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. 2020 Nov 9:11:585927.
doi: 10.3389/fpls.2020.585927. eCollection 2020.

Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit

María Muñoz-Amatriaín  1 , Javier Hernandez  2 , Dustin Herb  2 , P Stephen Baenziger  3 , Anne Marie Bochard  4 , Flavio Capettini  5 , Ana Casas  6 , Alfonso Cuesta-Marcos  7 , Claus Einfeldt  8 , Scott Fisk  2 , Amelie Genty  9 , Laura Helgerson  2 , Markus Herz  10 , Gongshe Hu  11 , Ernesto Igartua  6 , Ildiko Karsai  12 , Toshiki Nakamura  13 , Kazuhiro Sato  14 , Kevin Smith  15 , Eric Stockinger  16 , William Thomas  17 , Patrick Hayes  2
Affiliations

Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit

María Muñoz-Amatriaín et al. Front Plant Sci. .

Abstract

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.

Keywords: GWAS; barley; facultative; low temperature tolerance; meta-analysis; multi-environments.

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Figures

FIGURE 1
FIGURE 1
Phenotypic frequency distributions for 882 barley accessions. (A) Average winter survival across 10 locations. (B) Days to flowering under greenhouse conditions without vernalization. Full Pint, Maja, and Alba are the spring, facultative, and winter checks, respectively.
FIGURE 2
FIGURE 2
Principal component analysis of average winter survival across 10 locations. (A) Contribution of each location to variation across all sites (locations are defined in the text). (B) Overlay of the top 5%, bottom 5%, and rest of the accessions for winter survival. (C) Overlay of vernalization sensitivity (see text for definitions). (D) Overlay of head type (2-row, 6-row).
FIGURE 3
FIGURE 3
Diversity dendrogram based on SNP genotype data for the top 5% lines of barley accessions for average winter survival across 10 locations. Clades are numbered clockwise, starting with I. The% values are average winter survival for the clade. See Table 1 for more data on the accessions within each clade.
FIGURE 4
FIGURE 4
Principal component analysis of 882 barley accessions colored by head type (A) and accession origin (B).
FIGURE 5
FIGURE 5
Manhattan plots from the GWAS of 882 accessions. (A) Meta-analysis of winter survival. (B) Days to flowering without vernalization. -log10 (p-values) are shown for 4,875 SNPs with physical coordinates in the barley reference genome (Mascher et al., 2017). The dashed lines indicate the 0.01 FDR-corrected threshold [3.70 for (A) and 3.75 for (B)].
See this image and copyright information in PMC

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