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. 2022 Feb 21;11(4):566.
doi: 10.3390/plants11040566.

Identification of QTL Associated with Regrowth Vigor Using the Nested Association Mapping Population in Switchgrass

Santosh Nayak  1 , Hem Bhandari  1 , Malay C Saha  2 , Shahjahan Ali  2 , Carl Sams  1 , Vince Pantalone  1
Affiliations

Identification of QTL Associated with Regrowth Vigor Using the Nested Association Mapping Population in Switchgrass

Santosh Nayak et al. Plants (Basel). .

Abstract

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass species that is utilized as forage for livestock and biofuel feedstock. The stability of biomass yield and regrowth vigor under changing harvest frequency would help manage potential fluctuations in the feedstock market and would provide a continuous supply of quality forage for livestock. This study was conducted to (i) assess the genetic variation and (ii) identify the quantitative trait loci (QTL) associated with regrowth vigor after multiple cuttings in lowland switchgrass. A nested association mapping (NAM) population comprising 2000 pseudo F2 progenies was genotyped with single nucleotide polymorphism (SNP) markers derived from exome-capture sequencing and was evaluated for regrowth vigor in 2017 and 2018. The results showed significant variation among the NAM families in terms of regrowth vigor (p < 0.05). A total of 10 QTL were detected on 6 chromosomes: 1B, 5A, 5B, 6B, 7B, and 8A, explaining the phenotypic variation by up to 4.7%. The additive genetic effects of an individual QTL ranged from -0.13 to 0.26. No single QTL showed a markedly large effect, suggesting complex genetics underlying regrowth vigor in switchgrass. The homologs of candidate genes that play a variety of roles in developmental processes, including plant hormonal signal transduction, nucleotide biosynthesis, secondary metabolism, senescence, and responses to both biotic and abiotic stresses, were identified in the vicinity of QTL.

Keywords: nested association mapping (NAM) population; quantitative trait loci (QTL); regrowth vigor; single nucleotide polymorphism (SNP); switchgrass (Panicum virgatum L.).

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Conflict of interest statement

The authors declare that there are no conflict of interest.

Figures

Figure 1
Figure 1
Mean regrowth vigor score (The range of the score is from 0 to 9; 0 = no regrowth, 1 = the least vigorous, 9 = the most vigorous) across two years (2017 and 2018) of the founder parents of the nested association mapping (NAM) population, AP13, and Alamo check. Bars not sharing a common letter are significantly different at p < 0.05. Error bars indicate 95% confidence intervals of the mean.
Figure 2
Figure 2
Frequency distribution of regrowth vigor in the nested association mapping (NAM) population for (a) 2017, (b) 2018, and (c) the combined data across two years: 2017 and 2018.
Figure 3
Figure 3
Regrowth vigor scoring scale (0 to 9 rating scale: 0 = no regrowth, 1 = the least vigorous, 9 = the most vigorous).
See this image and copyright information in PMC

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