Genetic loci associated with winter survivorship in diverse lowland switchgrass populations

Authors: POUDEL, HARI - Agri Food - Canada; TILHOU, NEAL - University Of Wisconsin; SANCIANGCO, MILLICENT - Michigan State University; VAILLANCOURT, BRIANNE - Michigan State University; KAEPPLER, SHAWN - University Of Wisconsin; BUELL, C. ROBIN - Michigan State University; Casler, Michael

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/1/2021
Publication Date: 12/5/2021
Citation: Poudel, H., Tilhou, N., Sanciangco, M., Vaillancourt, B., Kaeppler, S., Buell, C., Casler, M.D. 2021. Genetic loci associated with winter survivorship in diverse lowland switchgrass populations. The Plant Genome. 14(3). Article e20159. https://doi.org/10.1002/tpg2.20159.
DOI: https://doi.org/10.1002/tpg2.20159

Interpretive Summary: Switchgrass is one of the energy grass candidates for development of perennial biomass systems to supply feedstock for bioenergy production. Significant breeding efforts are required to make switchgrass production systems more economically sustainable. One approach to improving sustainability is to identify late-flowering plants with sufficient winter hardiness to survive in the northern USA, where they can continue to grow and accumulate biomass up to killing frost. In order to speed up the tedious breeding process of identifying those plants, this project identified several highly significant DNA markers strongly associated with winter hardiness in two harsh environments. Several of these markers were significant across numerous populations, indicating a certain level of repeatability and consistency. These results can be used by switchgrass breeders to accelerate the breeding process of developing sustainable cultivars for biomass production in perennial systems.

Technical Abstract: High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk-segregant analysis (BSA). In this study, 29 lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 populations with differential winter survivorship were used for BSA. A maximum of 10% of the individuals (8-20 individuals per pool) were bulked to create survivor and non-survivor pools for each population and location. DNA pools were genotyped using exome capture sequencing and allele frequencies were used to conduct statistical tests for allelic differentiation. The BSA tests revealed nine QTL from tetraploid population and seven QTL from octoploid populations. Some markers were identified in multiple populations across a broad geographic landscape, while other markers were highly site-specific. QTL at position 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, 1 and 100 Mb on chromosome 9N are identified as most potentially useful based on the change in allele frequencies across multiple populations, relationship with the long-term minimum temperature of the coldest month of the site of origin of population, and biological significance of the chromosome region. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.