Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates.

Megan Taylor,Guillaume P Ramstein,Millicent D Sanciangco,Paul Grabowski,Joseph Evans,Jeffrey Volenec,C Robin Buell,Yiwei Jiang,Michael D Casler,Jianxin Ma,Carl-Erik Tornqvist,Xiongwei Zhao,Rebecca Doerge

doi:10.3389/fpls.2018.01250

Abstract

Switchgrass (Panicum virgatum) is a native prairie grass and valuable bio-energy crop. The physiological change from juvenile to reproductive adult can draw important resources away from growth into producing reproductive structures, thereby limiting the growth potential of early flowering plants. Delaying the flowering of switchgrass is one approach by which to increase total biomass. The objective of this research was to identify genetic variants and candidate genes for controlling heading and anthesis in segregating switchgrass populations. Four pseudo-F2 populations (two pairs of reciprocal crosses) were developed from lowland (late flowering) and upland (early flowering) ecotypes, and heading and anthesis dates of these populations were collected in Lafayette, IN and DeKalb, IL in 2015 and 2016. Across 2 years, there was a 34- and 73-day difference in heading and a 52- and 75-day difference in anthesis at the Lafayette and DeKalb locations, respectively. A total of 37,901 single nucleotide polymorphisms obtained by exome capture sequencing of the populations were used in a genome-wide association study (GWAS) that identified five significant signals at three loci for heading and two loci for anthesis. Among them, a homolog of FLOWERING LOCUS T on chromosome 5b associated with heading date was identified at the Lafayette location across 2 years. A homolog of ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5, a light modulator in the circadian clock associated with heading date was detected on chromosome 8a across locations and years. These results demonstrate that genetic variants related to floral development could lend themselves to a long-term goal of developing late flowering varieties of switchgrass with high biomass yield.

Highlights

Switchgrass is a C4 perennial bioenergy and forage grass
Day of year was chosen for calculating heading and anthesis dates and subsequently used for genome-wide association study (GWAS) analysis
Significant interactions for heading and anthesis dates involving genotypes, locations, and years may have contributed to variability in GWAS results

Summary

Introduction

Switchgrass is a C4 perennial bioenergy and forage grass. Switchgrass has been chosen as a herbaceous species for biofuel feedstock development due to its adaptation across climates, high biomass yields, tolerance to marginal conditions, and low input requirements. Upland ecotypes are adapted to northern climates with earlier flowering times and producing low biomass, while lowland ecotypes are adapted to southern climates with later flowering times and production of high biomass (Casler, 2012). A delay in flowering time could be achieved by the use of either upland or lowland ecotypes. For upland ecotypes, this would involve intensive selection for late flowering within adapted germplasm. This would involve intensive selection for late flowering within adapted germplasm For lowland ecotypes, this would involve intensive selection for cold tolerance and adaptability within populations from southern latitudes that are already 4–6 weeks later in flowering compared to northern populations (Casler and Boe, 2003; Casler et al, 2004). When short-day grasses are grown in long day conditions, tillers remain vegetative for a longer period of time, resulting in more phytomers and delayed and flowering (Van Esbroeck et al, 2003)

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