QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland

Abstract

Background: Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies.

Results: We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21-23.27% for FRH, 4.47-24.06% for NDVI, 4.35-32.77% for SE, and 4.61-29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55-0.64 H²) and NDVI (0.30-0.61 H²) implies the possibility of using the traits for indirect selection for biomass yield.

Conclusion: Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.

Keywords: Flowering date; QTL mapping; Spring emergence; Switchgrass; Winter dormancy.

Fig. 1

Frequency distribution of the phenotypic traits in AB (column A) and BV (column B) populations for two years of field evaluation. P1 The first portion of the BV population that was planted in April 2017; P2 The second portion of the BV population that was planted in May 2018; Red triangle = AP13; Green triangle = B6; Blue triangle = VS16

Fig. 2

a Parent plants in the greenhouse during winter (February 2020) showed dormant VS16 and AP13 and non-dormant B6; b Growth of B6 plant in Tifton, GA during winter (January 2020), six weeks after clipping in November showed that the plant is still actively growing

Fig. 3

QTL position and colocalization in the AP13 map of the AB population. QTLs are positioned at the right side of each LG; solid bars and whiskers on one or both ends represent coverage at LOD drop interval of 1.0 and 2.0, respectively. QTLs were mapped using LS means for each year and the BLUP value, and labeled with the trait they are associated with followed by year (LS means) or BLUP suffixes

Fig. 4

QTL position and colocalization in the B6 map of the AB population. QTLs are positioned at the right side of each LG; solid bars and whiskers on one or both ends represent coverage at LOD drop interval of 1.0 and 2.0, respectively. QTLs were mapped using LS means for each year and the BLUP value, and labeled with the trait they are associated with followed by year (LS means) or BLUP suffixes

Fig. 5

QTL position and colocalization in the B6 map of the BV population. QTLs are positioned at the right side of each LG; solid bars and whiskers on one or both ends represent coverage at LOD drop interval of 1.0 and 2.0, respectively. QTLs were mapped using LS means for each year in each planting date, and the BLUP value, and labeled with the trait they are associated with followed by year (LS means) or BLUP suffixes

Fig. 6

QTL position and colocalization in the VS16 map of the BV population. QTLs are positioned at the right side of each LG; solid bars and whiskers on one or both ends represent coverage at LOD drop interval of 1.0 and 2.0, respectively. QTLs were mapped using LS means for each year in each planting date, and the BLUP value, and labeled with the trait they are associated with followed by year (LS means) or BLUP suffixes