University of Idaho - Advancing wheat breeding

Idaho farmers can expect more varieties to be released from University of Idaho’s wheat breeding program that resist the fungal diseases dwarf bunt and common bunt thanks in large part to the work of a recent doctoral graduate, Pabitra Joshi.

Joshi, of Nepal, also became a licensed drone pilot for a research project using modeling and high throughput phenotyping — which involves collecting large amounts of data to assess phenotypic traits of plants — to assess potential yield, height, maturity, biomass and other traits among wheat cultivars at the U of I’s Aberdeen Research and Extension Center.

Joshi, who made a strong mark on Idaho agriculture during her four years as a U of I graduate student, received her doctorate in plant science in December 2024. She’s amassed a long list of accolades, including the Gerald O. Mott Meritorious Graduate Student Award from the Crop Science Society of America and the Borlaug Scholar in Plant Breeding award from the National Association of Plant Breeders. Joshi also secured a job with the U.S. Department of Agriculture (USDA) in Geneva, New York, where she will be working on genome sequence analysis, high throughput phenotyping for use in genomic selection and phenotyping of hemp.

Prior to moving to Idaho, Joshi earned a bachelor’s degree in agriculture from Agriculture and Forestry University in Nepal, where she had the opportunity to work with the maize breeding program at the National Maize Research Program, further deepening her passion for crop improvement and genetics. While at U of I, Joshi worked under advisor Jianli Chen, Idaho Wheat Commission’s D. Blaine Jacobson endowed professor of wheat breeding.

″My passion for genetics and crop breeding began during my undergraduate studies," Joshi shared. "In my country, wheat breeding plays a critical role in agriculture, yet there are very few experts in this field. That realization inspired me to contribute to this essential area of research.″

Investigating Disease Resistance

Joshi initially signed up for a master’s program at U of I. Based on her stellar performance, however, Chen urged her to bypass the master’s degree and continue working toward a doctorate. For her dissertation, Joshi identified two quantitative trait loci (QTLs) associated with common bunt and dwarf bunt resistance. A QTL is a DNA region close to a specific gene that influences the variation of a trait in a population of organisms.

She used a mapping population developed by crossing UI Silver — a hard white winter wheat developed by Chen’s program with strong and enduring resistance to the diseases — with a susceptible line, Shaan 89150. Mapping populations help crop breeders identify locations of genes controlling specific traits, which they map for use in marker-assisted selection. This mapping population was created using doubled haploid breeding — an advanced technique that cuts years off of the breeding process.

″I found there were two QTLs in chromosome 6D of wheat,″ Joshi said. ″I have developed primers to check wheat cultivars to see if they have that gene/loci present or not.″

Dwarf bunt and common bunt were devastating to wheat farmers until the advent of chemical fungicide in the 1950s. The diseases have made a resurgence in recent years as organic agriculture has gained in popularity and farmers have looked to cut back on input use.

Chen will now use the QTLs Joshi located, as well as other markers associated with resistance to the diseases, in screening wheat breeding lines.

Also for her dissertation, Joshi screened more than 170 winter wheat lines developed by U of I, Utah State University and Washington State University for the presence of the two QTLs she located. They were present in most of U of I and USU breeding lines, because the universities used the same known resistant landraces.

Her dissertation was recently accepted for publication in a future edition of the scientific journal Theoretical and Applied Genetics.

Joshi also participated in a separate project led by University of California-Davis that involved 20 doctoral students and 41 wheat breeders from 22 institutions in 20 states, called the Wheat Coordinated Agricultural Project (WheatCAP). The project, funded with a $15 million grant from the U.S. Department of Agriculture National Institute of Food and Agriculture, entails using technology such as high throughput phenotyping to breed wheat better suited for the challenges imposed by climate change.

″My work was to fly drones over our wheat breeding fields in Aberdeen and analyze that imagery and use it in our prediction models for specific traits,″ Joshi said.

While at U of I, Joshi made a point of mentoring other students and sharing her knowledge. She volunteered as a mentor with the International Peer Mentor Program, which provides support for incoming international students. She was also vice president of Randall Women in Science, a U of I organization devoted to promoting women in scientific fields.