I am interested in the characterization, maintenance, and utilization of crop genetic diversity as means of enhancing small farm viability, rural livelihoods, food security, and ecosystem integrity. This is to say that my work in the fields of plant genetics and breeding (traditional and molecular) stems not from a basic but a decidedly applied research interest with significant socioeconomic and ecological implications. For me, crop improvement is fundamentally about increasing the options available to both growers and consumers within a context of dynamic market forces, increasing land-use pressures, and uncertain environmental factors.
Motivated by this larger framework, the research objectives of my integrated plant breeding and plant molecular genetics/genomics program are: 1) To increase agricultural opportunities in New England by developing and providing improved germplasm to producers; 2) To develop molecular markers and genetic resources to support my breeding work and that of the larger plant improvement community, particularly in developing countries; and 3) To contribute to our understanding of the genetic bases of key traits at various scales, from individual plants (e.g. disease resistance) to whole farm systems (e.g. weed suppression) to landscapes (e.g. nutrient uptake).
In the field, classical breeding methods remain necessary for the practical development and delivery of improved plant varieties. In the lab, trait dissection, gene mapping, gene characterization, and molecular marker development can provide valuable information and support to breeding efforts. The integration of these field and lab components in one program insures that my basic genetic research stays consistently grounded in real-world production and is pursued with a firm commitment toward deployment.
A variety of research opportunities for students are available in my lab (http://www.unh.edu/halelab); please contact me if you are interested in learning more.
Ph.D., Horticultural and Agronomy, University of California - Davis
M.S., : International Agricultural Development, University of California - Davis
B.A., Religion, Dartmouth College
B.A., Physics, Dartmouth College
ANFS 933: Experimental Design/Analysis
BIOL 933: Experimental Design/Analysis
GEN 999: Doctoral Research
SAFS 733: Advanced Topics in SAFS
Jamnadass, R., Mumm, R. H., Hale, I., Hendre, P., Muchugi, A., Dawson, I. K., . . . Van Deynze, A. (2020). Enhancing African orphan crops with genomics. Nature Genetics, 52(4), 356-360. doi:10.1038/s41588-020-0601-x
Melo, A. T. O., & Hale, I. (2019). ‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information. BMC Bioinformatics, 20(1). doi:10.1186/s12859-019-2662-3
Bartaula, R., Melo, A. T. O., Kingan, S., Jin, Y., & Hale, I. (2019). Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid. BMC Plant Biology, 19(1). doi:10.1186/s12870-019-1893-9
Dawson, I. K., Powell, W., Hendre, P., Bančič, J., Hickey, J. M., Kindt, R., . . . Jamnadass, R. (2019). The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition. New Phytologist, 224(1), 37-54. doi:10.1111/nph.15895
Melo, A. T. O., & Hale, I. (2019). Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP. Bioinformatics, 35(17), 3215. doi:10.1093/bioinformatics/bty1073
Maccaferri, M., Harris, N. S., Twardziok, S. O., Pasam, R. K., Gundlach, H., Spannagl, M., . . . Cattivelli, L. (2019). Durum wheat genome highlights past domestication signatures and future improvement targets. Nature Genetics, 51(5), 885-895. doi:10.1038/s41588-019-0381-3
Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S. O., Gundlach, H., . . . Distelfeld, A. (2017). Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science, 357(6346), 93-97. doi:10.1126/science.aan0032
Melo, A. T. O., Bartaula, R., & Hale, I. (2016). GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. BMC Bioinformatics, 17(1). doi:10.1186/s12859-016-0879-y
Lowe, I., Jankuloski, L., Chao, S., Chen, X., See, D., & Dubcovsky, J. (2011). Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theoretical and Applied Genetics, 123(1), 143-157. doi:10.1007/s00122-011-1573-0
Lowe, I., Cantu, D., & Dubcovsky, J. (2011). Durable resistance to the wheat rusts: integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes. Euphytica, 179(1), 69-79. doi:10.1007/s10681-010-0311-z