Breeding Insight (BI)
Role: Director | Funded by USDA Agricultural Research Service (2019-2024)
Breeding of specialty crops and animals has lagged behind the major crops and livestock, despite the fact that these specialty species together have equal economic value to the major crops and provide critical nutrition and variety to human diets. One of the avenues for improving this situation is to accelerate breeding efforts by integrating the use of phenomics (trait analysis) with genomics and natural variation to increase the rate of genetic gain and to create novel healthy, nutritious, and sustainable specialty crops and animals. There are numerous challenges facing specialty crops, which hamper technology adoption and limit program efficiency. Breeding Insight is a new USDA-ARS initiative started in 2018 is creating new opportunities for ARS specialty breeders to assimilate tools, technologies (including software), and methods into their programs, allowing genomic insight to be used routinely in breeding. In the pilot phase, Breeding Insight supported breeding for grape, blueberry, sweetpotato, alfalfa, and rainbow trout, and North American Atlantic salmon. In 2021, BI was expanded to support ARS breeding programs of 7 additional species (cranberry, cucumber, lettuce, honeybee, lettuce, oat, and pecan). In future growth phases, BI (and its sister group, BI OnRamp) are expected to expand even further to support breeding programs of ~50 specialty crops, all national germplasm repositories for pre-breeding, ~15 specialty animals and 30 natural resource species across the US.
Breeding Insight OnRamp (BI OnRamp)
Role: Associate-Director | Funded by USDA Agricultural Research Service (2021-2023)
Breeding Insight OnRamp was founded in 2021 in response to the growing need for support and time to migrate historical data from decades-long breeding programs, and to allow public breeding efforts in major crops (eg., cotton and soybean) to benefit from BI technologies and services. Currently, BI OnRamp supports 4 ARS breeding programs in the southeastern area of the US: citrus, cotton, soybean, and sugarcane. In time, OnRamp is expected to expand to support more ARS geographic areas and species. BI OnRamp is directed by Dr. Amanda Hulse-Kemp out of North Carolina State University and assisted by Dr. Sheehan. BI and BI OnRamp are sister groups that work closely together on a regular basis with the same software infrastructure and mandates.
Peer-reviewed Publications
Dyrszka E, Sheehan M, Tanksley S, Casa A, Petiard V, Coque M, Mirleau-Thebaud V, Bascouert S, Gentou F, Lespinasse D, Cottet O (2012). Genetic Molecular tools for exploitation of genetic resource in wild species. Proceedings of the international sunflower conference, Mar del Plata, Argentina:101-105.
Ersoz ES, Wright MH, Pangilinan JL, Sheehan MJ, Tobias C, Casler MD, Buckler ES,Costich DE (2012). SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.). PLoS One 7(9):e44112
Sheehan MJ, Pawlowski WP (2012). Imaging chromosome dynamics in meiosis in plants. Methods in Enzymology 505:125–143.
Costich DE, Friebe B, Sheehan MJ, Casler MD, Buckler ES (2010). Genome‐size Variation in Switchgrass (Panicum virgatum): Flow Cytometry and Cytology Reveal Rampant Aneuploidy. The Plant Genome 3(3):130-114.
Sheehan MJ, Pawlowski WP (2009). Live imaging of rapid chromosome movements in meiotic prophase I in maize. PNAS 106:20989–20994.
Pawlowski WP, Sheehan MJ, and Ronceret A (2007). In the beginning: the initiation of meiosis. BioEssays 29:511-514.
Sheehan MJ, Kennedy LM, Costich DE, Muzynski M, Brutnell TP (2007). Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize. Plant Journal 49:338-353.
Sawers RJ, Sheehan MJ, Brutnell TP (2005). Cereal phytochromes: targets of selection, targets for manipulation? Trends in Plant Science 10: 138-143.
Sheehan MJ, Farmer P, Brutnell TP (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167: 1395-1405.
Xu B, Sheehan MJ, Timko MP (2004). Differential induction of ornithine decarboxylase (ODC) gene family members in transgenic tobacco (Nicotiana tabacum L. cv. Bright Yellow 2) cell suspensions by methyl-jasmonate treatment. Plant Growth Reg 44 (2):101-116
Wang J, Sheehan M, Brookman H, Timko MP (2000). Characterization of cDNAs differentially expressed in roots of tobacco (Nicotiana tabacum cv Burley 21) during the early stages of alkaloid biosynthesis. Plant Science 158:19-32.
Wang J, Sheehan M, Timko MP (2000). Differential Expression of two members of the nuclear gene family encoding Arginine Decarboxylase in tobacco (Nicotiana tabacum L). J. Plant Biochem and Biotechnology 9:57-65.
Book chapters and reports
Mejia-Guerra MK, Zhao D, Sheehan MJ (2021) Genomic Resources for Breeding in Alfalfa: Availability, Utility, and Adoption. In: Yu LX., Kole C. (eds) The Alfalfa Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-74466-3_11
Sheehan MJ, Dawe RK, Pawlowski WP (2013). Live imaging of chromosome dynamics. Chapter 8 in WP Pawlowski, M Grelon, and S Armstrong (eds.) Plant Meiosis: Methods and Protocols, Methods in Molecular Biology, vol. 990, 91-104.
Ronceret A, Sheehan, MJ, Pawlowski WP (2007). Chromosome dynamics in meiosis. Chapter 6 in D.P.S. Verma and Z. Hong (eds.) Plant Cell Monographs (9): Cell Division Control in Plants. Springer-Verlag Berlin Heidelberg, Heidelberg, Germany, p. 103-124.
