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

• Published in: Grassland research (Online) 2022-03, Vol.1 (1), p.31-42
• Main Authors: Tilhou, Neal W., Kaeppler, Shawn M., Casler, Michael D.
• Format: Article
• Language: English
• Subjects: Biomass; Breeding; Cultivars; Datasets; Deoxyribonucleic acid; DNA; DNA sequencing; Domestication; Ecotypes; Experiments; Gene frequency; Gene sequencing; Genetic testing; Genomes; genomic prediction; Germplasm; grassland establishment; Grasslands; Panicum virgatum; Polygenic inheritance; polygenic traits; Seedlings; Seeds; selection; Survival; Sward; Winter
• ISSN: 2097-051X; 2770-1743
• DOI: 10.1002/glr2.12007

Background Switchgrass sward establishment results in up to 90% seedling mortality. The degree of selection during sward establishment has not been reported using modern genetic methods. Methods Pooled leaf samples were sequenced from replicated swards of 46 half‐sib families from two breeding groups (lowland and hybrid) before and through 3 years of stand establishment. Pooled allele frequencies were then assessed using fixation indices (Fst) and an independent data set was used to predict the polygenic impact of establishment selection on two traits (heading date and winter survivorship). Last, the DNA pools were assigned survival rankings to predict the sward survival genomically estimated breeding values within the training data set. Results Strong and parallel selection occured in both breeding groups. Five genomic regions exceeded the significant threshold of 99.9% in >10 families, indicating consistent selection across families and breeding groups. Polygenic trait predictions determined that establishment selection was partially associated with winter survivorship but resulted in variable heading date alterations. The genomewide variation is consistent with selection for a small number of related parental lines. Conclusions This study observed strong selection for a small number of hybrid and coastal ecotype individuals which are promising germplasm sources for improved sward survival. This confirms prior reports of sward selection during grassland establishment and highlights the strength of pooled DNA sequencing for survival traits. Grassland sward establishment can result in >90% seedling mortality. Pooled switchgrass leaf DNA indicated intense selection during establishment in two diverged breeding populations and that a few parental individuals were over‐represented in surviving swards. This confirms prior reports of grassland establishment selection and provides a novel genomic selection training strategy.