Summary

ABSTRACTWheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is responsible for significant yield losses worldwide, which can be minimized by deploying Pst resistance genes. Yr78 is an adult plant resistance gene that has remained effective against the post-2000 virulent Pst races. In this study, we first generated a high-resolution map of Yr78 based on 6,124 segregating chromosomes. Yr78 was mapped in an 11.16 Mb region on the short arm of chromosome 6B, including 15 annotated protein-coding genes in the ‘Chinese Spring’ Ref Seq. v1.1 genome. Using exome capture data, we yielded five major haplotypes in the candidate gene region, with the H1 haplotype associated with Yr78. The H1 resistant haplotype was identified in Spelt, Cadenza, and Lancer. Especially, 67% of the European Spelt accessions have the H1 haplotype, suggesting its origin from Spelt wheat and the value of sequenced genomes carrying the resistance allele in developing Yr78 precise map. By manually reannotating the non-repetitive regions of the Spelt genome published by the Pan Genome project, we are able to delimit the proximal border of the Yr78 candidate region with new markers developed from the resistance/susceptible haplotype analysis. Besides, luckily we found a natural deletion in a recombinant line R136 from the mapping population, which has a breakpoint within the Yr78 candidate gene region and is resistant against Pst. This deletion line delimits the distal border of the Yr78 candidate region furthermore. And finally, we mapped Yr78 within a 604 kb interval based on the Chinese Spring Ref Seq. v1.1 genome, between CDM164 (CS-6BS 111,985,311 bp) and CDM161(CS-6BS 111,381,697). This new candidate region excludes the previous 15 candidate genes and low confidential genes, and only includes the NOR-B2 locus. The NOR-B2 locus has not been assembled in any of the current wheat genomes due to its highly repetitive nature. Based on the published number of ribosomal genes in chromosome 6BS, the unassembled region in Chinese Spring was estimated to be ~37 Mb. More, we explored in detail the NOR-B2 region by re-analyzing data from three different genomic projects that attempted to provide a better cover of NOR-B2. In spite of all these efforts, we could not find a likely candidate for Yr78. The optical mapping of this region has shown the presence of non-repetitive regions within the NOR-B2 region. We hypothesize that the Yr78 gene is likely located within the non-repetitive regions of this complex and unassembled region of the wheat genome. This result highlights the importance of completing the currently unassembled regions of the wheat genome. Although the unassembled NOR-B2 region limited our ability to identify a candidate gene for Yr78, our precise mapping and detailed haplotype analyses of the region yielded useful tools for the deployment of this valuable resistance gene in wheat breeding programs. We developed two tightly linked molecular markers CDM158 (CS-6BS 106,540,703) and CDM160-2 (CS-6BS 108,227,904) for the H1 haplotype that will facilitate the deployment of Yr78 in wheat breeding programs. In the practice side, we created several valuable germplasms containing Yr78. First, we transferred Yr78 from hexaploid wheat into the tetraploid durum variety Kronos and demonstrated increased Pst resistance 39% IT and 35% SEV in the field test. This germplasm has been submitted to GRIN-Global as ‘Kronos-Yr78’ assigned as PI 702944. Since Yr78 has not been detected in wild or cultivated tetraploid wheat, this material can be a novel tool to improve Pst resistance in durum wheat. The second genetic stock developed in this thesis includes the combination of the closely linked Pst adult plant resistance genes Yr78 and Yr36 in phase. We successfully screened out the recombinant progenies containing homozygous Yr36+Yr78. So breeders can deploy both genes together using a single set of flanking markers. To increase the value of this germplasm, we developed an additional line with the Yr5 and Yr15 resistance genes in addition to the combined Yr36+Yr78. This germplasm provides a single source of multiple Pst resistance genes for common wheat breeding programs. These lines are currently growing to increase seeds for Pst resistance level test and submission to GRIN-Global.

Plant breeding is the art and science of developing new crops and plant products that serve an immense range of industries. The scientific training for plant breeders often involves making discoveries in plant genetics to develop new tools for plant breeders. The first part of this Thesis describes the discovery, validation, and deployment of WHEAT ORTHOLOG OF APO1 (WAPO1), a gene that increases the spikelet number per spike (SNS) and yield potential in wheat. The path from discovery to deployment of WAPO1 was a three-step, forward genetics approach that first involved construction of a high‑resolution genetic map, followed by candidate gene evaluation and functional validation experiments to demonstrate that WAPO-A1, the A genome homeolog of WAPO1, is a causal gene for SNS. With causality established, an extensive germplasm screen was performed to discover and characterize novel alleles for WAPO-A1. To raise durum yield potential, a WAPO-A1 allele associated with higher SNS was deployed into durum wheat and raised SNS significantly. If this increase in SNS translates into higher yield, plant breeders could make targeted introgressions of WAPO-A1 alleles into widely grown durum varieties to improve durum yield. Beyond scientific training and crop-specific knowledge, plant breeders also need to be competent in a wide variety of technical and soft skills. The second part of this Thesis is an assessment of students’ learning and skill development in the Student Collaborative Organic Plant-breeding Education (SCOPE) program: a student-led collective that uses technical training, social learning, and mentorship to prepare students for a career in plant breeding. Two educational theories – Experiential Learning and Situated Learning – served as the conceptual basis for this study’s design, implementation, and interpretation of results. To determine how well students were acquiring new technical and soft skills, I conducted a mixed methods study of anonymous surveys and analysis of student writing pieces from the SCOPE program. This study found that most students participated in all plant breeding activities and were building new knowledge and skills accordingly. SCOPE staff were the primary mentors to all students, while graduate students played dual roles as mentors to undergraduate students and mentees to staff and faculty advisors. However, undergraduate students rarely achieved proficiency in advanced skills, and few mastered more basic skills despite frequent practice and training. I suspect the unclear leadership role of undergraduate participants in the SCOPE community hampered learning and skills acquisition. If given a clear role and more responsibility, students would likely gain confidence in their training and take greater initiative and responsibility for their own learning. To make these suggestions a reality, this study concludes with recommendations for feasible undergraduate-led projects that would hopefully improve undergraduate skills development and benefit the SCOPE community.