Browsing by Subject "plant breeding"

Now showing 1 - 5 of 5
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    Developing genomic tools to breed for climate-adapted plant varieties
    (2023-03) Della Coletta, Rafael
    Climate change is a major threat to global food security, as current plant varieties used by farmers may not adapt to new growing environments. To mitigate this problem, plant breeders must use all available tools to speed up the development and release of new climate-adapted varieties. In this dissertation, I discuss how the recent advances in crop genomics due to improvements in sequencing technology, genome assembly methods, and computational resources are revolutionizing plant breeding. Particularly, I argue that the analysis of the complete catalog of genetic variation of a crop can provide useful information for plant breeders. I demonstrate that modeling this pan-genome information can increase the accuracy of multi- environment genomic prediction models, a tool widely used by breeders to develop new plant varieties. I also show how utilizing prior information on genetic variants associated with certain phenotypes can help simulate traits that are more realistic and relevant for breeders using digital breeding, a tool where breeders can test many different experiments before deployment in their breeding programs. Finally, I developed a new tool that identifies genetic variants associated with specific environmental factors via network analysis of common datasets available to plant breeders.
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    The Development of Plant Breeding at Minnesota
    (St. Paul, MN: Department of Agronomy and Plant Genetics, University of Minnesota, 2009) Hayes, H.K.
    Following his retirement as chief of the Division of Agronomy and Plant Genetics at the University of Minnesota in 1952, H. K. Hayes compiled a record and observations of the division's research through his tenure, and that of the successor Department of Agronomy and Plant Genetics over about the next 10 years. His manuscript was never published. This book provides a snapshot of the historical traditions of the University of Minnesota Department of Agronomy and Plant Genetics. For a more comprehensive history of the department, please see the book "Agronomy and Plant Genetics at the University of Minnesota" published in 2000 by the Minnesota Agricultural Experiment Station (Minnesota Report 247-2000) and available at http://purl.umn.edu/50613.
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    The Enigma of Genetic Linkage in Molecular Breeding for Maize
    (2017-06) Sleper, Joshua
    Linkage among quantitative trait loci prevents the release of hidden genetic variation, but also preserves desirable gene combinations. This dissertation, which includes three studies, shows the continuing enigma of linkage in maize (Zea mays L.) breeding. The first study aimed to determine if the additional recombinations in doubled haploids induced from F2 instead of F1 plants leads to a larger genetic variance and a superior mean of the best lines. In two maize populations, inducing doubled haploids from F2 plants did not improve the mean, and it increased the genetic variance for moisture, but not for yield and plant height. The second study aimed to determine if multi-allelic markers or haplotypes improve the prediction accuracy of genomewide selection in three-way breeding populations, which could have three alleles per locus. In both simulated and empirical maize populations, accounting for multiple alleles did not improve the prediction accuracy over a biallelic model. The third study aimed to determine if genomewide markers can be used to partition trait effects into independent and correlated portions, and if selection on the independent portion was more effective than selection on the entire trait. Results from four cycles of selection showed that selection only for the independent portion did not lead to higher responses for yield, moisture, and plant height. Overall, genetic linkage both assists and confounds molecular breeding efforts in maize.
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    Evaluating genomewide marker-based breeding methods in traditional and wild relative-derived barley populations
    (2016-04) Tiede, Tyler
    The genetic improvement of plants for human use is the primary goal of plant breeding. Through repeated processes of population development and selection, breeders have produced highly productive plants that are adapted to a vast array of environments and cultivation practices. The challenges that drove plant breeders in the past, such as increasing production, novel or increasingly prevalent abiotic and biotic stresses, and evolving end-user demands persist today and are compounded with unprecedented population growth. Genomic selection (GS), a genomewide marker-based selection method, has been shown to be an efficient and effective breeding tool. Its general applicability to plant breeding and principles guiding its use have been established by simulation and empirical cross-validation studies. More recently, studies have demonstrated genetic gains over multiple cycles of selection in a variety of crop species. In the first chapter we provide additional evidence for the effectiveness of GS in an actual breeding program by demonstrating significant gains of 164.74 kg ha-1 and -1.41 ppm for grain yield and DON, respectively, two unfavorably correlated quantitative traits, across three cycles of selection in a spring six-row barley breeding population. With its general effectiveness established, the next step is to increase the accuracy of GS and thereby increase genetic gains. For this, we first showed that updating the training population (TP) with phenotyped lines from recent breeding cycles, specifically selected lines, had an overall positive effect on prediction accuracy. Additionally, we investigated four recently-proposed algorithms that seek to optimize the composition of a TP. Overall the optimization algorithms improved prediction accuracy when compared to a randomly selected TP subset of the same size, but which algorithm performed best was dependent on the trait being predicted and other factors discussed within. This retrospective investigation highlighted the importance of maintaining and optimizing the TP when using GS in real breeding situations to maximize prediction accuracy, thereby maximizing gain from selection and resource utilization. Furthermore, genetic gains depend on genetic variation. Exotic germplasm can be exploited to introduce genetic variability into elite breeding populations to drive genetic gains and address new or changing breeding targets. Wide crosses between elite and exotic germplasm have been widely used to identify large-effect QTL and breed for improved disease or insect resistance. The utility of exotic germplasm to improve quantitative traits, which includes many important agronomic traits, has not been tested as widely. In the second chapter we select parents from an advanced backcross population constructed from 25 wild barley (Hordeum vulgare L. spp spontaneum) accessions crossed to the common high-yielding malting barley cultivar, Rasmusson. We extended the genomic selection framework to identify parent combinations that, with ideal recombination, should produce progeny with large numbers of exotic introgressions with favorable effects. We compared the marker-based crossing strategy to the traditional methods of crossing the topmost performing parents or the most genetically diverse parents. After one round of marker-based progeny selection from these crosses we identified breeding lines, harboring exotic introgressions, which consistently yielded higher than Rasmusson across five trial locations. While none of these lines were statistically better than Rasmusson, there is compelling evidence that the introgression of wild alleles contributed to increased yield. The three parent selection strategies were not significantly different for their ability to identify superior progeny.
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    Understanding the genetic architecture of secondary domestication traits in Field Pennycress (Thlaspi arvense L.)
    (2022-12) Tandukar, Zenith
    Thlaspi arvense L. (Field Pennycress) is a newly domesticated winter annual oilseed capable of improving ecosystems and intensifying agricultural productivity without new land displacement. Pennycress is a winter hardy cover crop that provides ecosystem services such as reduced soil erosion and nutrient loss in between fall corn harvest and spring soybean planting. However, pennycress is currently limited by its small seed size and unimproved oil production. This dissertation builds on the limited research on pennycress breeding and genetics and aims to establish and characterize a global diversity panel of wild pennycress accessions, two biparental recombinant inbred populations, and three independent EMS-derived mutants to contribute knowledge and resources to understand important seed and agronomic characteristic traits in pennycress. Chapter 1 presents a literature review focused on the status of pennycress breeding and genetics, as well as factors that may shed light to understanding the genetic and physiological control of seed size and oil content. Chapter 2 presents a genetic dissection of seed size, oil content, and protein content via genome-wide association studies in a diversity panel. Chapter 3 explores and characterizes the phenotypic and genotypic diversity in two recombinant inbred populations developed for field pennycress, whereas chapter 4 reports the characterization of three independent wax mutants in pennycress and the implications of waxes on total seed oil content in pennycress.