Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

Abstract

Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using crossvalidation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence-based GS when sequencing resources were restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes for reduced sequencing costs in GS. INTRODUCTIONSwitchgrass (Panicum virgatum L.) is a perennial bioenergy grass that is native to the United States and is capable of producing large quantities of low-input biomass (Casler, 2012;. Bioenergy crops have an important role in

Strong parallel evidence of selection during switchgrass sward establishment in hybrid and lowland ecotypes

“…Heading date repeatability was 0.97 for lowland and 0.79 for hybrid breeding populations. The generally high repeatability in the lowland models is due to population structure (Tilhou & Casler, 2021). Visually, there was a pattern of earlier heading date GEBVs among late flowering families and later heading date among the early flowering families within both breeding groups (Figure 2c,d).…”

“…The FLOMAS data set used 724 individuals of lowland and hybrid ecotype ancestry with observations of heading date (2 years) and winter survival (3 years). The experimental design and sequencing methods for FLOMAS was previously reported in Tilhou and Casler (2021). A combined marker array of DNA pools and individuals was created by converting pooled DNA allele frequencies (0–1) to mean allele dosage (0–2).…”

Biomass yield improvement in switchgrass through genomic prediction of flowering time

“…In this study, the experimental units for the GP training data were unreplicated, randomized greenhouse‐grown spaced plants (previously described in Tilhou & Casler, 2021). The training population nursery was established in row plots in 2016 at a single location (Arlington, WI; 43° 18′ N; 89° 21′ W).…”

“…The training populations used in this experiment could predict flowering time with accuracy sufficient for gain equivalent to or greater than phenotypic selection for flowering time. Further, these gains could be maintained with substantial reductions in phenotyping effort (Tilhou & Casler, 2021; Table S2). Assuming selection of the top 10% of a population (selection intensity: 1.75), the repeatability, variance, and predictive ability estimates from progeny validation indicate that Midwest and Hybrid breeding groups could delay anthesis by 3.4 (MT 3.7) and 7.1 (MT 7.8) days in one selection cycle, respectively.…”

Switchgrass sward establishment selection is consistent across multiple environments and fertilization levels

“…Performance data was collected on 24 hybrid SPACE half‐sib families. The exact experimental design and sequencing methods for FLOMAS were previously reported by Tilhou and Casler (2021). Briefly, the FLOMAS data set included 422 hybrid individuals with measurements of the heading date (2 years) and winter survival (3 years).…”