High-resolution genetic mapping of maize pan-genome sequence anchors

Nature Communications

Volumn 6, Issue , 2015, Pages

  Lu, Fei ^a   Romay, Maria C ^a   Glaubitz, Jeffrey C ^a   Bradbury, Peter J ^b   Elshire, Robert J ^a   Wang, Tianyu ^c   Li, Yu ^c   Li, Yongxiang ^c   Semagn, Kassa ^d   Zhang, Xuecai ^e   Hernandez, Alvaro G ^f   Mikel, Mark A ^f   Soifer, Ilya ^b   Barad, Omer ^b   Buckler, Edward S ^a,b  

^a Department of Obstetrics Gynecology   (United States)

^b United States Department of Agriculture/Agricultural Research Service ^*  (Israel)

^c INSTITUTE OF PLANT PROTECTION   (China)

^d INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Kenya)

^e INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^f UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ANALYSIS; GENETIC VARIATION; MAIZE; MUTATION; PHENOTYPE;

ARTICLE; CROP; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME SIZE; INBRED STRAIN; MACHINE LEARNING; MAIZE; NONHUMAN; PHENOTYPIC VARIATION; PLANT BREEDING; PLANT GENOME; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENETICS;

ZEA MAYS;

CHROMOSOME MAPPING; GENOME, PLANT; MACHINE LEARNING; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

EID: 84928018963     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7914     Document Type: Article

References (42)

1. Adams, K. L. & Wendel, J. F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8, 135-141 (2005).
2. Bennetzen, J. L. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr. Opin. Genet. Dev. 15, 621-627 (2005).
3. Brenchley, R. et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705-710 (2012).
4. Jia, J. et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496, 91-95 (2013).
5. Paterson, A. H. et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556 (2009).
6. Schnable, P. S. et al. The B73 maize genome: Complexity, diversity, and dynamics. Science 326, 1112-1115 (2009).
7. Michael, T. P. & Jackson, S. The first 50 plant genomes. Plant Genome 6 (2013).
8. Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
9. Consortium, T.W.T.C.C.. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713-720 (2010).
10. Springer, N. M. et al. Maize Inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5, e1000734 (2009).
11. Swanson-Wagner, R. A. et al. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20, 1689-1699 (2010).
12. Ellis, J., Dodds, P. & Pryor, T. Structure, function and evolution of plant disease resistance genes. Curr. Opin. Plant Biol. 3, 278-284 (2000).
13. McHale, L. K. et al. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 159, 1295-1308 (2012).
14. Chia, J.-M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803-807 (2012).
15. Morgante, M., De Paoli, E. & Radovic, S. Transposable elements and the plant pan-genomes. Curr. Opin. Plant Biol. 10, 149-155 (2007).
16. Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2011).
17. Fu, H. & Dooner, H. K. Intraspecific violation of genetic colinearity and its implications in maize. Proc.. Natl Acad. Sci. USA 99, 9573-9578 (2002).
18. Brunner, S., Fengler, K., Morgante, M., Tingey, S. & Rafalski, A. Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17, 343-360 (2005).
19. Le Rouzic, A., Boutin, T. S. & Capy, P. Long-term evolution of transposable elements. Proc.. Natl Acad. Sci. USA 104, 19375-19380 (2007).
20. SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. The paleontology of intergene retrotransposons ofmaize. Nat. Genet. 20, 43-45 (1998).
21. Tenaillon, M. I., Hufford, M. B., Gaut, B. S. & Ross-Ibarra, J. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol. Evol. 3, 219-229 (2011).
22. Jiang, N., Bao, Z., Zhang, X., Eddy, S. R. &Wessler, S. R. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569-573 (2004).
23. Morgante, M. et al. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37, 997-1002 (2005).
24. Long, M., Betran, E., Thornton, K. & Wang, W. The origin of new genes: Glimpses from the young and old. Nat. Rev. Genet. 4, 865-875 (2003).
25. Freeling, M. Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453 (2009).
26. Hirsch, C. N. et al. Insights into the maize Pan-genome and Pan-transcriptome. Plant Cell 26, 121-135 (2014).
27. Glaubitz, J. C. et al. TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9, e90346 (2014).
28. Bradbury, P. J. et al. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635 (2007).
29. Romay, M. C. et al. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 14, R55 (2013).
30. Tian, F. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159-162 (2011).
31. Holmes, G., Hall, M. & Prank, E. in Advanced Topics in Artificial Intelligence Vol. 1747 (ed Foo, N.) 1-12 (Springer, 1999).
32. Hall, M. et al. The WEKA data mining software: An update. SIGKDD Explor. Newsl 11, 10-18 (2009).
33. Gore, M. A. et al. A first-generation haplotype map of maize. Science 326, 1115-1117 (2009).
34. Zarrei, M., MacDonald, J. R., Merico, D. & Scherer, S. W. A copy number variation map of the human genome. Nat. Rev. Genet. 16, 172-183 (2015).
35. Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853 (2007).
36. Schatz, M., Witkowski, J. & McCombie, W. R. Current challenges in De novo plant genome sequencing and assembly. Genome Biol. 13, 243 (2012).
37. Li, Y.-h. et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32, 1045-1052 (2014).
38. McMullen, M. D. et al. Genetic properties of the maize nested association mapping population. Science 325, 737-740 (2009).
39. Flint-Garcia, S. A. et al. Maize association population: A high-resolution platform for quantitative trait locus dissection. Plant J. 44, 1054-1064 (2005).
40. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Method 9, 357-359 (2012).
41. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
42. Zhang, Z. et al. Mixed linear model approach adapted for genome-wide association studies. Nat. Genet. 42, 355-360 (2010).