Talk by Peter L. Morrell in the Tritaceae Genomics & Genetics session at PAG 2018. The title was "Barley landrace environmental association."

1. Barley Landrace
Environmental
Association
Plant & Animal Genome 2018

2. Questions
• Can we identify genetic
variants that contribute
to environmental
adaptation in barley?
• In particular, are their
detectable variants that
could contribute to
cold temperature
adaptation?
• Cold adaptation per se
poorly explored relative
to flowering time
Poets et al. 2015

3. Study Design
• 784 geo-referenced landraces
from USDA NSGC Core
• Across historic range of
cultivation
• Genotyping on the barley
iSelect 9K - 6,152 SNPs
• Exome capture resequencing
of 137 landraces from our lab
• 137 more from IPK &
collaborators

4. Barley Landrace
Distribution
• Barley was cultivated from
Europe to East Asia
• By 3 - 5K YBP
• Ultimately from equator to the
Arctic Circle
• 0 - 66˚ N latitude

5. Barley Adaptation to
Eurasia
Pinhasi et al. 2005

6. ATGCAGTT
TTGCAGTT
CTGCAGTT
ATGCGGTT
TTGCGGTT
CTGCGGTT
Genetic varaints Phenotypes
Genetic positions of Chromosomes (cM)
+
●
●
●
●
●
●
●● ●●
●● ●
●●●●
● ●● ●● ●●● ●● ●●● ● ● ●● ●● ●● ● ●●●● ●●● ● ●● ● ●●● ● ●● ●●● ●● ● ●● ● ●●●●●●● ● ●● ●● ●●● ●●●● ●● ●●● ●● ●● ●● ●● ●●● ●● ●● ●● ●●● ● ● ●●● ● ● ●●● ●● ●● ●● ● ● ●●● ● ●●●●● ●● ●● ● ●● ●●● ●●●● ●● ●●● ●● ●● ●●● ●●● ● ●● ●●● ●●● ● ●●● ●● ●● ● ●● ●●●● ●● ●●● ●● ● ●●● ● ●● ●● ● ●●● ● ● ● ●●●●● ●●● ●● ●● ●●● ● ●● ●● ●●●● ●●● ●●● ●●● ●● ●●● ● ●● ●● ●● ●●● ● ●● ●● ● ●● ●● ● ●● ● ●●● ●● ●●● ●● ● ●● ●●● ● ●●● ●● ●● ●● ●●●● ●● ●●● ● ●● ● ●● ●● ●● ● ●●● ●●● ●●●● ●●● ●● ●●● ●●●● ●●●● ●●● ●● ●●●● ● ● ●● ● ●●● ●● ● ●● ●●● ● ● ●● ●●● ●● ●●●●●● ●● ● ●●● ● ●●● ●● ●● ●● ●●●● ● ● ●● ●● ●● ●● ●●● ●● ●● ●● ● ● ●● ● ● ●●● ●●● ● ●● ● ●● ● ●●●●● ● ● ● ●● ●●● ●● ● ● ● ●● ● ●● ●● ● ●● ●● ●● ●● ● ●● ●● ●● ●●● ●● ●● ●●●● ● ●● ●●● ●●● ● ●● ● ●●●● ●● ●● ●● ●●●● ●● ●●● ●● ●●● ●●●●●● ●● ●● ●● ● ●● ●●● ● ●●● ●● ● ● ●●● ● ● ●● ●●●● ●● ●● ● ●●● ●● ● ●●● ● ● ●● ● ● ●● ● ●● ● ●● ●●●● ● ●●● ●●●●● ●●● ● ● ●● ●●● ●● ●● ● ●●● ●● ●● ● ●●● ● ●● ● ●●● ●● ●● ●● ●● ●●● ●● ●● ●●● ● ●● ●● ●● ● ●● ● ●● ●● ● ● ●●● ●●● ● ● ●●●● ●●● ●●●●● ● ●●●● ●● ●●● ●●● ●● ●●●● ●●●●● ●●●●● ● ● ●● ●● ● ●● ●● ● ●●● ●●● ●●●● ● ●●●●● ● ●● ● ●●●● ● ●● ●● ●●● ●●● ● ● ●●● ●● ● ●● ● ●●●● ●●● ●●● ●● ● ●● ●● ●●● ●● ●● ●●● ● ●● ● ●●●●●● ● ●● ● ●● ●● ●● ●● ●● ●● ●●● ●● ● ●● ●● ● ●●●● ●● ●●●● ●●● ●●● ● ●● ●●●● ●● ● ●● ● ●● ●●● ● ● ●●●● ●● ●● ●● ●●● ●● ● ●● ●●●● ●● ●● ●● ● ●●● ● ●●● ●● ●●●●● ●● ● ●● ●●● ●●● ●●● ●●● ●● ●● ●●● ●● ●●●● ●●●● ●● ●●● ● ●●● ● ● ●●●●● ● ●● ●● ● ● ●● ●● ● ●●● ●● ●● ●●● ●●● ●●●● ●● ● ●●● ●● ●● ●●●●● ●●●● ●● ●● ● ●● ●● ●●● ●● ●● ●● ●●● ●● ●●●●● ●●● ● ●●● ● ●● ●●● ●●●●●● ●●● ● ●●● ●● ●●● ●● ● ●● ●● ●● ●● ● ●●●● ● ●●●●●● ●● ● ●●●●● ● ●●● ● ● ●●● ●●●● ●● ●●●●● ●● ●● ● ●● ●●●● ● ●●● ●● ● ●● ● ●●● ● ●●● ●● ●● ● ● ●● ●●● ● ●● ● ●●●● ● ●● ● ●●●● ●●● ●● ●● ●● ●● ●●●●● ● ●● ● ●●● ●● ●● ●●● ●● ●● ●● ● ●● ●●● ● ●●● ● ● ●● ● ●● ●●●● ●● ● ●●●●● ●●● ● ●●●● ●● ●●● ●● ●● ● ●● ●●● ● ●●●●● ●● ●● ●●●● ● ● ●● ●●● ●● ●●●● ●●● ●● ● ●● ●● ●●● ●● ● ●● ●● ●● ●●● ●● ●● ●● ●● ● ●● ●● ●● ● ●●● ● ● ●● ●●●● ● ●●● ● ●● ●● ●● ●● ●● ●●●●● ●● ●●●● ●● ●● ● ●●●● ●● ●●● ●● ●● ●●● ●● ●●●● ●●● ● ●●● ●● ●●●●● ●●● ●●● ● ●● ● ● ●●● ●● ●● ● ●●● ● ●● ●● ● ● ●●● ●● ●● ●● ●● ●● ● ●● ● ●●● ● ●●●● ●●● ● ●● ●● ●● ●● ●●● ● ● ●●● ●● ● ●● ●● ● ●●● ● ● ●● ●●●●● ●● ●●● ● ●● ● ●●●● ●● ● ● ●● ●●● ● ● ●●●●● ●● ●●● ●● ● ●● ● ●●●● ●●● ● ● ● ●● ●●●● ●● ● ●● ●● ●● ●● ●●●● ● ●●● ●● ● ●● ●● ●● ●● ● ●● ● ●● ●●● ●● ● ●●● ●● ●●● ●●● ● ●● ● ●● ●● ●● ●●● ●●● ● ● ●●● ●● ●●● ● ●● ● ●● ● ●● ● ●● ● ● ● ●●● ●● ● ●● ●●● ●● ●●● ● ● ●● ●● ●● ● ●● ●● ●● ●●●● ●● ●● ● ● ●● ● ●● ●●●● ●● ● ●●●● ● ● ●● ●● ●●● ●● ●● ●●● ●● ● ●●● ● ●●● ● ●● ●● ● ●●●● ●● ●● ●● ●●● ●●● ●●● ●●●● ●●● ● ●●●● ● ●●● ● ●● ● ●●●● ●● ●● ● ● ●● ●● ●● ● ●● ● ●●● ● ●● ● ●● ● ● ●●● ● ● ● ●● ● ●● ●●●● ●● ●● ●●● ●● ●●●● ●●● ●●● ●● ●●● ● ●●● ●●●● ● ●●● ●● ●● ● ●●●● ● ●●● ●● ●●● ●●● ●● ●●● ●● ●●●● ● ●●●●● ●● ●● ● ●●● ●● ● ●● ●● ●●● ●●●●● ● ●● ●● ●●●●● ● ●●● ●● ● ●● ●● ●● ●● ●● ●● ● ●●●● ●● ●● ●●● ●●● ●● ● ●●●● ● ●●● ● ●● ● ●●● ●●● ●● ●● ● ●● ● ●● ●● ●●●● ●●●● ●● ● ●● ●● ● ●● ●●● ● ●● ●● ●● ●● ●● ●● ●● ●●●● ● ●● ●● ●● ● ●●● ● ●●● ●●●● ●● ● ●●● ● ●●● ●●● ●●● ●●●● ●● ● ●● ●● ●●●● ●● ● ●●●● ●●● ●●● ●● ●●●● ● ●● ● ●●● ●●● ●●● ●● ● ●● ● ●● ● ●● ●● ●●● ●●●● ●● ● ●●● ●●● ●● ●● ● ●● ●●● ● ●● ●●● ● ●● ●●●● ●●●●● ●● ●● ● ●● ●● ●● ● ● ●● ●●● ●● ●● ●● ● ● ●● ● ●●● ●●● ● ●● ●● ●● ●●● ●●●●● ● ●● ●● ●● ●● ●● ●●● ● ●● ● ●● ●●● ●● ● ● ●●● ●●●● ●● ●●● ● ●● ● ● ●●● ●● ●●● ● ●● ●● ●●●● ● ●● ●●●●● ●● ●●● ●● ● ●● ●● ●● ●● ●●● ●● ●● ●● ●● ●●●● ● ●●●● ●● ● ●● ●● ●●● ●● ● ●● ●● ●●●● ● ● ●●● ●● ●● ●● ● ●●●●● ● ●● ● ●●● ● ●●● ●●●● ● ●● ●●● ●● ●●● ●●● ●● ●●●● ●●● ● ●● ● ●●● ●● ● ●●●●● ● ●●● ●● ●●● ●● ●● ●●●●● ●●●● ●● ●●● ●● ●● ●● ● ●●●● ●● ● ●●● ● ●● ●● ●● ●● ● ●● ●●● ●● ● ● ● ●● ● ●●● ●● ●● ●●●● ● ●● ●● ● ● ●● ●● ● ● ●● ● ● ●● ● ●● ●● ●●● ● ●● ● ● ●● ● ●●● ●●● ●● ●● ●● ●●● ●●● ●●● ● ●●●● ● ●● ●●●● ● ●●● ● ●● ●● ●● ●●● ● ●●●● ● ●●●● ●●●● ● ●● ●● ● ●● ●●● ●●● ● ●● ●●● ●● ●●● ● ●● ●●● ● ●● ● ● ●● ●●● ● ●● ● ● ●● ● ●●● ● ●●● ●●●● ●●● ●●● ●● ●●● ●●●●● ●●● ● ●● ●● ●● ● ● ● ●● ●● ●●●● ●● ●● ●●● ●●●● ●● ●● ●●●● ● ●● ● ●● ●● ●● ● ●● ●●● ●●● ●●● ●● ●●● ●●●● ● ● ●● ●●● ●● ● ●● ●● ●●● ● ●● ●● ●● ● ●●● ●●●● ● ●●● ● ●● ●● ●●● ●●●● ● ● ● ●●● ● ●●● ● ●● ●● ● ●● ●● ●● ●●● ● ●● ●● ●● ●● ●● ●● ●● ●● ●● ● ●● ●●●●● ●●● ● ●●● ●● ● ● ●● ●●●● ● ●●●● ● ●● ●●● ● ●● ●●● ●●●● ●●●● ● ●● ●● ● ●●● ●● ●● ●● ●●● ●●●●● ●●●● ● ●●●● ● ●● ●● ● ●● ●●● ●●● ●●● ●● ●●● ●● ●●● ● ●●● ●● ●● ●●● ●● ●●● ●●● ●●● ●●●●● ●●●●●●● ● ●●● ● ● ●● ●● ●● ●●●●●● ●● ●●● ●● ●●● ●●●● ●●● ● ●● ● ●● ●● ● ●●● ●● ●● ● ●● ● ●●● ●●● ●● ●● ●●● ● ●●● ●●● ●● ● ●●● ●●● ●●● ●● ● ● ● ● ●● ●●● ●● ● ●● ●●●● ●● ●● ●● ● ●● ●●● ●●● ●● ● ●● ● ● ●●● ● ● ●● ●●● ●●●● ●●● ●●● ●● ●● ● ●● ●● ●● ●●● ●●● ● ●● ●● ● ●● ● ●● ●● ●● ● ●● ● ● ●●● ● ●● ● ●● ● ●●●● ●●● ●● ● ●●● ●● ● ● ● ●● ● ●● ● ●● ● ●● ●●● ●●● ● ● ●● ●● ●● ● ● ● ● ●● ● ●●● ●● ● ●●● ●●●● ●● ●●● ●● ●●●● ●● ● ● ●●● ●●● ●● ●● ●●● ● ●● ●●● ● ●● ●●●● ●● ● ●●● ●● ●● ●●● ●●● ●●● ●● ●●● ●● ● ● ●● ●● ●●●●● ●●● ● ● ●●●● ●● ● ●●●● ●●●● ●● ●●● ●● ●● ●●● ● ●●● ● ●●● ● ●● ● ●● ●● ●● ● ●● ●●●● ●● ●●● ● ●● ●● ●●● ●● ●● ●●● ●●●● ●●● ●●● ●●●● ●● ●●● ● ●●● ●● ●●●● ●●● ●●●● ●●● ●● ●●●● ● ●●● ● ●● ●●● ●● ●● ● ● ●●● ●●● ●● ●●● ●● ●●● ● ● ●● ● ● ●●●●● ● ●●●● ● ● ●● ●●● ● ●●● ●●●● ●●●● ●● ● ●● ● ●●● ●● ●● ● ●●● ●●●● ●● ●●● ● ●● ●●●● ●●●● ●● ●● ● ● ●●●● ●● ●● ●● ● ●●● ●●●● ●● ●● ● ●● ●●●●● ● ●● ● ●●● ● ● ●●● ●● ● ●●● ● ●● ●●● ● ●● ●●● ● ●● ● ● ●● ●● ●●●● ●● ●●●● ●● ● ●●●●● ●●● ●●● ● ●●● ●● ●●● ● ●●● ●● ●●●● ●● ● ● ●●●● ●●●● ●● ●● ●● ●● ●● ●● ●● ●● ● ●● ●● ● ●●● ● ●● ●● ● ●●●●● ●● ●● ●●● ●● ● ●● ● ●● ●●● ●● ●●● ● ● ●●●●●● ●● ● ●●● ● ● ● ●●● ● ● ●● ●● ●● ●● ●● ●●●● ●●● ●● ● ●● ●● ●●● ● ●●● ● ●●● ● ●●● ●● ●● ● ●● ● ●● ●●● ●●●● ● ●●● ●●●● ●● ● ●● ●● ● ●● ●●● ●●● ●● ●● ●● ●●●● ● ●●● ● ●● ●● ●●●● ● ●●● ●● ●●●●● ● ●● ●●● ●● ● ●●● ● ●● ●● ●●● ● ● ●● ●● ●● ●●● ●● ●● ● ●● ●●●● ●●● ● ●● ●● ● ●●● ● ●●●● ●●●● ● ●● ●● ● ●●● ●● ●● ●●●●● ● ●●● ●●●● ●● ●●●●● ●●● ●● ●●● ●●● ● ● ●● ● ●● ●● ●●●● ●● ●● ●● ●● ●●●● ● ●●● ●● ●● ●●● ● ●● ●● ●● ● ●● ●●● ●●● ●●● ●● ●● ● ●● ●● ●● ● ●● ●●●●● ● ● ● ●● ●●● ●● ●● ● ●● ● ● ●●●●● ●● ● ●● ● ●●● ●● ●●●● ●● ● ●● ●● ● ●● ●● ●● ● ●●●●● ●● ●●● ●● ● ● ●●● ●●● ●●● ● ●●●● ●● ●●● ●● ●●●● ● ●●● ●● ● ●● ● ●● ●● ●●●●● ●● ●● ● ●●● ●● ● ● ●●● ● ●● ● ●● ●●● ●● ● ●● ●● ● ● ● ●● ●●● ● ● ● ●● ●● ●●● ● ●●● ●●● ●● ●● ●●●● ●● ●● ●● ● ●● ●● ●● ●● ● ●● ●●● ●●●●●● ●● ● ● ●● ● ●● ● ●●● ●●● ● ●●● ●● ●● ●●● ●● ●●● ●●●● ●● ● ●●● ●● ● ●●●●●● ●●● ●● ●● ●● ● ●●●● ●● ●●● ●● ●● ●●●● ● ●● ● ● ●● ●●●● ●●● ●● ●●●● ●●● ●● ●●● ●● ●● ●● ●● ●● ●● ●● ● ●● ●● ● ●● ●● ● ●● ● ● ●●● ● ●●● ● ●● ● ● ●●●●● ● ●● ●● ●● ●●● ●●● ● ●● ● ●●●● ●● ●● ● ●●●●● ● ●●● ●● ● ●●● ●●●● ●● ●●● ●● ●● ●● ●●● ●●● ● ●●●●●●●● ●● ● ● ●● ●● ●● ● ● ●● ● ●●● ● ●●●● ●●● ●●●●● ●● ●●● ●● ●● ●●●●●● ● ● ●●●● ● ● ●● ● ●● ● ●● ●● ●● ●● ●●● ● ●● ●● ● ●●●●● ● ● ●●●● ●●● ●●● ●● ●●● ●● ●●● ●●●●● ● ● ● ●● ●●● ● ●● ●● ●● ●●● ● ●● ●● ● ●● ●● ●● ● ● ● ●● ●●● ● ●●●● ●●●● ●●● ● ●● ● ● ●● ● ●●● ● ●● ●●●● ●● ● ●●● ●●●●● ●● ●●● ●● ●●●●●● ● ●●● ●● ●● ●● ●●●●● ●● ●●● ● ●● ●● ●●● ●● ●● ●● ●● ●●● ● ● ● ●● ●●● ● ●● ● ●●●●●● ●● ●●● ● ●●● ● ●● ● ●●● ●● ●●● ● ●● ●● ●●●● ● ● ●●●●● ●●● ●● ● ●● ●●● ● ●●● ●● ● ●●● ●●● ● ●● ●●● ●● ●● ●●●●● ●● ●● ● ● ●●● ●●●● ●● ●● ● ● ●●●●● ● ●● ●● ●●● ●● ●● ●●● ●● ●● ●● ●● ●● ●● ● ● ●● ●● ●●●● ● ●●● ●●●●● ●● ●●● ● ●● ● ●●●● ●● ● ●● ●● ●● ●● ●● ●● ●●●● ● ●● ●● ● ●● ●●● ● ● ●● ●●● ●● ● ●●●●●●● ● ●●●● ●● ●● ●●● ●● ● ●●● ● ● ●●● ● ●● ●● ●● ● ● ● ●●●●● ●●●● ● ●● ● ●● ● ●● ●●● ●●● ● ●● ●●● ● ●● ● ●●● ● ●● ●● ● ●●● ● ●● ● ●● ●● ●● ●●● ● ●● ● ●● ●● ● ●●● ●●●● ● ● ●●● ●●●● ●● ●●● ●●● ●● ●●● ●●● ● ●● ●● ●●● ●●● ●● ●● ●● ● ●● ●●●● ●● ●●● ● ●●●● ●● ● ●●● ●● ●●● ●●● ● ●● ●●●● ● ● ●● ●●● ●● ● ●● ●● ●●● ●●●● ●● ●● ●●●● ●●● ●● ●●● ●● ● ●●● ●● ●● ●● ● ● ●●● ● ● ● ●●●● ●● ●● ●● ●● ●●● ●● ●●● ● ●●●●● ● ● ●●●● ● ●● ● ●●● ●● ●● ●● ●● ●●●● ●●● ●● ●●● ●●● ● ●● ● ●●● ●● ●●● ●● ●● ●●● ●● ●●● ● ●●●●●● ● ● ●●● ● ●● ●●● ●● ●●● ● ●●● ● ●● ● ●● ●●● ●● ●●● ●● ●●●●● ●● ● ● ●● ●●● ●●●● ●● ● ●● ● ●●●● ●● ● ● ●● ●● ● ●● ●● ●● ●● ● ●● ●●●●● ● ●● ●● ● ●● ●● ● ●●● ●●● ●● ● ●●● ●●● ● ●●● ●● ● ●● ●●● ●●● ● ●●● ● ●●● ●●●● ●●● ● ●●●●● ●● ●●● ● ●●● ●●●● ●● ●● ● ●● ● ●● ●● ● ●● ●● ● ●●●● ●●● ●● ●● ●● ●● ● ●● ●●●● ●●● ●● ●●● ● ● ●● ●● ●●●● ● ●● ● ● ●● ● ●●● ●●●● ●● ●● ●●● ● ●●● ●● ●●●● ●● ●●●● ●●● ● ●● ●● ●●● ●● ●● ●● ●●● ● ●● ●● ●● ●●● ● ●●● ●●● ●●●● ●●●● ●● ●● ●●● ●●● ● ●● ● ●● ●●● ●● ●●● ● ●●● ●● ●●● ●●● ●● ●●●● ●● ●● ●● ●● ●●● ●●● ●● ●●● ●●●● ● ●● ●● ●●● ● ●● ●●● ●●● ●● ●●● ●● ● ●●● ●●● ●● ● ●●●● ● ●● ● ●● ●● ●●● ●●● ●● ●● ●● ●● ●● ●●● ●● ●● ●●● ● ●●● ● ●● ● ● ●● ●●●●● ●●●●● ●● ●● ●●● ●● ●●●● ●● ● ●●●●● ●● ●● ● ●●●●● ●●● ● ●● ●● ● ●● ●
.bio11
−log10(p)
1 2 3 4 5 6 7 8
123456
Mixed model
P-value
Temperature
(C°)
# of plant accessions
Mixed Model Association to bioclimatic variables
Allele Frequency Differentiation - FST
Coop et al. 2009

7. Fang et al. 2014

8. Primary Results
• 12 associations to “cloned”
flowering time or cold-
tolerance genes
• 5 associations to loci relate
to cold tolerance
• 14 Fst outliers, primarily
involved flowering time and
cold tolerance
T A T V P Y STOP
A C T G C C A C G G T G C C C T A C T G A
T A T V P Y STOP
A C T G C C A C G G T A C C C T A C T G A
Reference
Alternative
…
…
SNP: 11_20784
Known cold tolerance gene: MLOC_15214.4
0 50 100 150
0
20
40
60
BIO17 Precipitation of Driest Quarter
X11_20784, Chro: 6H, 75.16cM, P−value: 2.563e−04
0
200
400
600
800
1000
1200
1400
●
●●●
●
●
●●
●
●
●
●● ●
●
●●
●●●●
●● ●●●●●●
●
●●●●
●
●
●
●
●
●●
●
●● ●
●
●
●●●
●
●
●●●
●
●●
●●
●
●
●●●●●●●●
●
●
●
●
●
●
● ●●●●●●●●●●●●
●
●●●
●
●●
●●●●
●●●●●●●●●●●●
●
●●
●
●
●
●
●
●
●
●●
●
●
●
●●
●
●●●
●
●
●
●●●●● ●
● ●
●
●
●
●
●
●
●●
●●
●
●
●●●●●●●
●
●
●
●
●●●●●●●
●
●●●●●●●●●
●
●
●●
●
●
●●
●
●●●●●●●●
●●
●●●
●
●●●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●●●
●
●
●
●
●
●●
●
●
●
●
●●
●
●
● ●
●
●
●●●●●●
●
●●●●●●
●
●
●
●
●
●● ●
●●
●
●
●
●●●●
●●
● ●●
●
●●
●●
●●●
●
●
●
●●●
●
●
●
●●
●●●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●●
● ●●●
●
●
●●
●
●
●
●
●
●
●
●●
●
●
●● ●●
●●●
●●
●●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●●
●
●●
●
●●
●
●
●●●●●
●
●
● ●●●
●
●
●
●
●
●●●● ●●
●
●●
●
●●●●
●
●●●
●●●●●
●
●●●●●●
●
● ●
●
●
●
●●●
●
●
●
●●
●
●
●●
●
●
●
●●
●●
●●
●
●
●
●
●
●
●●●●●●●●●
●
●
●●
●●
●
●
●●●●●●●●●●●●●
●
●
●●●●
●●●●●
●●●●●●●●●●●●●●●●●
●
●●
●
●
●●
●
● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●
●
●
●●●●●●
●
●●
●●
●
●
●
●●
●
●
●●
●
●
●
●
●
●
●●
●
●
●
●
●●●●●●●●●
●
●
●●●●●●●●●●●●●●●
●●●●●●●●●●●●●
●
●
●
●
●●●
●●
●●
●
●●●●●●●
●
●
●
●
●●
●
●
● ●
●
●●
●●
●
●
●●●
●●
●
●
●
●●
●●● ●
●
●●
●●●●
●●
●
●●●●
●●●●●●●●●
●
●
●
●●●●●●● ●●●●
●●●●
● ●
●●
●●●●●●
●●●
●
●●●●●
●●●
●
●
●●
●●
●
●
●
●
●
●
●●
●●
●●●●
BIO17 Precipitation of Driest Quarter
100150
tionofDriestQuarter
75.16cM,P−value:2.563e−04
0
200
400
600
800
1000
1200
1400
●
●●●●
●●●●●●●●
●●●●
●●●●
●●●●●●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●●
●
●
●●
●
●●●●●●●●
●●
●●●
●
●●●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●
●●●●●●●
●
●●●●●●
●
●●
●●●●
●
●
●●●
●
●
●●●●
●
●
●
●
●
●
●●
●●
●
●
●●
●
●
●
●
●
●
●●
●
●●
●
●●●
●
●●●
●●●
●●
●
●
●
●●●●●●●●●●●●●●●
●●●●●●●
●
●
●
●●●
●●
●
●
●
●●
●●●●
●
●●●●●●●●●
●●●●
●●
●●
●●●●●●
●●●
●
●●●●●●
●
●●
●●
●
●
●
●●
●●●●
100150
tionofDriestQuarter
tionunavailable,P−value:2.597e−04
0
200
400
600
800
1000
1200
1400
●
●●●●
●●●●●●●●
●●●●
●●●●
●●●●●●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●●
●
●
●●
●
●●●●●●●●
●●
●●●
●
●●●●●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●
●●●●●●
●
●●●●●●
●
●●
●●●●
●
●
●●●
●
●
●●●●
●
●
●
●
●
●
●●
●●
●
●
●●
●
●
●
●
●
●
●●
●
●●
●
●●●
●
●●●
●●●
●●
●
●
●
●●●●●●●●●●●●●●●
●●●●●●●
●
●
●
●●●
●●
●
●
●
●●
●●●●
●
●●●●●●●●●
●●●●
●●
●●
●●●●●●
●●●
●
●●●●●●
●
●●
●●
●
●
●
●●
●●●●
Bio17 Precipitation of Driest Quarter
Li et al. - in prep.

9. LD around association
“hits”
●
●
●
●
●●●●●●●●●●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●●●
●
●
●
●
●
●●●
●
●●●
●
●
●●
●
●
●
●●
●
●●●●●●●
●
●●
●
●●●●●
●
●●●●
●
●
●
●●●
●
●●
●●●● ●
●
●●
●
●
LD decay for SNPs around SNP: 11_10085
( chr2H : 758851026 bp )
Physical Distance (Kb)
LDestimate(r2
)
−100 −80 −60 −40 −20 0 20 40 60 80 100
0.00.20.40.60.81.0
●
●
●●
●
●●●●●●●●●●
●
●●
●●
●
●
●
●
●
●●●●●●●●
●
●●●
●
●
●●●
●
●
●
●
●
●
●
●
●●●●●●●●●
●
●
●
●●●●
●●●
●
●●●
●●●●●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●●●●●●
●●
●●●
●
●●●●●● ●●●●●●●●●● ●●●●●●●
●
●●●●●●●●●●●●●
●
●
●●●
●
●●●●●●
●
●
●●
●●●
●
●●●●
●
●●●
●
●●
●
●
●
●●●
●
●●●
●
●
●
●●
●
●
●
●●●
●●
●
●
●
●
●●
●
●
●●
●●
●
●●●●●●●●
●●●●●●●●●●●●●●●●●●
●●●●
●
●
●●
●
LD decay for SNPs around SNP: 11_20742
( chr3H : 17409756 bp )
Physical Distance (Kb)
LDestimate(r2
)
−100 −80 −60 −40 −20 0 20 40 60 80 100
0.00.20.40.60.81.0
Li et al. - in prep.

10. LD around association
“hits”
●
●●●●
●
●
●
●
●
●
●
●
●
●
●●● ●●●
●
●●●●
●
● ●
●
●
●
●●●●
●
●●
●
●
●
●●
●
●
●
●●
●
●
● ●
●●●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●
●
●
●●
●
●
●
●
●
●
●●●
LD decay for SNPs around SNP: 11_10143
( chr7H : 537951457 bp )
Physical Distance (Kb)
LDestimate(r2
)
−100 −80 −60 −40 −20 0 20 40 60 80 100
0.00.20.40.60.81.0
Li et al. - in prep.
●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
●
●●●
●
●●
●
●
●
●
●
●●
●
●
●
●●●
●
●
●
●●
●
LD decay for SNPs around SNP: 11_20784
( chr6H : 507569812 bp )
Physical Distance (Kb)
LDestimate(r2
)
−100 −80 −60 −40 −20 0 20 40 60 80 100
0.00.20.40.60.81.0

11. ●●●●
●
●●●●●●●●●●●●●●●●●●●●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●●
●●
●
●
●
●
●
●
●●
●
LD decay for SNPs around SNP: SCRI_RS_137464
( chr6H : 374867096 bp )
Physical Distance (Kb)
LDestimate(r2
)
−100 −80 −60 −40 −20 0 20 40 60 80 1000.00.20.40.60.81.0
LD decay for SNPs around SNP: SCRI_RS_137464
( chr6H : 374867096 bp )
Physical Distance (Kb)
LDestimate(r2
)
HvPRR1/HvTOC1 HORVU6Hr1G057640
11_10513
556
A/C
535
T/C
580
T/C
592
C/T
608
T/C
609
G/T
618
T/C
621
C/T
632
A/T
644
T/G
645
A/C
647
T/C
658
A/C
669
C/T
670
G/A
673
G/A
710
T/C
714
G/T
716
A/C
717
T/C
726
C/T
728
G/C
734
G/C
745
A/G
754
T/A
856
C/A
1003
G/A
1056
C/G
1169
G/A
1172
G/A
1180
T/C
1188
A/G
1336
C/T
2003
C/T
2011
C/T
2081
T/C
2117
G/T
2318
G/A
2332
C/T
2421
T/C
2579
G/A
2664
G/A
2724
C/T
2737
C/T
2739
T/G
2751
C/G
2767
C/T
2865
C/T
0 2995
Red: Nonsynonymous SNP
Blue: Significant associated SNP
LD with significant associated SNP (r2>0.4)
HvPRR1/HvTOC1
556
A/C
535
T/C
580
T/C
592
C/T
608
T/C
609
G/T
618
T/C
621
C/T
632
A/T
644
T/G
645
A/C
647
T/C
658
A/C
669
C/T
670
G/A
673
G/A
710
T/C
714
G/T
716
A/C
717
T/C
726
C/T
728
G/C
734
G/C
745
A/G
754
T/A
856
C/A
1003
G/A
1056
C/G
1169
G/A
1172
G/A
1180
T/C
1188
A/G
1336
C/T
2003
C/T
2011
C/T
2081
T/C
2117
G/T
2318
G/A
2332
C/T
2421
T/C
2579
G/A
2664
G/A
2724
C/T
2737
C/T
2739
T/G
2751
C/G
2767
C/T
2865
C/T
0 2995

12. HvPrr1/HvTOC1
SCRI_RS_137464 - chr6H:374867096

13. Summary
• Recover previously
characterized loci: Cbf3,
PhyC, Ppd-H1, Vrn1
• At least one locus directly
associated with freezing
tolerance
• Environmental association in
barley landraces will benefit
greatly from resequencing,
increased SNP density

14. Li Lei Chaochih Liu Corey Carter
Skylar Wyant Paul Hoffman
Fumi Katagiri

15. Code and Data Sharing
• https://github.com/MorrellLab/
Env_Assoc
• https://github.com/MorrellLab/
sequence_handling
• Sequences - NCBI Sequence
Read Archive