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Plant & Animal Genome 2019 - The fate of deleterious variants

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The fate of deleterious variants in a barley genomic prediction population

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Plant & Animal Genome 2019 - The fate of deleterious variants

  1. 1. The fate of deleterious variants in a barley genomic prediction population What happens when heterosis is not an option? barleyworld.org
  2. 2. The fate of deleterious variants • How common are dSNPs in elite barley lines and what is their fate through rounds of selection? • Are dSNPs uniformly distributed in the genome or concentrated in regions of low recombination? • Does any class of SNPs explain a larger proportion of phenotypic variance? Questions
  3. 3. dSNPs in genomic prediction experiment 21 exomes 01 genome 5,215 genotyped 676 phenotyped 7 UMN 8 ND 6 BA F3 98 Selected 300 Random F3 105 Selected 101 Random F3 48 Selected 49 Random 21 Parents (Cycle 0) 1,872 F3 Progeny (Cycle 1) 1,904 F3 Progeny (Cycle 2) 1,439 F3 Progeny (Cycle 3) 78 Crosses/Families Yield Trials Yield Trials Yield Trials 33 Families, 20 Parents 33 Families, 41 Parents 30 Families, 40 Parents 47 Families, 58 Parents 16 Families, 30 Parents 32 Families, 55 Parents 80 Crosses/Families 60 Crosses/Families Kono et al. 2018 - bioRxiv
  4. 4. What is a deleterious variant (dSNP)? • A variant that reduces fitness • Typical inferred based on sequence conservation • In humans, validated by association with Mendelian disorders Species dSNPs/genome Method Publication human 800 Conservation Chun & Fay 09 human 400 Disease Causing Xeu et al. 12 barley 1000 Conservation Kono et al. 16 soybean 800 Conservation Kono et al. 16
  5. 5. How are deleterious variants identified? A•••••••T••A••T ... Banana ••T••••A•••A••A ... Switchgrass ••••••••••••••C ... Purple False Brome ••T•••••••••••A ... Foxtail Millet •••••••••••A••A ... Maize •••••C•••••T••C ... Wild Red Einkorn ••••••••••••••T ... Cutgrass •••••C••••••••C ... Goatgrass ••••••••••••••T ... Asian Rice •••••••••••A••A ... Milo Barley GTCCCTTTCCCGCTM ... Consensus •••••••C••••••C ... N D DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD H Y CCCCYY--YYYCCCCCCCCCCCCCCCCCCCCCCCCCCC C F FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF R T TTTMTTTTTTTTTTTTTTTDTTTTTTTTTTTTTTTTTT A T VVAAVVVAVAAAVSVVVTVVVVIVAAAALATTTVVVVV A V VVVVVIVVVIIIIIVVVV-VVV-VVVVVVVVVVVVVVV D E EDDEEEEEEEE-EEEEEEEEEEEEEEEVVEEEEEEEEE Q L LLLLLLL-LMLLLLLLLLLLLL-LLLLLLLLLLLLLLL D N NDDDNNNNNDDDDNDNNNNDDDDDDDDDDNNNNNNDNN V I VVLVVVMMVVVVVVVSVIIIIVMVVVVVIVVVVVIVVV A V AAAAAAAAAAAAAAAAAA-AVT-TA-SAAATTTTTAAT D E DDDDDDDN-DDDDDDDDDNEDD-EEEEEEEDDDDDDDD A P EKSKEEEKEENAENEEEEDAAPAAAEKKEEGGEEEEEE E D RNKKKRK-KKKKKNSSKDPESSPS-KS-SN---KKHHN E D EEEEEEQDDEEEEEEEDEEEDEEDDDDEEEEEEEEEED E A TATTMTTSTTTTATSSCA-SPPMASREECGSSSMTAAT Deleterious Tolerated https://github.com/MorrellLAB/BAD_Mutations Predict! All Variants SNPs Coding SNPs Nonsynonymous SNPs Length Polymorphisms Noncoding SNPs Synonymous SNPs Kono et al. 2016 - MBE
  6. 6. Distribution of fitness effects Neher 2013 - Ann. Rev. Ecol. Syst.
  7. 7. Do annotation tools work? • Chun & Fay 2009 likelihood ratio test (LRT) approach controls for local variation in divergence rate • LRT outperforms other approaches, all better with deeper alignments • LRT implemented in BAD_Mutations Python program Kono et al. 2018 - G3
  8. 8. Genomic prediction retrospective • Selection on unfavorably correlated quantitative traits • Realistic scenario for understanding role of dSNPs
  9. 9. Site frequency spectrum of founders • dSNPs are mostly rare • SFS impacted by family structure of breeding programs Kono et al. 2018 - bioRxiv [0,0.1] (0.2,0.3] (0.4,0.5] (0.6,0.7] (0.8,0.9] Derived Allele Frequency Proportion 0.00.10.20.30.40.50.6 [0,0.1] (0.2,0.3] (0.4,0.5] (0.6,0.7] (0.8,0.9] Noncoding Synonymous Nonsynonymous Deleterious
  10. 10. Distribution of variants • Blue - exome capture density • Green - recombination rate cM/Mb • blue lines - exome capture SNPs • purple triangles - genotyped SNPs Kono et al. 2019 - in review chr1H chr2H chr3H chr4H chr5H chr6H chr7H 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 0 5 10 0 5 10 0 5 10 0 5 10 0 5 10 0 5 10 0 5 10 Physical Position (Mb)
  11. 11. Imputation of genotypes in progeny • 497,754 SNPs in parents • 3,885 dSNPs • 384 SNPs genotyped in progeny • AlphaPeel can us complex pedigree in imputing genotypic state & phase • Imputation subject to multiple rounds of Mendel testing - Plink 1.9 Whalen et al. 2018 - Genet Sel Evol www.yonka.com/fr
  12. 12. Genomic prediction • Grain yield and fungal disease resistance 5 year- locations • Unfavorably correlated quantitative traits • Lines selected based on GEBV - have improved disease resistance, stable yield Kono et al. 2018 - bioRxiv; Tiede & Smith 2018 Mol Breeding
  13. 13. Proportion of phenotypic variance explained • Linear mixed model in GEMMA software • “SNP heritability” for SNPs genotyped and imputed from parents to progeny • Yield heritability 0.198 genotyped, 0.250 imputed SNPs • Association finds regions associated w/ better disease resistance, poorer yield! • Linkage in population precludes estimation of variance explained by SNP classes Fang et al. 2013 - G3
  14. 14. dSNPs & phenotypes • Number of homozygous dSNPs reduced over cycles • Other classes of variants also become more homozygous Kono et al. 2019 - bioRxiv 150 200 250 300 40005000600070008000 Yield Homozygous Derived Deleterious SNPs YieldBLUE(kg/ha) ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● C0 r=−0.01 C1 r=−0.04 C2 r=−0.02 C3 r= −0.11 150 200 250 300 05101520253035 DON Conc. Homozygous Derived Deleterious SNPs DONBLUE(ppm) ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● C0 r=−0.3 C1 r=0 C2 r=−0.06 C3 r= −0.13 150 200 250 300 5060708090100110 Height Homozygous Derived Deleterious SNPs HeightBLUE(cm) ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● C0 r=0.13 C1 r=0.15 C2 r=0.04 C3 r= 0.2
  15. 15. Fate of dSNPs ● ● ● ● ● ● ● ● ● ● DAF in Parents ProportionofVariantsFixedforAncestralAllele ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.00.10.20.30.40.5 [0,0.1] (0.2,0.3] (0.4,0.5] (0.6,0.7] (0.8,0.9] ● ● ● ● Noncoding Synonymous Nonsynonymous Deleterious Cycle NumberofHomozygousDeleteriousSNPs ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ●●●●●●●●●●●●●●●●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 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● ●●● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● Random Selected Parents C1 C2 C3 150200250300 Kono et al. 2019 - bioRxiv
  16. 16. SFS all SNPs • dSNPs are rare and get rarer over breeding cycles • Other classes more frequently approaching fixation [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Cycle 1 Derived Allele Frequency Proportion 0.00.10.20.30.40.50.60.7 [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Noncoding Synonymous Nonsynonymous Deleterious [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Cycle 2 Derived Allele Frequency Proportion 0.00.10.20.30.40.50.60.7 [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Noncoding Synonymous Nonsynonymous Deleterious [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Cycle 3 Derived Allele Frequency Proportion 0.00.10.20.30.40.50.60.7 [0,0.05] (0.1,0.15] (0.2,0.25] (0.3,0.35] (0.4,0.45] (0.5,0.55] (0.6,0.65] (0.7,0.75] (0.8,0.85] (0.9,0.95] Noncoding Synonymous Nonsynonymous Deleterious 1872 progeny 1,904 progeny Kono et al. 2019 - bioRxiv 1,439 progeny

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