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Document Type

Thesis - University Access Only

Award Date


Degree Name

Master of Science (MS)

Department / School

Plant Science

First Advisor

Xing-You Gu


Weeds are unwanted plants that adapted to human-disturbed environments and compete with crops for limited natural resources. The goal of this project was to elucidate genetic and evolutionary mechanism of weed adaptation and competitiveness in agro-ecosystems using combinative approaches of ecology, genetics and genomics to provide fundamental knowledge to improve or devise new weed management strategies. The objectives of this project were: 1) to identify quantitative trait loci (QTL) for wild and crop-mimic traits in weedy rice (Oryza sativa) under controlled conditions; 2) to determine haplotype patterns for genomic segments clustered with the QTLs in U.S. weedy red rice populations; and 3) to develop a permanent segregation population to facilitate ecological genetics research on weed adaptation and competitiveness in the model system of weedy rice across agroecosystems. An F2 population of 500 plants from the cross between a cultivated (EM93- 1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A total of 49 QTL were detected for the wild (21) and crop-mimic (28) traits, indicating that the conspecific weed-crop differentiation involved many genomic segments. About 90% of the QTL were located on 14 genomic segments, indicating that genes responsible for weed adaptation and competitiveness tend to link with each other. A core collection of 28 U.S. weedy red rice lines and 14 AAgenome wild rice (O. spp) lines were determined for haplotype variants for the QTLenriched genomic segments. The haplotype analysis revealed that U.S. weedy red rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars. Based on haplotype patterns for the 14 QTL cluster regions, 27 of the 28 weedy rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types. A total of 442 recombinant inbred lines (RILs) were developed by a single-seed-decent technique from the F2 to F9 generations. Evaluation of five traits (i.e. hull color, pericarp color, awn, plant height and flowering time) revealed that flowering time has large phenotypic variation across generations unlike plant height and other qualitative traits. Flowering time and plant height also showed significant difference in distribution pattern between greenhouse and field condition, indicating that quantitative traits associated to weed adaptation expressed differently in different ecological conditions. A preliminary experiment using a subpopulation of 94 RILs detected 14 QTL associated with eight adaptive traits. A majority of the 14 QTL corroborated with those detected in the F2 population. Evaluation for seed aging was added into RIL population and detected two QTL on chromosome 1 and 9. This population of >400 RILs is unique and valuable for ecological genetics/genomics research on weed adaptation and competitiveness, in terms of genetic, evolutionary, developmental or molecular bases underlying phenotypic plasticity and genotype-by-environment interactions in various agro-ecosystems with different weed management practices.

Library of Congress Subject Headings

Rice -- Genetics
Ecological genetics


Includes bibliographical references (pages 131-144)



Number of Pages



South Dakota State University


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