Genomic selection for perennial groundcover and intercrop breeding systems

Overview

This solution applies genomic selection (GS) to the challenge of breeding for intercropping (B4I), an underexploited strategy for improving intercrop systems. Conventional B4I is limited to late-stage testing with small entry numbers because the number of possible species combinations is too large to evaluate directly. The proposed approach enables rapid, early-stage selection for intercrop-ability by predicting performance using a sparse co-testing field design combined with phenomic and genomic data.

The primary application is perennial groundcover (PGC) systems, specifically kura clover (KC) grown alongside corn. PGC systems offer documented agronomic benefits including weed suppression, improved soil water infiltration, and reduced nitrogen fertilizer requirements without sacrificing corn yields. However, scale-up is hindered by slow KC establishment and the difficulty of germinating corn in a living KC stand. This approach targets both problems simultaneously by breeding KC for corn-compatible canopies and fast establishment, and by identifying corn hybrids suited to no-till planting into PGC.

Technical specifications

Core methodology:

• Genomic prediction adapted from hybrid breeding and genotype-by-environment interaction (GxE) prediction frameworks
• Sparse co-testing field design where each entry from one crop is tested with multiple partners from the other crop, keeping trial sizes tractable
• Integration of phenomic and genomic data to predict unmeasured intercrop-ability traits
• Leveraging a nearly complete genome assembly and pan-genome project for kura clover (developed with JGI and HudsonAlpha)

Three planned validation trials:

• KC Nursery Alone vs. Under Corn: Cloned KC lines evaluated in monoculture versus interplanted with corn to determine whether selection under monoculture is predictive of performance under corn
• Corn-KC Training Population: Sparse field testing of genotyped corn and KC lines, each tested with multiple partners from the other species, to assess the accuracy of intercrop-ability genomic prediction
• PGC Variety Trial: Intercrops and monocultures of 3–6 KC accessions with corn to evaluate KC impacts on corn yield and corn impacts on KC productivity

Technology readiness level

The underlying genomic selection methodology is well-validated in related breeding contexts, including hybrid prediction and GxE prediction. Genetic variance in PGC systems has not yet been estimated for either kura clover or corn in this configuration. Current data comes from two ongoing trials involving corn hybrids but only one kura clover accession, which cannot represent the full corn-KC PGC potential. Additional kura clover seed is being increased for the proposed trials. The proposed work would generate the first systematic estimates of genetic variance and genomic prediction accuracy for intercrop-ability in a PGC system, representing an early-to-mid stage development effort requiring field validation before deployment.