Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Nature Genetics

Volumn 49, Issue 6, 2017, Pages 959-963

  Ramu, Punna ^a   Esuma, Williams ^b   Kawuki, Robert ^b   Rabbi, Ismail Y ^c   Egesi, Chiedozie ^c,d,e   Bredeson, Jessen V ^f   Bart, Rebecca S ^g   Verma, Janu ^a   Buckler, Edward S ^a,h   Lu, Fei ^a  

^a Department of Obstetrics Gynecology   (United States)

^b National Crops Resources Research Institute NaCRRI   (Uganda)

^c INTERNATIONAL INSTITUTE OF TROPICAL AGRICULTURE   (Nigeria)

^d National Root Crops Research Institute Umudike   (Nigeria)

^e Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^h ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ARTICLE; CASSAVA; DOMESTICATION; GENE DELETION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENETIC VARIATION; GENOTYPE; HAPLOTYPE MAP; INDEL MUTATION; MOLECULAR CLONING; NONHUMAN; PLANT BREEDING; PLANT GENETICS; PLANT GENOME; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME SEQUENCING; GENETICS; HAPLOTYPE; MANIHOT; MUTATION;

GENETIC VARIATION; GENOME, PLANT; HAPLOTYPES; MANIHOT; MUTATION; PLANT BREEDING; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 85017648395     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3845     Document Type: Article

References (49)

1. Raven, P., Fauquet, C., Swaminathan, M.S., Borlaug, N. & Samper, C. Where next for genome sequencing? Science 311, 468-468 (2006).
2. Olsen, K.M. & Schaal, B.A. Evidence on the origin of cassava: phylogeography of Manihot esculenta. Proc. Natl. Acad. Sci. USA 96, 5586-5591 (1999).
3. Allem, A.C. The closest wild relatives of cassava (Manihot esculenta Crantz). Euphytica 107, 123-133 (1999).
4. Wang, W. et al. Cassava genome from a wild ancestor to cultivated varieties. Nat. Commun. 5, 5110 (2014).
5. McDonald, M.J., Rice, D.P. & Desai, M.M. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature 531, 233-236 (2016).
6. McKey, D., Elias, M., Pujol, B. & Duputie, A. The evolutionary ecology of clonally propagated domesticated plants. New Phytol. 186, 318-332 (2010).
7. Charlesworth, D. & Willis, J.H. The genetics of inbreeding depression. Nat. Rev. Genet. 10, 783-796 (2009).
8. Rojas, M.C. et al. Analysis of inbreeding depression in eight s1 cassava families. Crop Sci. 49, 543-548 (2009).
9. Nuwamanya, E., Herselman, L. & Ferguson, M. Segregation of selected agronomic traits in six S1 cassava families. J. Plant Breed. Crop Sci. 3, 154-160 (2011).
10. Bredeson, J.V. et al. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat. Biotechnol. 34, 562-570 (2016).
11. Prochnik, S. et al. The cassava genome: current progress, future directions. Trop. Plant Biol. 5, 88-94 (2012).
12. Browning, B.L. & Browning, S.R. Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 98, 116-126 (2016).
13. Chia, J.-M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803-807 (2012).
14. Tennessen, J.A. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69 (2012).
15. Fu, W. et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493, 216-220 (2013).
16. Davydov, E.V. et al. Identifying a high fraction of the human genome to be under selective constraint using GERP. PLoS Comput. Biol. 6, e1001025 (2010).
17. Rodgers-Melnick, E. et al. Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc. Natl. Acad. Sci. USA 112, 3823-3828 (2015).
18. Mackay, T.F.C. et al. The Drosophila melanogaster Genetic Reference Panel. Nature 482, 173-178 (2012).
19. Kumar, P., Henikoff, S. & Ng, P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073-1081 (2009).
20. Mezmouk, S. & Ross-Ibarra, J. The pattern and distribution of deleterious mutations in maize. G3 (Bethesda) 4, 163-171 (2014).
21. Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170 (2010).
22. Keller, P.J. & Knop, M. Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots. PLoS Genet. 5, e1000533 (2009).
23. Hussin, J.G. et al. Recombination affects accumulation of damaging and disease-associated mutations in human populations. Nat. Genet. 47, 400-404 (2015).
24. Haddrill, P.R., Halligan, D.L., Tomaras, D. & Charlesworth, B. Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biol. 8, R18 (2007).
25. Jorgensen, K. et al. Cassava plants with a depleted cyanogenic glucoside content in leaves and tubers: distribution of cyanogenic glucosides, their site of synthesis and transport, and blockage of the biosynthesis by RNA interference technology. Plant Physiol. 139, 363-374 (2005).
26. Conn, E.E. Cyanogenic compounds. Annu. Rev. Plant Physiol. 31, 433-451 (1980).
27. Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402 (2010).
28. Ros, R., Munoz-Bertomeu, J. & Krueger, S. Serine in plants: biosynthesis, metabolism, and functions. Trends Plant Sci. 19, 564-569 (2014).
29. Benstein, R.M. et al. Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis. Plant Cell 25, 5011-5029 (2013).
30. Marsden, C.D. et al. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proc. Natl. Acad. Sci. USA 113, 152-157 (2016).
31. Agrawal, A.F. & Whitlock, M.C. Inferences about the distribution of dominance drawn from yeast gene knockout data. Genetics 187, 553-566 (2011).
32. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997/ (2013).
33. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
34. Hohenlohe, P.A. et al. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6, e1000862 (2010).
35. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
36. Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635 (2007).
37. Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290 (2004).
38. International Cassava Genetic Map Consortium (ICGMC). High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations. G3 (Bethesda) 5, 133-144 (2015).
39. Rahman, A.Y.A. et al. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics 14, 75 (2013).
40. Sato, S. et al. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res. 18, 65-76 (2011).
41. Chan, A.P. et al. Draft genome sequence of the oilseed species Ricinus communis. Nat. Biotechnol. 28, 951-956 (2010).
42. Dai, X. et al. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res. 24, 1274-1277 (2014).
43. Wang, Z. et al. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J. 72, 461-473 (2012).
44. Tuskan, G.A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604 (2006).
45. Harris, R.S. Improved pairwise alignment of genomic DNA. PhD thesis, Pennsylvania State University (2007).
46. Beissinger, T.M., Rosa, G.J., Kaeppler, S.M., Gianola, D. & de Leon, N. Defining window-boundaries for genomic analyses using smoothing spline techniques. Genet. Sel. Evol. 47, 30 (2015).
47. Du, Z., Zhou, X., Ling, Y., Zhang, Z. & Su, Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-W70 (2010).
48. Supek, F., Bosnjak, M., Skunca, N. & Smuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800 (2011).
49. Henn, B.M. et al. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc. Natl. Acad. Sci. USA 113, E440-E449 (2016).