Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: Maize RIL Populations: To map much of the segregating variation in maize, 25 RIL mapping populations were created. We have selected 25 diverse lines that capture 80% of the nucleotide polymorphism in maize. To provide a uniform evaluation background, each line was crossed to B73 (the standard US inbred) to form 25 mapping populations (each population with over 200 recombinant inbred lines). A final seed increase was completed for these inbreds during the 2008 summer season and this germplasm was deposited with the Maize Stock Center for use by the maize research community. Over the past year, genotypic data from the 25 populations (7,200 RILs were scored for more than 1,500 informative SNP loci) have been correlated with phenotypic data collected earlier to perform joint linkage and association analyses for candidate genes. From these studies, several candidate genes responsible for agronomically important phenotypes were identified. The most notable of these were a variant lycopene E-cyclase that resulted in increased amounts of B-carotene in maize grain and barren inflorescence-2, a regulatory gene that affects maize kernel shape and volume. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Two undergraduates were trained in maize field propagation, phenotyping for ear and tassel traits, DNA isolation, sequencing and other molecular biology and data analysis techniques. An additional educational board was created on the topic of biofuels (to complement the previous boards on the history and culture of maize and Barbara McClintock) and posted online in both English and Spanish. Two maize breeders visited to work on the project during the summer.
Publications
- Canaran P, ES Buckler, JC Glaubitz, L Stein, Q Sun, W Zhao, and D Ware. 2008. Panzea: an update on new content and features. Nucleic Acids Res. 36: D1041-D1043.
- Harjes CE, TR Rocheford, L Bai, TP Brutnell, CB Kandianis, SG Sowinski, AE STapelton, R Vallabhaneni, M Williams, ET Wurtzel, JB Yan and ES Buckler. 2008. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science USA. 319: 330-333.
- Liang CZ, P Jaiswal, C Hebbard, S Avraham, ES Buckler, T Casstevens, B Hurwitz, S McCouch, JJ Ni, A. Pujar, D Ravenscroft, L Ren, W Spooner, I Tecle, J Thomason, CW Tung, XH Wei, I Yap, K Youens-Clark, D Ware and L Stein. 2008 Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 36: D947-D953.
- Pressoir, G, PJ Brown, W Zhu, N Upadyayula, T Rocheford, ES Buckler and S Kresovich. 2009. Natural variation in maize architecture is mediated by alleleic differences at the PINOID co-ortholog barren inflorescence-2. Plant J. in press.
- Stich B, J Mohring, HP Piepho, M Heckenberger, ES buckler and AE Melchinger. 2008. Comparison of mixed-model approaches for association mapping. Genetics. 178:1745-1754.
- Thuillet AC, MI Tenaillon, LK Anderson, SE Mitchell, S Kresovich, SM Stack, B Gaut and J Doebley. 2008. A weak effect of background selection on trinucleotide microsatellites in maize. J. Hered. 99: 45-55.
- Weber AL, WH Briggs, J Rucker, BM Baltazar, JD Sanchez-Gonzalez, P Feng, ES Buckler and J Doebley. 2008. The genetic architecture of complex traits in teosinte (Zea mays ssp parviglumis): New evidence from association mapping. Genetics 180: 1221-1232.
- Yu JM, JB Holland, MD McMullen and ES Buckler. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics. 178: 539-551.
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Progress 01/01/07 to 12/31/07
Outputs
Maize RIL Populations: To map much of the segregating variation in maize, 25 RIL mapping populations were created. We have selected 25 diverse lines that capture 80% of the nucleotide polymorphism in maize. In order to provide a uniform evaluation background, each line was crossed to B73 (the standard US inbred) to form 25 mapping populations (each population with over 200 recombinant inbred lines). Seed increase was also continued for these inbreds during the 2007 summer and winter seasons. This year, these populations were genotyped (7,200 RILs were scored for more than 1,500 informative SNP loci). This genotypic data together with the phenotypic information collected in 2005-2006 is now being used to perform joint linkage and association analyses for candidate genes.
Impacts
Two undergraduates were trained in maize field propagation, phenotyping for ear and tassel traits, DNA isolation, sequencing and other molecular biology and data analysis techniques.
Publications
- Bradbury PJ, Z Zhang, DE Kroon, TM Casstevens, Y Ramdoss and ES Buckler. 2007. TASSEL: software for association mapping of complex traits in diverse samples Bioinformatics 23 (19): 2633-2635.
- Tracy WF, SR Whitt and ES Buckler. 2007. Recurrent mutation and genome evolution: Example of Sugary 1 and the origin of sweet maize. Crop Sci. 46: S49-S54 Suppl. 1.
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Progress 01/01/06 to 12/31/06
Outputs
Maize RIL Populations: To map much of the segregating variation in maize, 25 RIL mapping populations were created. We have selected 25 diverse lines that capture 80% of the nucleotide polymorphism in maize. In order to provide a uniform evaluation background, each line was crossed to B73 (the standard US inbred) to form 25 mapping populations (each population with over 200 recombinant inbred lines). Seed increase was also continued for these inbreds during the 2006 summer and winter seasons. These populations will be genotyped next year and together with the phenotypic information collected in 2005-2006 a joint linkage and association analysis will be performed for candidate genes. RIL DNAs. This year, SNP selections were finalized and DNA extractions for 7,000 RILS were formatted for high-throughput genotyping. Phenotyping maize inflorescence architecture: In addition to the trait scored in the field (specifically tassel and maturity traits), we have continued to
score kernel (fruit-seed) shape traits from the previous year's harvest. Data analysis and statistical methodology in association mapping: In this area, progress has continued this year. We have dealt with one of the major limiting constraint in doing association mapping (correctly controlling for population structure). We developed a new methodology that was published Nature Genetics that allows to effectively control for population structure (so far our method has proven very effective at improving both the level of false positive as well as increasing the power in our maize sample, in a human data set as well as in the model organism Arabidopsis thaliana)
Impacts
Two undergraduates were trained in maize field propagation, phenotyping for ear and tassel traits, DNA isolation, sequencing and other molecular biology and data analysis techniques.
Publications
- Yu, J.*, Pressoir, G.*, Briggs, W.H., Vroh Bi, I., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S., and E.S. Buckler. 2006. A Unified Mixed-Model Method for Association Mapping Accounting for Multiple Levels of Relatedness. Nature Genetics 38:203-208.
- Kresovich, S., A.M. Casa, A.J. Garris, S.E. Mitchell, and M.T. Hamblin. 2006. Improving the connection between effective crop conservation and breeding. In: Plant Breeding: Hallauer Symposium, pp. 90-96, Blackwell, Oxford.
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Progress 01/01/05 to 12/31/05
Outputs
Maize RIL Populations: To map much of the segregating variation in maize, 25 RIL mapping populations are being created. We have selected 25 diverse lines that capture 80% of the nucleotide polymorphism in maize. In order to provide a uniform evaluation background, each line was crossed to B73 (the standard US inbred) to form 25 mapping populations (each population with over 200 recombinant inbred lines). DNA extraction for these 7000 recombinant inbred lines was performed during this summer. Seed increase was also carried out for these inbreds during the 2005 summer and winter seasons. These populations will allow starting next year to carry on a joint linkage and association analysis for candidate genes. Phenotyping maize inflorescence architecture: In addition to the trait scored in the field last year, we scored this year kernel (fruit-seed) shape traits from previous years harvest. Association mapping for inflorescence architecture in maize: All genes mentioned in
previous report have been sequence across the 25 diverse lines as well as in a panel of teosintes (maize wild ancestor). 12 of these genes have been sequenced in the association mapping panel which resulted in three of these genes showing strong association with the maize architecture. We selected SNPs for genotyping from 20 additional genes which will be scored across the association mapping panel next year. As we are waiting for additional data, publications have yet to be submitted for these associations. Data analysis and statistical methodology in association mapping: This is the area in which the most progress was made this year. We have dealt with one of the major limiting constraint in doing association mapping (correctly controlling for population structure). We have developed a new methodology that is to be published very soon in Nature Genetics that allows to effectively control for population structure (so far our method has proven very effective at improving both the
level of false positive as well as increasing the power in our maize sample, in a human data set as well as in the model organism Arabidopsis thaliana)
Impacts
Nine undergraduates were trained in maize field propagation, phenotyping for ear and tassel traint, DNA isolation, sequencing and other molecular biology and data analysis techniques.
Publications
- Yu, J.*, Pressoir, G.*, Briggs, W.H., Vroh Bi, I., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S., and E.S. Buckler. 2006. A Unified Mixed-Model Method for Association Mapping Accounting for Multiple Levels of Relatedness. Nature Genetics in press * Both authors equally contributed to this work Flint-Garcia, S.A., A.-C. Thuillet, J. Yu, G. Pressoir, S.M. Romero, S.E. Mitchell, J. Doebley, S. Kresovich, M.M. Goodman, and E.S. Buckler. 2005. Maize association population: a high-resolution platform for quantitative trait locus dissection. The Plant Journal 44:1054-1064.
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Progress 01/01/04 to 12/31/04
Outputs
The objectives of this work were to determine which genes have been under selection during maize domestication and improvement, and to identify genes and alleles that control key agronomic traits. To this end, a high-throughput, high-resolution system including pipelines for data analysis for SNPs and DNA sequences was devised. Also, interesting candidate genes were researched and the decision was made to concentrate on assaying genes that may be important in maize inflorescence architecture including the CLE gene family (18 genes), td1, td1B, Fea2, Erecta-like genes, Wushel-like genes, Moc-like genes, bd1, bd1B, Bif2 and other Pinoid-like genes, Knox-like genes, UFO-like genes, and SKP1-like genes. Lines and populations to be assayed in this study were grown over the summer and phenotyping for ear and tassel traits was completed in October of this year. So far we have sequenced eight candidate genes in a test population consisting of 30 diverse maize inbred lines.
Several of the CLE genes have shown promising results. Over the next year, all gene candidates will be sequenced in 300 maize inbred lines and 16 lines of the wild relative, teosinte. These genes will then be tested for association(s) between their SNPs and indels and inflorescence phenotypic variation. Publications regarding the CLE genes and inflorescence architecture traits will be submitted sometime in 2005. Preliminary results will be presented at the Maize Genetics Conference in March of 2005.
Impacts
Eight undergraduates were trained in maize field propagation, phenotyping for ear and tassel traint, DNA isolation, sequencing and other molecular biology and data analysis techniques.
Publications
- No publications reported this period
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