Altendorf, Kayla2020-08-252020-08-252020-04https://hdl.handle.net/11299/215182University of Minnesota Ph.D. dissertation. April 2020. Major: Applied Plant Sciences. Advisor: James Anderson. 1 computer file (PDF); xiii, 210 pages.Chapter 1 Perennial plants provide extensive environmental services, and increasing their prevalence on the agricultural landscape is one way to improve sustainability. Direct domestication of intermediate wheatgrass (Thinopyrum intermedium) as a perennial grain crop is underway, and selection has focused primarily on improving seed size and yield. Breeders are limited by the lack of understanding of yield and its relationship with component traits in this species. We characterized a large population (n = 1168) of IWG spaced plants in St. Paul, MN and Salina, KS in 2017 and 2018 for a series of 13 yield component traits. Family by environment by year interaction was highly significant (P < 0.001) for all traits, indicating that family performance and rankings were variable across environments. In year two in St. Paul, yield plant-1 and reproductive tiller numbers nearly doubled, while all other yield components, including yield spike-1, thousand grain weight, spikelets spike-1 and florets spikelet-1 significantly decreased. Bivariate correlation analyses between component traits revealed consistent trends across environments and highlighted positive associations of seven traits with grain yield. Structural equation modeling (SEM) was conducted using an initial path model that more clearly delineated relationships into direct and indirect effects. When yield is measured on a yield spike-1 basis, floret site utilization was the primary contributor to yield, followed by spikelets spike-1, florets spikelet-1 and thousand grain weight. When measured on a plant-1 basis, reproductive tiller number was the most significant contributor to yield in all environments. Considering the limited indirect effects of biomass and maturity component traits, and the potential for strong indirect selection for tillering when selecting for yield plant-1, we suggest a two-step selection procedure on yield spike-1 and floret site utilization and explored alternative methods for collecting data on this labor-intensive trait. Future work should test the predictive ability of yield spike-1 and floret site utilization in IWG spaced plants and seed production swards. Chapter 2 Intermediate wheatgrass (IWG) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop for human consumption. Selection targets for this crop are numerous, and breeding may be made more efficient by improving knowledge of the underlying genetic control for traits of interest. Nested association mapping (NAM) has proven useful in dissecting the genetic control of important agronomic traits in a wide range of crop species. This work introduces an intermediate wheatgrass NAM developed by crossing ten phenotypically divergent donor parents to a low-shattering common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genome wide association mapping (GWAS) and linkage mapping both combined across and within families, we characterize the genetic control of flowering time measured in two different ways across two locations and two years. We detected 35 QTL in GWAS and 20 in linkage mapping, demonstrating the complex genetic control of flowering time that is variable across years and locations as well as within families. The IWG NAM population was effective at detecting previously identified QTL, as well as a new QTL that aligns closely to the well-characterized flowering time orthogene from barley, Ppd-H1. Results demonstrated the utility of the NAM for understanding of the genetic control of flowering time and should be applied to additional traits of interest in IWG. Chapter 3 Perennial grain crops have the potential to improve agricultural sustainability, but few existing species produce sufficient grain yield to make this an economically viable option. The perennial forage species intermediate wheatgrass (Thinopyrum intermedium; IWG) has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection at the current pace will be required to achieve yields on par with annual small grain crops. Marker aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we utilize the IWG Nested Association Mapping (NAM) population, with 1,168 F1 progeny across ten families to dissect the genetic control of brittle rachis, floret shattering, free-threshing ability, tillering, floret site utilization, plant height, and thousand grain weight. We used genome wide association analysis (GWAS) with 8,003 SNP markers and linkage mapping using within-family and combined analyses using a custom genetic map, with a robust phenotypic dataset collected from four unique year by location combinations. A total of 32 QTL in GWAS and 18 in linkage mapping were detected in at least two environments, and most large effect QTL were in common across the two analysis methods. We reveal that the genetic control of domestication traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary across families. However, in many cases these QTL align closely with putative orthogenes for known domestication traits in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.enDomesticationGenetic mappingIntermediate wheatgrassNested association mappingYield componentsThesis or Dissertation