Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Agronomy, Horticulture, and Plant Science

First Advisor

Sharon Clay


Cover crops provide soil health benefits to crop production. However, spring termination timing must be critically managed to prevent crop competition and yield loss. This study examined the influence of termination timing of fall-seeded rye (Secale cereale) on early corn (Zea mays) growth, gene expressions, and yield. Treatments included no cover crop, rye termination before corn planting, at corn planting, at V2, and at V4 corn. Rye was drill-seeded at 56 kg ha-1 in October 2018 and 2019. Corn was planted in mid-May 2019 (wet season) and 2020 (dry season). Rye biomass was 21 (2019) or 28 (2020) kg ha-1, 75 (2019) or 62 (2020) kg ha-1, 722 (2019) or 634 (2020) kg ha-1, and 1,120 (2019) or 702 (2020) kg ha-1 at before corn planting, corn planting, V2, and V4 rye termination, respectively. Transcriptome analysis of V4 samples in rye termination at V4 versus no cover crop resulted: 1) reduced corn growth and plant tissue nitrogen in both years; 2) 25 differentially expressed genes (DEGs) in 2019 and 322 (13X more) in 2020; 3) upregulated N metabolism ontology in 2019; and d) upregulated photosynthesis, carbon fixation and light signaling ontologies in 2020. Also, significant pathways including photosynthesis, carbon fixation in photosynthetic organisms, and carbon metabolism were altered regardless of climate conditions at V4 rye termination and can be attributed to corn-rye interactions. In V8 (2019) samples, response to cold and response to abscisic acid were upregulated, whereas photosynthesis and protein transport were downregulated at V4 rye termination versus no cover crop. In 2019, yield loss (16%) did not occur until V4 rye termination versus no cover crop. In 2020, yield was 19, 29, and 38% less when rye was terminated at corn planting, V2, and V4, respectively. This study suggests that during a wet season, delaying rye termination time until V2 may alter specific DEGs and pathways, but can provide more rye biomass without reducing corn yield. Inversely, during a dry season, delaying termination until planting or beyond can negatively impact corn development and significantly reduce corn yield.

Number of Pages



South Dakota State University

Available for download on Thursday, May 15, 2025



Rights Statement

In Copyright