Diversifying crop systems by developing intercropping breeding strategies for improving forage yield and quality in oat-legume mixtures

Kigoni, Milcah

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https://hdl.handle.net/2142/132677 Copy

Description

Title

Diversifying crop systems by developing intercropping breeding strategies for improving forage yield and quality in oat-legume mixtures

Author(s)

Kigoni, Milcah

Issue Date

2025-12-03

Director of Research (if dissertation) or Advisor (if thesis)

Arbelaez Velez, Juan David

Doctoral Committee Chair(s)

Arbelaez Velez, Juan David

Committee Member(s)

• Rutkoski, Jessica
• Villamil, Maria Bonita
• Sacks, Erik J.

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Oat
• Pea
• Intercrop breeding
• Intercropping
• Forages
• Oat-Pea Mixtures
• High throughput phenotyping
• phenomics
• UAV/drone

Abstract

Intercropping is a critical yet underutilized strategy for enhancing agricultural system resilience in U.S. Midwest cropping systems. Chapter 1 reviews the historical, economic, and ecological factors that have entrenched monoculture in the Midwest, highlighting the resulting vulnerabilities to climate variability, soil degradation, and input dependence. We build a case for spatial re-diversification through intercropping to enhance agroecosystem resilience and productivity. The chapter examines benefits of intercropping alongside adoption barriers, including yield penalties and management complexities. From a breeding perspective, we explore opportunities for addressing these challenges, with emphasis on cereal-legume mixed intercropping. We highlight recent technological advances with the potential to accelerate progress in breeding for intercrop systems. Finally, we outline practical strategies and discuss future priorities for intercrop breeding and research. One particularly promising application of cereal-legume intercropping is in forage systems, where mixtures enhance both yield and quality compared to monocultures, offering a sustainable approach for meeting rising global demand for high-quality livestock feed. In the Midwest, oat (Avena sativa L.) is commonly intercropped with field pea (Pisum sativum L.) to improve forage performance. Despite these advantages, breeding progress for forage mixtures remains slow due to the logistical challenges of evaluating numerous genotype combinations under field conditions. To address this constraint, efficient intercrop breeding requires preliminary understanding of genetic variation, trait heritability and correlations, and the relationship between monoculture and mixture performance to streamline selection strategies. We used oat-pea mixtures as a use case for the potential of cereal-legume intercropping systems. In chapter 2 presents a comprehensive oat-pea mixed intercropping case study, whereby 24 spring oat and 5 field pea genotypes were evaluated in monoculture and intercrop conditions across three seasons for forage yield (YLD), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), total digestible nutrients (TDN), and relative feed value (RFV). Genetic variance, heritability, general mixing ability (GMA), and specific mixing ability (SMA) were analyzed using mixed models; intercrop advantage was evaluated using net effect ratio (NER) and transgressive overyielding index (TOI). Forage traits exhibited moderate to high heritability (H² = 0.48–0.66) with substantial genetic variance. GMA effects were highly significant for all oat traits, while SMA effects were non-significant, indicating mixture performance is determined by genotype additive effects. Monoculture performance predicted 38–74% of mixture GMA variance, highest for fiber traits (TDN r² = 0.74; NDF r² = 0.64). Transgressive overyielding for crude protein was frequent (76–93 mixtures per season exceeding best monoculture by up to 38%), and positive net effects (NER = 1.07–1.14) indicated improved land-use efficiency. These results support staged breeding strategies combining early-generation monoculture screening for highly heritable and predictable traits followed by targeted mixture evaluation in advanced trials for traits less predictable from monoculture. Accelerating genetic gain for forage yield and quality in cereal-legume intercrop mixtures requires innovative phenotyping strategies to address the logistical challenge of evaluating yield and quality across numerous species and genotype combinations. While UAV-based high-throughput phenotyping is well established in monocrops, few studies examine its application in intercropping field experiments. As detailed in chapter 3, we tested the utility of UAV-derived multispectral vegetation indices (VIs) for predicting forage yield and nutritive quality traits in oat–pea mixtures, evaluated as described above. Five VIs—three near-infrared-based (NDVI, GNDVI, NDRE) and two green-band indices (EXG, EXGR)—were incorporated as secondary traits in multivariate mixed models to assess predictive ability in cross-validation studies. VIs exhibited moderate to high heritability (H² = 0.37–0.79) and significant correlations with forage traits in mixtures ranging between 0.19 to 0.57. Models combining all five VIs achieved the highest predictive ability (0.32–0.83). A novel pattern emerged: green-band VIs were particularly effective for predicting CP and RFV, reflecting sensitivity to pea canopy-cover and leaf area, whereas NIR-based VIs were more associated with yield and fiber, characteristic of oat biomass. These complementary associations indicate that VIs capture species composition and biomass partitioning in mixed stands. Integrating NIR- and green-band indices was essential for maximizing prediction accuracy. UAV-based VIs are effective for high-throughput selection in oat-pea intercrop breeding. Finally, accelerating the rate of genetic gain for these complex forage traits requires reducing the breeding cycle time. In Chapter 4, we developed and validated a novel greenhouse protocol, ‘Single-Seed-SpeedBulks,’ that combines ‘speed breeding’ (22 h extended photoperiod) with a high-density, modified single-seed descent (mSSD) method using sand media to accelerate the development of uniform fixed oat breeding germplasm. Our results showed that plants grown in high-density sand under 22 h of light flowered approximately 20 days earlier than those grown under standard 16 h control conditions, while about 85% of plants produced a single seed, closely matching single-seed descent assumptions and substantially reducing space and labor requirements. We translated these findings into a standard operating procedure that advances oat populations from F2 to near-homozygous F4 lines within one year, thereby shortening breeding cycle. Integrating this protocol into spring oat breeding pipelines can accelerate the rate of genetic gain by speeding the development of oat lines to be trialed for cereal–legume intercropping systems.

Graduation Semester

2025-12

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/132677

Copyright and License Information

Copyright 2025 Milcah Kigoni

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