Progress 05/09/13 to 02/19/18
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. This is the final report for this project, which as replaced by project 6070-21220-016-00D, "Genetics of Disease Resistance and Food Quality Traits in Corn." 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. We also defined the ten most important genomic regions containing photoperiod response genes in tropical maize inbreds. We assayed sequence variation at a key photoperiod response gene from 3 � 5 plants each of a set of more than 350 maize heirloom landrace varieties distributed from Canada to southern Chile. This information has provided insight into which genes appear to have been under selection during the spread of maize from its tropical origin in Mexico to the higher latitudes of the United States. We determined the genetic nature of resistance to southern corn leaf blight disease at an unprecedented level of resolution for a complex disease resistance trait. We determined that at least 30 genes are involved in the control of this resistance, and that resistance genes are dispersed across many different maize lines, suggested that targeted breeding could be used to combine them to achieve higher levels of disease resistance. Association mapping in diverse populations was used to identify 350 candidate genes for Southern leaf blight resistance. By screening publicly available mutant stock resources we identified lines with transposon insertions in or near 161 of these genes. About 1500 sub- families derived from these lines were genotyped and evaluated for resistance to Southern leaf blight (and other foliar diseases) in multiple environments in replicated field trials. F2:3 populations were constructed to test whether the mutations of interest are specifically associated with variation in resistance. Genes with repeatable associations across experiments underwent functional evaluation using insertional mutant analysis, gene expression analysis, and resequencing. Lines overexpressing 6 candidate gene disease resistance genes were constructed and tested in the field for altered disease resistance phenotypes. Several loci associated with the maize hypersensitive defense response were identified with extremely high precision using association mapping. We have analyzed a number of distinct data sets to identify genes associated with resistance to southern corn leaf blight disease. Several lines have been identified with enhanced resistance to multiple diseases. We measured the response to recurrent selection for ear rot resistance and yield in a diverse corn population, demonstrating that selection for resistance to ear rot alone resulted in improved resistance to mycotoxin contamination. These data were also used to develop a training population for genomic selection for improved resistance to Fusarium ear rot and mycotoxin contamination. For each of the five years of this project, we screened 50 or more advanced lines from the USDA Germplasm Enhancement of Maize (GEM) project and the North Carolina State University maize inbred development programs for resistance to Fusarium ear rot and fumonisin contamination resistance and southern leaf blight. Results were provided to cooperators for their use in making selections for improved maize varieties. Accomplishments 01 Demonstration that a gene involved in the synthesis of lignin is also important for resistance to at least two diseases. Maize diseases cause significant yield losses. Genes that confer resistance to multiple diseases are a valuable tool to protect the maize crop. The gene that encodes the enzyme caffeoyl-CoA O-methyltransferase was identified as a gene that conferred significant levels of resistance to two maize diseases; southern corn leaf blight and grey leaf spot. ARS researchers at Raleigh, North Carolina, used a variety of methods to identify the gene, these include; using mutants in which the gene was mis-expressed, using transgenic plants in which the gene was over- expressed and mapping the position of the gene in the maize genome. This finding helps us understand one of the ways that plants can defend themselves against disease. Several maize breeding companies have shown interest in this work and it is likely that they will consider this gene when breeding future varieties of maize.
Impacts
(N/A)
Publications
- Nelson, R., Wiesner-Hanks, T., Wisser, R., Balint Kurti, P.J. 2018. Navigating complexity to breed disease-resistant crops. Nature Reviews Genetics. 19:21-33.
- Yang, Q., He, Y., Kabahuma, M., Chaya, T., Kelly, A., Borrego, E., Bian, Y. , El Kasmi, F., Yang, L., Teixeira, P., Kolkman, J., Nelson, R., Kolomiets, M., Dangl, J., Wisser, R., Caplan, J., Li, X., Lauter, N.C., Balint Kurti, P.J. 2017. A maize caffeoyl-CoA O-methyltransferase gene confers quantitative resistance to multiple pathogens. Nature Genetics. 49:1364- 1372.
- Cooper, J., Balint Kurti, P.J., Jamann, T. 2018. Identification of quantitative trait loci for Goss�s wilt of maize caused by Clavibacter michiganensis subsp. nebraskensis. Crop Science. 58:1192-1200.
- Sermons, S.M., Balint Kurti, P.J. 2018. Large scale field inoculation and scoring of maize southern leaf blight and other maize foliar fungal diseases. Bio-protocol.
- Ovenden, B., Milgate, A., Lisle, C.J., Wade, L.J., Rebetzke, G.J., Holland, J.B. 2017. Selection for water-soluble carbohydrate accumulation and investigation of genetic � environment interactions in an elite wheat breeding population. Theoretical and Applied Genetics. 130:2445-2461.
- Isik, F., Holland, J.B., Maltecca, C. 2017. Genetic data analysis for plant and animal breeding. Springer, New York. 400 pp. Book Chapter.
- Ovenden, B., Milgate, A., Wade, L.J., Rebetzke, G.J., Holland, J.B. 2018. Accounting for genotype�by-environment interactions and non-additive genetic variation in genomic selection for water-soluble carbohydrate concentration in wheat. Genetics. 8:1909-1919.
- Wills, D.M., Fang, Z., York, A., Holland, J.B., Doebley, J. 2018. Defining the role of the MADS-box gene, Zea agamous like1, in maize domestication. Journal of Heredity. 109:333-338.
- Gonzales, J.S., Corral, J.R., Garcia, G.M., Ojeda, G.R., De La Cruz, L.L., Holland, J.B., Medrano, R.M., Romero, G.G. 2018. Ecogeography of teosinte. PLoS One. 13:e0192676.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. Additional topcross hybrid seed of landrace introgression lines was made for field testing and preliminary yield trials were conducted. Mapping populations to fine-map resistance to quantitative disease resistances were developed and genotyped. Sequencing and field evaluations of a large set of lines was performed to evaluate genomic selection for ear rot resistance and yield in a diverse corn population. Allele frequencies of markers associated with Fusarium ear rot associated resistance were estimated for different geographic subpopulations. Germplasm Enhancement of Maize breeding lines were screened for resistance to Fusarium ear rot, southern leaf blight and northern leaf blight resistances. Genes with repeatable associations across experiments underwent functional evaluation using insertional mutant analysis, gene expression analysis, and resequencing. Maize near-isogenic line populations (lines that have a common genetic background but differ for a small number of genome segments introduced from diverse parents) were screened for the identification of disease resistance loci. Association mapping in diverse populations was used to identify 350 candidate genes for Southern leaf blight resistance. By screening publicly available mutant stock resources, we identified lines with transposon insertions in or near 161 of these genes. About 1,500 sub- families derived from these lines were genotyped and evaluated for resistance to Southern leaf blight (and other foliar diseases) in multiple environments in replicated field trials. ARS scientists in Raleigh, North Carolina, created transgenic lines over-expressing or silencing 12 of the candidate genes and have tested 5 of them for resistance to Southern leaf blight. We have unequivocally shown that one gene, encoding a caffeoyl-CoA O-methyltransferase, is associated with resistance to both SLB and to GLS. Several other genes showed significant effects in initial trails that are being repeated this year. Accomplishments 01 High depth targeted sequencing of 20 candidate genes in diverse maize landrace populations. Most of the genetic variation in maize resides in outcrossed �landrace� (heirloom-type) populations from the Americas. Inexpensive, low coverage sequencing methods have enabled the genetic analysis of large populations. Such methods are poor at accurately identifying two different variants at the same gene in the same individual, however. This is not a problem when inbred lines (with only one variant at almost all genes) are sequenced, but it hinders the analysis of genetic variation in diverse, outcrossed (�highly heterozygous�) plants such as those found in landrace collections. ARS scientists in Raleigh, North Carolina, used a new approach to target a subset of genes of interest and obtain high depth sequence information that allows us to accurately identify when individuals carry two different sequence variants at a genomic position. This method can be performed cost-effectively at large scale, so we were able to obtain sequence information at 20 genes of interest from more than two thousand plants representing hundreds of maize landrace populations collected from the entire range of maize in the Americas.
Impacts
(N/A)
Publications
- Olukolu, B., Bian, Y., De Vries, B., Tracy, W.F., Wisser, R., Holland, J.B. , Balint Kurti, P.J. 2016. The genetics of leaf flecking in maize and its relationship to plant defense and disease resistance. Plant Physiology. 172(3):1787-1803.
- Jamann, T., Sood, S., Wisser, R., Holland, J.B. 2017. High-Throughput resequencing of maize landraces at genomic regions associated with flowering time. PLoS One. 12:e0168910.
- Rebetzke, G., Richards, R., Holland, J.B. 2017. Population extremes for assessing trait value and correlated response of genetically complex traits. Field Crops Research. 201:122-132.
- Xue, S., Bradbury, P., Casstevens, T., Holland, J.B. 2016. Genetic architecture of domestication-related traits in maize. Genetics. 204:99- 113.
- Bian, Y., Holland, J.B. 2017. Enhancing genomic prediction with genome- wide association studies in multiparental maize populations. Heredity. 118:585�593.
- Andres, R.J., Coneva, V., Frank, M.H., Tuttle, J.R., Samayoa, L.F., Han, S. , Kaur, B., Zhu, L., Fang, H., Bowman, D.T., Rojas-Pierce, M., Haigler, C. H., Jones, C., Holland, J.B., Chitwood, D.H., Kuraparthy, V. 2016. Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Proceedings of the National Academy of Sciences. 114:E57-E66.
- Lennon, J., Krakowsky, M.D., Goodman, M., Flint Garcia, S.A., Balint Kurti, P.J. 2017. Identification of Teosinte (Zea mays ssp. parviglumis) alleles for resistance to southern leaf blight in near isogenic maize lines. Crop Science. doi:10.2135/cropsci2016.12.0979.
- Zhang, X., Valdez-Lopez, O., Arenalo, C., Stacey, G., Balint Kurti, P.J. 2017. Genetic dissection of the maize (Zea mays L.) MAMP response. Theoretical and Applied Genetics. 130:1155. doi:10.1007/s00122-017-2876-6.
- Zhang, X., Yang, Q., Rucker, E., Thomason, W., Balint Kurti, P.J. 2017. Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis). Theoretical and Applied Genetics. 130(6):1285-1295.
- Yang, Q., Balint Kurti, P.J., Xu, M. 2017. Quantitative disease resistance: dissection and adoption in maize. Molecular Plant Pathology. doi.org/10.1016/j.molp.2017.02.004.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. Topcross hybrid seed of landrace introgression lines were made for field testing. Mapping populations to fine-map resistance to quantitative disease resistances were developed and genotyped. Sequence variation at 20 photoperiod and flowering response genes from 3�5 plants each of a set of more than 350 maize heirloom landrace varieties distributed from Canada to southern Chile was assayed. Sequencing and field evaluations of a large set of lines was performed to evaluate genomic selection for ear rot resistance and yield in a diverse corn population. Germplasm Enhancement of Maize breeding lines were screened for resistance to Fusarium ear rot and southern corn leaf blight resistances. A combination of association mapping in two diversity populations was used to identify 350 candidate genes for Southern leaf blight resistance. By screening publicly available mutant stock resources we identified lines with transposon insertions in or near 161 of these genes. About 1, 500 sub-families derived from these lines were genotyped and evaluated for resistance to Southern leaf blight (and other foliar diseases) in multiple environments in replicated field trials. F2:3 populations were constructed to test whether the mutations of interest are specifically associated with variation in resistance. These populations are being tested this summer. Lines overexpressing 6 candidate gene disease resistance genes were constructed and are being tested this summer for altered disease resistance phenotypes. Maize near-isogenic line populations (lines that have a common genetic background but differ for a small number of genome segments introduced from diverse parents) were used to identify several alleles conferring multiple disease resistance. Accomplishments 01 Characterization of genes modulating the defense response of plants. Corn varieties differ in their ability to respond to pathogen infection, often due to the presence or absence of so-called resistance (R) proteins which are responsible for the recognition and subsequent rapid response to specific pathogens. One defense response involves the production of compounds such as lignin that strengthen cell walls (�lignin�). Two different proteins in the lignin biosynthesis pathway were found to physically interact with a protein and to modulate its activity. The unravelling of the molecular details of this interaction provide a detailed pictures of how plants recognize pathogens and then transmit molecular signals to modulate the defense response.
Impacts
(N/A)
Publications
- Holland, J.B., Murphy, P., Graham, G., Senior, L. 2015. Charles W. Stuber: Maize geneticist and pioneer of marker-assisted selection. Plant Breeding Reviews. 39:1-22.
- Lennon, J., Krakowsky, M.D., Goodman, M., Flint Garcia, S.A., Balint Kurti, P.J. 2016. Identification of alleles conferring resistance to gray leaf spot in maize derived from its wild progenitor species teosinte (Zea mays ssp. parviglumis). Crop Science. 56:209-218.
- Horne, D., Eller, M., Holland, J.B. 2015. Responses to recurrent index selection for reduced fusarium ear rot and lodging and for increased yield in maize. Crop Science. 56:85-94.
- Bian, Y., Holland, J.B. 2015. Ensemble learning of QTL models improves prediction of complex traits. G3, Genes/Genomes/Genetics. doi: 10.1534/g3. 115.021121.
- Nelson, P.T., Krakowsky, M.D., Coles, N.D., Holland, J.B., Bubeck, D.M., Smith, J.C., Goodman, M.M. 2016. Genetic characterization of the North Carolina State University maize lines. Crop Science. 56:259-275.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. The final set of landrace introgression lines was created. Mapping populations to fine-map resistance to quantitative disease resistances were developed and genotyped. Sequence variation at a key photoperiod response gene from 3 � 5 plants each of a set of more than 350 maize heirloom landrace varieties distributed from Canada to southern Chile was assayed. Responses to recurrent selection for ear rot resistance and yield in a diverse corn population was measured. Germplasm Enhancement of Maize breeding lines were screened for resistance to Fusarium ear rot and southern corn leaf blight resistances. Genes with repeatable associations across experiments underwent functional evaluation using insertional mutant analysis, gene expression analysis, and resequencing. Maize near-isogenic line populations (lines that have a common genetic background but differ for a small number of genome segments introduced from diverse parents) were screened for the identification of disease resistance loci. A combination of association mapping in the Nested Association Mapping (NAM) and diversity populations was used to identify 350 candidate genes for Southern leaf blight resistance. By screening publicly available mutant stock resources we identified lines with transposon insertions in or near 161 of these genes. About 1500 sub-families derived from these lines were genotyped and evaluated for resistance to Southern leaf blight (and other foliar diseases) in multiple environments in replicated field trials. Accomplishments 01 Selection for resistance to Fusarium ear rot of corn also resulted in reduced mycotoxin contamination. Fusarium ear rot of corn is an important disease that causes ear mold and results in contamination of grain by the mycotoxin fumonisin. Resistance to this disease is complex, affected by many genes and the environment. A maize population was subjected to three generations of selection for resistance to Fusarium ear rot. Evaluation of the original and selected generations of this population demonstrated that resistance to ear rot was improved, and also that the selected population had significantly lower contamination by fumonisin. This is the first direct demonstration that visual selection for resistance to ear rot can result in better resistance to mycotoxin contamination. Breeders can use this information to plan their breeding programs and new improved inbred lines are being selected from this population.
Impacts
(N/A)
Publications
- Bian, Y., Yang, Q., Balint Kurti, P.J., Wisser, R., Holland, J.B. 2014. Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population. Biomed Central (BMC) Genomics. 15:1068.
- Pratt, R., Holland, J.B., Balint Kurti, P.J., Coles, N., Zwonitzer, J., Casey, M., Mcmullen, M.D. 2015. Registration of the Ki14 � B73 recombinant inbred mapping population of maize. Journal of Plant Registrations. 9(2) :262-265.
- Samayoa, L.F., Malvar, R., Olukolu, B., Holland, J.B., Butron, A. 2015. Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel. Journal of Experimental Botany. 15:35.
- Jamann, T., Balint Kurti, P.J., Holland, J.B. 2015. QTL mapping using high- throughput sequencing. In: Alonso, J., Stepanova, A.N., editors. Methods in Molecular Biology: Plant Functional Genomics: Methods and Protocols. New York, NY: Springer. p. 257-285.
- Balint Kurti, P.J., Holland, J.B. 2015. New insight into a complex plant- fungal pathogen interaction. Nature Genetics. 47:101-103.
- Ogut, F., Bradbury, P., Holland, J.B., Bian, Y. 2015. Joint multiple family QTL analysis predicts within-family variation better than single family analysis of the maize nested association mapping population. Heredity. 114:552-563.
- Hirsch, C.N., Flint Garcia, S.A., Beissinger, T.M., Eichten, S.R., Deshpande, S., Barry, K., Mcmullen, M.D., Holland, J.B., Buckler IV, E.S., Springer, N., Buell, R.C., de Leon, N., Kaeppler, S.M. 2014. Insights into the effects of long-term artificial selection on seed size in maize. Genetics. 198(1):409-421.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. We developed BC5F2:3 generations of landrace introgression lines. We evaluated mapping populations to fine-map resistance to quantitative disease resistances. We assayed sequence variation at a key photoperiod response gene from 3 � 5 plants each of a set of more than 350 maize heirloom landrace varieties distributed from Canada to southern Chile. We planted the second year of an experiment to measure the direct response to recurrent selection for ear rot resistance and yield in a diverse corn population. We also planted an experiment to evaluate 100 lines from each of three selection cycles to an elite tester line to measure the effect of selection for improved performance in partly inbred lines on the performance of hybrids made from those lines. We planted experiments to screen Germplasm Enhancement of Maize breeding lines for resistance to Fusarium ear rot and southern corn leaf blight resistances. We have analyzed a number of distinct data sets to identify genes associated with resistance to southern corn leaf blight disease. Genes with repeatable associations across experiments are undergoing functional evaluation using insertional mutant analysis, gene expression analysis, and resequencing. We have begun to evaluate the near-isogenic line populations developed for the identification of disease resistance loci. Several lines have been identified with enhanced resistance to multiple diseases. Accomplishments 01 Identification of genes associated with resistance to an ear rot disease of corn. We evaluated most of the USDA maize seed bank inbred line collection for resistance to Fusarium ear rot, an important disease that causes ear mold and is related to mycotoxin contamination of grain. Resistance to this disease is complex, affected by many genes and the environment. No genes are known to provide immunity to this disease. The genes involved in conferring partial resistance have also been unknown. DNA sequence variations in several genes were found to be associated with levels of ear rot disease in the inbred line collection. These genes were previously unknown to be involved in disease resistance, so this information provides insight into the possible mechanisms of partial natural resistance to this disease. Breeders can use this information to identify new sources of resistance, and molecular biologists can further study these genes to determine how they might be related to disease resistance.
Impacts
(N/A)
Publications
- Santa-Cruz, J.H., Kump, K.L., Arellano, C., Goodman, M., Krakowsky, M.D., Holland, J.B., Balint Kurti, P.J. 2014. Evaluation of two southern leaf blight resistance QTL for their effect on yield and disease resistance in isogenic maize hybrids. Crop Science. 54(3):882-894.
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Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): 1. Develop novel maize genetic resources and analysis tools to enable high resolution dissection of complex agronomic traits. 1A. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. 1B. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. 1C. Develop new strategies for the analysis of complex trait phenotypes. 2. Identify favorable alleles for disease resistance and agronomic traits in exotic maize germplasm. 2A. Geographic distribution of disease resistance alleles in maize. 2B. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. 2C. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. 2D. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). 2E. Identification of disease resistance and yield genes from wild relatives. 3. Identify genes and mechanisms underlying quantitative disease resistance and defense response in maize. Approach (from AD-416): 1. Create new genetic stocks to identify favorable alleles for yield improvement derived from exotic maize germplasm. Develop near-isogenic line (NIL) populations for the identification of disease resistance loci. Develop new strategies for the analysis of complex trait phenotypes. 2. Geographic distribution of disease resistance alleles in maize. Enrichment of novel disease resistance alleles from exotic maize in adapted genetic backgrounds. Identifying new sources of resistance to Southern leaf blight (SLB), Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Identify resistance loci from lines with elite levels of multiple disease resistance (MDR). Identification of disease resistance and yield genes from wild relatives. 3. Select candidate genes and order at least 50 insertional mutant lines. Screen plants for desired insertional events and self. Identify P. sorghi isolate that induces HR on the line W22. We developed BC5 generations of landrace introgression lines. We created and evaluated a set of experimental hybrids to identify appropriate testers to evaluate yield potential of these lines. We developed BC3F3 populations to fine-map resistance to quantitative disease resistances. We isolated DNA from 3 � 5 plants each of a set of more than 350 maize heirloom landrace varieties distributed from Canada to southern Chile and developed assays to evaluate their genetic variations at several candidate photoperiod genes. We planted an experiment to measure the direct response to recurrent selection for ear rot resistance and yield in a diverse corn population. We also crossed 100 lines from each of three selection cycles to an elite tester line to measure the effect of selection for improved performance in partly inbred lines on the performance of hybrids made from those lines. We planted experiments to screen GEM breeding lines for resistance to Fusarium ear rot and southern corn leaf blight resistances. We have analyzed a number of distinct data sets to identify genes associated with resistance to southern corn leaf blight disease. Genes with repeatable associations across experiments are undergoing functional evaluation using insertional mutant analysis, gene expression analysis, and resequencing. We have begun to evaluate the NIL populatins developed for the identification of disease resistance loci. Several lines have been identified with enhanced resistance to multiple diseases. Accomplishments 01 Identification of genes and pathways associated with the maize defense response. We created a series of specialized mapping populations which carried an autoactive defense response gene. Genome wide association analyses of these populations has identified a set of genes associated with protein degradation and programmed cell death which appear to be associated with the control of the hypersenstivie defense response in maize. This information is primarily of use to researchers trying to understand how this important defense response is controlled by the plant. Ultimately it may lead to improved disease resistant varieties created by transgenic or conventional approaches.
Impacts
(N/A)
Publications
- Willcox, M., Davis, G., Warburton, M.L., Windham, G.L., Abbas, H.K., Betran, J., Holland, J.B., Williams, W.P. 2013. Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds. Molecular Breeding. 32(1):15-26.
- Olukolu, B., Negeri, A., Dhawan, R., Venkata, B.P., Sharma, P., Garg, A., Gachomo, E., Marla, S., Chu, K., Hasan, A., Ji, J., Chintamanani, S., Green, J., Holland, J.B., Wisser, R., Shyu, C., Johal, G., Balint Kurti, P. J. 2013. A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize caused by a maize auto-active resistance gene. Genetics. 193:609-620.
- Veturi, Y., Kump, K., Walsh, E., Ott, O., Poland, J.A., Kolkman, J., Nelson, R., Balint Kurti, P.J., Holland, J.B., Wisser, R. 2012. Multivariate mixed linear model analysis of longitudinal data: an information-rich statistical technique for analyzing disease resistance data. Phytopathology. 102(11):1017-1025.
- Hizbai, B., Gardner, K., Wight, C., Danda, R., Molnar, S., Johnson, D., Fregeau-Reid, J., Yan, W., Rossnagel, B., Holland, J.B., Tinker, N. 2012. Quantitative trait loci affecting oil content, oil composition, and other agronomically important traits in Oat (Avena sativa L.). The Plant Genome. 5:164-175.
- Hung, H.Y., Holland, J.B. 2012. Diallel analysis of resistance to fusarium ear rot and fumonisin contamination in maize. Crop Science. 52:2173-2181.
- Green, J., Appel, H., Rehrig, E., Harnsomburana, J., Chang, J., Chintamanani, S., Balint Kurti, P.J., Shyu, C. 2012. PhenoPhyte: A flexible affordable method to quantify visual 2D phenotypes. Plant Physiology. 8:45.
- Benavente, L., Ding, X., Redinbaugh, M.G., Nelson, R., Balint Kurti, P.J. 2012. Virus-induced gene silencing in diverse maize lines using the Brome Mosaic virus-based silencing vector. Maydica. 57(3/4):206-214.
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