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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Dairy Forage Research » Research » Publications at this Location » Publication #359074
Title: Quantitative trait loci for freezing tolerance in a lowland x upland switchgrass population

Author
item POUDEL, HARI - University Of Wisconsin
item SANCIANGCO, MILLICENT - Michigan State University
item KAEPPLER, SHAWN - University Of Wisconsin
item BUELL, C - Michigan State University
item Casler, Michael

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary: Switchgrass is undergoing development as a biomass crop to support the bioenergy industry. Late flowering time and increased freezing tolerance are two key traits to aid in developing high-biomass varieties for use in the northern USA. This research identified six regions within switchgrass chromosomes that contained genes regulating freezing tolerance. These six regions combined accounted for over 70% of the variability in freezing tolerance within a diverse switchgrass population. DNA markers within these six regions can be utilized by switchgrass breeders to make significant genetic improvements in freezing tolerance of late-flowering switchgrass populations for the northern USA.

Technical Abstract: Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass grown in northern latitudes in the USA. A better understanding of the genomic architecture for freezing tolerance in switchgrass will aid the development of lowland switchgrass cultivars with improved winter survival. The objectives of this study were to conduct a freezing tolerance assessment, generate a genetic map using single nucleotide polymorphism (SNP) markers and identify QTL (quantitative trait loci) associated with freezing tolerance in a lowland x upland switchgrass population. An F2 mapping population was generated from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. The segregating progenies were screened for freezing tolerance in a controlled-environment facility. Two clonal replicates of each genotype were tested at six different treatment temperatures ranging from -15 to -5°C at an interval of 2°C in two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype. Survivorship of the F2 population ranged from 89% at -5°C to 5% at -15°C with an average LT50 of -9.7°C. Genotype had a significant effect on all traits except tiller number at -15°C. A linkage map was constructed from bi-allelic SNP markers genotyped using exome capture sequencing. The final map consisted of 1618 markers and 2626 cM with an average inter-marker distance of 1.8 cM. Six significant QTL were identified, one on each of the chromosomes 1K, 5K, 5N, 6K, 6N and 9K for the following traits: tiller number, tiller emergence days and LT50. A comparative genomics study revealed important freezing tolerant genes/proteins such as COR47, DREB2B, zinc finger-CCCH, WRKY, GI, HSP70, and NRT2 among others that reside within the 1.5 LOD confidence interval of the identified QTL. Markers associated with freezing tolerance can be used for breeding lowland switchgrass with higher winter survival suitable for areas with freezing winters.