Inbreeding drives maize centromere evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 8, 2016, Pages E987-E996

  Schneider, Kevin L ^a   Xie, Zidian ^a   Wolfgruber, Thomas K ^a   Presting, Gernot G ^a  

^a UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CENTROMERE PROTEIN A; CENTROMERE PROTEIN C; HISTONE H3; REPETITIVE DNA; UNCLASSIFIED DRUG; RETROPOSON;

ARTICLE; CENTROMERE; DOMESTICATION; GENE LOCUS; GENETIC VARIABILITY; GERMPLASM; HAPLOTYPE; INBREEDING; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT GENE; PRIORITY JOURNAL; TANDEM REPEAT; TRANSPOSON; GENETIC EPIGENESIS; GENETICS; PLANT CHROMOSOME; RETROPOSON;

CENTROMERE; CHROMOSOMES, PLANT; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; INBREEDING; RETROELEMENTS; ZEA MAYS;

EID: 84959377846     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1522008113     Document Type: Article

References (45)

1. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: Stable inheritance with rapidly evolving DNA. Science 293(5532):1098-1102.
2. Henikoff S, Malik HS (2002) Centromeres: Selfish drivers. Nature 417(6886):227.
3. Matsuoka Y, et al. (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99(9):6080-6084.
4. Piperno DR, Flannery KV (2001) The earliest archaeological maize (Zea mays L.) from highland Mexico: New accelerator mass spectrometry dates and their implications. Proc Natl Acad Sci USA 98(4):2101-2103.
5. Doebley J, Stec A (1991) Genetic analysis of the morphological differences between maize and teosinte. Genetics 129(1):285-295.
6. Doebley J, Stec A (1993) Inheritance of the morphological differences between maize and teosinte: Comparison of results for two F2 populations. Genetics 134(2):559-570.
7. Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize-Teosinte F2 population: Implications for the origin of maize. Proc Natl Acad Sci USA 87(24):9888-9892.
8. Dorweiler J, Stec A, Kermicle J, Doebley J (1993) Teosinte glume architecture 1: A genetic locus controlling a key step in maize evolution. Science 262(5131):233-235.
9. Hufford MB, et al. (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44(7):808-811.
10. Hufford MB, et al. (2013) The genomic signature of crop-wild introgression in maize. PLoS Genet 9(5):e1003477.
11. Ross-Ibarra J, Tenaillon M, Gaut BS (2009) Historical divergence and gene flow in the genus Zea. Genetics 181(4):1399-1413.
12. Wolfgruber TK, et al. (2009) Maize centromere structure and evolution: Sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet 5(11):e1000743.
13. Gorinsek B, Gubensek F, Kordis D (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol Biol Evol 21(5):781-798.
14. Miller JT, Dong F, Jackson SA, Song J, Jiang J (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150(4):1615-1623.
15. Neumann P, et al. (2011) Plant centromeric retrotransposons: A structural and cytogenetic perspective. Mob DNA 2(1):4.
16. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16(6):721-728.
17. Sharma A, Presting GG (2014) Evolution of centromeric retrotransposons in grasses. Genome Biol Evol 6(6):1335-1352.
18. Sharma A, Schneider KL, Presting GG (2008) Sustained retrotransposition is mediated by nucleotide deletions and interelement recombinations. Proc Natl Acad Sci USA 105(40):15470-15474.
19. Albert PS, Gao Z, Danilova TV, Birchler JA (2010) Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 129(1-3):6-16.
20. Lamb JC, Birchler JA (2006) Retroelement genome painting: Cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 173(2): 1007-1021.
21. Bilinski P, et al. (2015) Diversity and evolution of centromere repeats in the maize genome. Chromosoma 124(1):57-65.
22. Lee HR, et al. (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci USA 102(33): 11793-11798.
23. McMullen MD, et al. (2009) Genetic properties of the maize nested association mapping population. Science 325(5941):737-740.
24. Nagaki K, et al. (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36(2):138-145.
25. Wang K, Wu Y, Zhang W, Dawe RK, Jiang J (2014) Maize centromeres expand and adopt a uniform size in the genetic background of oat. Genome Res 24(1):107-116.
26. Chia JM, et al. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44(7):803-807.
27. Tian F, Stevens NM, Buckler ES, 4th (2009) Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. Proc Natl Acad Sci USA 106(Suppl 1):9979-9986.
28. Lamb JC, Meyer JM, Birchler JA (2007) A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region. Chromosoma 116(3):237-247.
29. Miracle MP (1965) The introduction and spread of maize in Africa. J Afr Hist 6(1): 39-55.
30. Bukowski R, et al. (2015) Construction of the third-generation Zea mays haplotype map. bioRxiv doi: dx.doi.org/10.1101/026963.
31. Liu Y, et al. (2014) Genetic diversity and linkage disequilibrium estimation among the maize breeding germplasm for association mapping. Int J Agric Biol 16(5):851-861.
32. Troyer AF (1999) Background of U.S. hybrid corn. Crop Sci 39(3):601-626.
33. Buckler ES, et al. (2009) The genetic architecture of maize flowering time. Science 325(5941):714-718.
34. Shi J, et al. (2010) Widespread gene conversion in centromere cores. PLoS Biol 8(3): e1000327.
35. Wright SI, et al. (2005) The effects of artificial selection on the maize genome. Science 308(5726):1310-1314.
36. Larièpe A, et al. (2012) The genetic basis of heterosis: Multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics 190(2):795-811.
37. Graham GI, Wolff DW, Stuber CW (1997) Characterization of a yield quantitative trait locus on chromosome five of maize by fine mapping. Crop Sci 37(5):1601-1610.
38. Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J (2012) Teosinte as a model system for population and ecological genomics. Trends Genet 28(12):606-615.
39. Carneiro M, Ferrand N, NachmanMW (2009) Recombination and speciation: Loci near centromeres are more differentiated than loci near telomeres between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 181(2):593-606.
40. Stump AD, et al. (2005) Centromere-proximal differentiation and speciation in Anopheles gambiae. Proc Natl Acad Sci USA 102(44):15930-15935.
41. Guerrero AA, et al. (2010) Centromere-localized breaks indicate the generation of DNA damage by the mitotic spindle. Proc Natl Acad Sci USA 107(9):4159-4164.
42. Sharma A, Wolfgruber TK, Presting GG (2013) Tandem repeats derived from centromeric retrotransposons. BMC Genomics 14(1):142.
43. McVey M, Lee SE (2008) MMEJ repair of double-strand breaks (director's cut): Deleted sequences and alternative endings. Trends Genet 24(11):529-538.
44. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25.
45. Clark RM, Tavaré S, Doebley J (2005) Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol Biol Evol 22(11): 2304-2312.