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Barley environmental association - Plant & Animal Genome 2018

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

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Barley environmental association - Plant & Animal Genome 2018

  1. 1. Barley Landrace Environmental Association Plant & Animal Genome 2018
  2. 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. 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. 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. 5. Barley Adaptation to Eurasia Pinhasi et al. 2005
  6. 6. ATGCAGTT TTGCAGTT CTGCAGTT ATGCGGTT TTGCGGTT CTGCGGTT Genetic varaints Phenotypes Genetic positions of Chromosomes (cM) + ● ● ● ● ● ● ●● ●● ●● ● ●●●● ● ●● ●● ●●● ●● ●●● ● ● ●● ●● ●● ● ●●●● ●●● ● ●● ● ●●● ● ●● ●●● ●● ● ●● ● ●●●●●●● ● ●● ●● ●●● ●●●● ●● ●●● ●● ●● ●● ●● ●●● ●● ●● ●● ●●● ● ● ●●● ● ● ●●● ●● ●● ●● ● ● ●●● ● ●●●●● ●● ●● ● ●● ●●● ●●●● ●● ●●● ●● ●● ●●● ●●● ● ●● ●●● ●●● ● ●●● ●● ●● ● ●● ●●●● ●● ●●● ●● ● ●●● ● ●● ●● ● ●●● ● ● ● ●●●●● ●●● ●● ●● ●●● ● ●● ●● ●●●● ●●● ●●● ●●● ●● ●●● ● ●● ●● ●● ●●● ● ●● ●● ● ●● ●● ● ●● ● ●●● ●● ●●● ●● ● ●● ●●● ● ●●● ●● ●● ●● ●●●● ●● ●●● ● ●● ● ●● ●● ●● ● ●●● ●●● ●●●● ●●● ●● ●●● ●●●● ●●●● ●●● ●● ●●●● ● ● ●● ● ●●● ●● ● ●● ●●● ● ● ●● ●●● ●● ●●●●●● ●● ● ●●● ● ●●● ●● ●● ●● ●●●● ● ● ●● ●● ●● ●● ●●● ●● ●● ●● ● ● ●● ● ● ●●● ●●● ● ●● ● ●● ● ●●●●● ● ● ● ●● ●●● ●● ● ● ● ●● ● ●● ●● ● ●● ●● ●● ●● ● ●● ●● ●● ●●● ●● ●● ●●●● ● ●● ●●● ●●● ● ●● ● ●●●● ●● ●● ●● ●●●● ●● ●●● ●● ●●● ●●●●●● ●● ●● ●● ● ●● ●●● ● ●●● ●● ● ● ●●● ● ● ●● ●●●● ●● ●● ● ●●● ●● ● ●●● ● ● ●● ● ● ●● ● 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  7. 7. Fang et al. 2014
  8. 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. 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. 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. 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. 12. HvPrr1/HvTOC1 SCRI_RS_137464 - chr6H:374867096
  13. 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. 14. Li Lei Chaochih Liu Corey Carter Skylar Wyant Paul Hoffman Fumi Katagiri
  15. 15. Code and Data Sharing • https://github.com/MorrellLab/ Env_Assoc • https://github.com/MorrellLab/ sequence_handling • Sequences - NCBI Sequence Read Archive

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