Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population.

Hari P Poudel,Michael D Casler,C Robin Buell,Millicent D Sanciangco,Shawn M Kaeppler

doi:10.3389/fpls.2019.00372

Abstract

Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass when grown in northern latitudes in the United States. A better understanding of the genetic architecture of 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 × upland switchgrass population. A pseudo-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 for two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype with the hypothesis that upland genotype is the source for higher tiller number and early tiller emergence. Survivorship of the pseudo-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 single nucleotide polymorphism markers generated 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 each on 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 tolerance genes/proteins, such as COR47, DREB2B, zinc finger-CCCH, WRKY, GIGANTEA, HSP70, and NRT2, among others that reside within the 1.5 LOD confidence interval of the identified QTL.

Highlights

Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass (Panicum virgatum L.) when grown in northern latitudes in the United States (Lemus et al, 2002; Milano et al, 2016)
The objectives of this study were to: (1) conduct a freezingtolerance screening of a pseudo-F2 switchgrass population in controlled environment chambers, (2) construct a genetic map using single nucleotide polymorphism (SNP) markers generated through exome-capture sequencing, and (3) identify quantitative trait loci (QTL) associated with freezing tolerance in a lowland x upland switchgrass mapping population
The effect of cycle was significant for tiller emergence and tiller number combined analysis, probably because of the extra 7 days of cold acclimation in the samples used in cycle 2

Summary

Introduction

Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass (Panicum virgatum L.) when grown in northern latitudes in the United States (Lemus et al, 2002; Milano et al, 2016). For the sustainable and economical use of switchgrass as a biomass crop, a minimum of 20 Mg ha−1 yr−1 dry matter biomass yield that survives multiple years is desirable (Taliaferro, 2002; Casler, 2012). To achieve this goal, two traits mainly form the focus in switchgrass breeding programs: late flowering to extend the growing season and winter survivorship to ensure stand longevity. Identification of freezing tolerance QTL using the first strategy is the focus of this research

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Conclusion