Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Agronomy, Horticulture, and Plant Science

First Advisor

Xingyou Gu


epistatic, oryza sativa, plant height, QTL, rice, seed dormancy


Seed dormancy (SD) is an adaptive trait of both ecological and agricultural importance. Cereal crops have been selected for reduced SD to promote germination, which also caused the pre-harvest sprouting (PHS) problem in crop production. The previous research identified a set of quantitative trait loci (QTL) for SD, including qSD1- 2 and qSD8, in the conspecific weedy and cultivated rice (Oryza sativa). qSD1-2 carries a dormancy-enhancing allele from the cultivated rice and has a pleiotropic effect on plant height. qSD8 carries a dormancy-enhancing allele from the weedy rice and tightly links to qAL8 for awn length. The objectives of this research were: 1) to assemble the qSD1-2 and qSD8 alleles in the same genetic background as isogenic lines for fundamental research; and 2) to evaluate additive (a) and dominance (d) and epistatic (i) effects of these two loci on germination ability and its associated traits for use of the QTL alleles to breed cultivars resistant to PHS. Single plants that are heterozygous for the qSD1-2 and qSD8 regions were selected from the BC1F1 to BC1F5 generations of a backcross (BC) to synchronize the genetic background. From the BC1F6 generation all the nine digenic genotypes for the two loci were identified as isogenic lines (ILs). A total of 144 plants for the nine ILs were grown in a greenhouse, and evaluated for SD by a standard germination test (30°C) at 0 and 10 days of after-ripening (DAR), low-temperature (15°C) germination (LTG) ability, plant height, flowering time and percentage of awned seeds per panicle. QTL analysis confirmed the effects of qSD1-2 on SD and plant height, and the associations of qSD8 with the SD and awn traits. The analysis also identified new effects of the two QTL regions on LTG and flowering time, and the qSD8 region on plant height. Multiple linear regression analysis revealed that the qSD1-2 and qSD8 loci influence the SD and flowering time traits by their main (a and/or d) effects, and the plant height and LTG traits by both main and epistatic effects. The regression analysis also revealed that qSD1- 2 had no effect, while qSD8 alone had only a small effect (6.5%) on the awn trait. This research provided new data to support the coevolution of SD with the adaptive traits awn, plant height, flowering time and LTG. The four homozygotes for the qSD1-2 and qSD8 loci were purified as a set of ILs. These lines are valuable for mapbased cloning qSD8 and for research molecular mechanisms regulating the SD development/release in the model system of rice. The dormancy-enhancing allele at qSD1-2 is common in rice semidwarf cultivars. The estimated genetic component effects suggest that an addition of the dormancy-enhancing allele at qSD8 to the genetic background of a semidwarf variety could reduce germination significantly (11% due to the additive effect). However, this addition may cause short-awned seeds, reduce LTG (8%), but have little influence on plant height and flowering time.


Includes bibliographical references



Number of Pages



South Dakota State University


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