 51:2056-2066.

Sanchez-Gonzales, J.J., De La Cruz, L., Vidal, V.A., Parra, R.J., Taba, S., Santacruz, F., Sood, S., Holland, J.B., Ruiz, J.A., Carvajal, S., Aragon, F., Chavez, V.H., Morales, M.M., Barba, R. 2011. Three New Teosintes (Zea spp., Poaceae) From Mexico. American Journal of Botany. 98:1537-1548.

Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M.A., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B., Phyajarvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S.M., Ross-Ibarra, J., McMullen, M.D., Buckler IV, E.S., Zhang, G., Xu, Y., Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 40:803-807. DOI: 10.1038/ng.2313.

Brown, P.J., Upadyayula, N., Mahone, G.S., Tian, F., Bradbury, P., Myles, S., Holland, J.B., Flint Garcia, S.A., McMullen, M.D., Buckler IV, E.S., Rocheford, T.R. 2011. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genetics. 7(11):e1002383.

Bloom, J.C., Holland, J.B. 2012. Genomic localization of the maize cross-incompatibility gene, Gametophyte factor 1 (ga1). Maydica. 56:1782.

Blecher, A., Zwonitzer, J., Santa Cruz, J., Krakowsky, M.D., Chung, C., Nelson, R., Arellano, C., Balint Kurti, P.J. 2011. Analysis of quantitative disease resistance to southern leaf blight and of multiple disease resistance in maize, using near-isogenic lines. Theoretical and Applied Genetics. 124:433-445.

Balint Kurti, P.J., Stapleton, A. 2011. Application of an antibiotic resets the maize leaf phyllosphere community and increases resistance to southern leaf blight. Acta Horticulturae. 905:57-62.

Chaikam, V., Negeri, A., Dhawan, R., Puchaka, B., Chintamanani, S., Gachomo, E.W., Zillmer, A., Doran, T., Weil, C., Balint Kurti, P.J., Johal, G. 2011. Use of Mutant-Assisted Gene Identification and Characterization (MAGIC) to identify novel genetic loci that modify the maize hypersensitive response. Theoretical and Applied Genetics. 123(6):985-997.

Last Modified: 7/24/2014
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