Group: Mackay Lab
PhD, Cornell University
Office: 3532A Thomas Hall
Website: Visit our Lab Home Page
Phenomics and high-throughput sequencing have drastically increased the information available to crop geneticists and breeders. From this information, linkage and association mapping of alleles and genomic prediction of breeding values have greatly enhanced our knowledge of genetic architecture. New analytical approaches are needed to efficiently use this architectural knowledge in the optimization of mapping efforts and to better inform breeding practices. Drawing techniques from the disciplines of combinatorial optimization, statistical mechanics, and locally weighted regressions, this project will optimize the selection of mapping and genomic prediction populations for multi-environment trials. These techniques will incorporate prior genetic knowledge in an adaptive sequential manner to better balance exploration and exploitation of the diversity within the landscape of potential genotypes. By implementing related techniques, scientists will be able to use this understanding of a population's orientation on the landscape to direct cross-pollination and selection decisions that better exploit genetic diversity and allow breeders to more rapidly converge on a desired phenotype for a given crop application and environment.
Peiffer J, Spor A, Koren O, Jin Z, Buckler E, and Ley R. (2012). Biodiversity and Heritability of the Maize Rhizosphere Under Field Conditions. PNAS. (in review).
Peiffer J, Kaushik S, Sakai H, Arteaga-Vazquez M, Sanchez-Leon N, Ghazal H, Vielle-Calzada J-P, and Meyers B. (2008). A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS. BMC Plant Biology. 8:43.
Myles S, Peiffer JA, Brown PJ, Ersoz ES, Zhang Z, Costich DE, and Buckler ES. (2009). Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design. The Plant Cell. 21:2194–2202.
Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz E, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, and Buckler ES. (2009). A First-Generation Haplotype Map of Maize. Science. 326:1115–1117.
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, etal. (2009). The Genetic Architecture of Maize Flowering Time. Science. 325:714–718.