Insights into the effects of long-term artificial selection on seed size in maize

Genetics

Volumn 198, Issue 1, 2014, Pages 409-421

  Hirsch, Candice N ^a   Flint Garcia, Sherry A ^b,c   Beissinger, Timothy M ^d   Eichten, Steven R ^a   Deshpande, Shweta ^e   Barry, Kerrie ^e   McMullen, Michael D ^b,c   Holland, James B ^b,f   Buckler, Edward S ^b,g,g   Robin Buell, C ^h   de Leon, Natalia ^d   Kaeppler, Shawn M ^d  

^a UNIVERSITY OF MINNESOTA   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c UNIVERSITY OF MISSOURI   (United States)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

^e DOE JOINT GENOME INSTITUTE   (United States)

^f NORTH CAROLINA STATE UNIVERSITY   (United States)

^g Department of Obstetrics Gynecology   (United States)

^h MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL SELECTION; CHROMOSOME 1; CHROMOSOME 2; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 6; CHROMOSOME 7; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; EFFECTIVE POPULATION SIZE; ENDOSPERM; FEMALE; GENE CONTROL; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENE MAPPING; GENETIC VARIABILITY; GENOTYPE; GRAIN YIELD; HETEROZYGOSITY; INTROGRESSION; LINKAGE ANALYSIS; MAIZE; MALE; MICROSATELLITE MARKER; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; PLANT CHROMOSOME; PLANT GENETICS; QUANTITATIVE TRAIT LOCUS; SEED SIZE; SEED WEIGHT; SELECTIVE SWEEP; SINGLE NUCLEOTIDE POLYMORPHISM; ANATOMY AND HISTOLOGY; BIOLOGICAL MODEL; GENETIC SELECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; PLANT GENOME; PLANT SEED; QUANTITATIVE TRAIT;

DNA COPY NUMBER VARIATIONS; GENE FREQUENCY; GENOME, PLANT; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; SEEDS; SELECTION, GENETIC; ZEA MAYS;

EID: 84937511064     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.167155     Document Type: Article

References (72)

1. Abendroth, L. J., R. W. Elmore, M. J. Boyer, and S. K. Marlay, 2011 Corn growth and development. PMR 1009. Iowa State University Extension, Ames, Iowa
2. Akey, J. M., G. Zhang, K. Zhang, L. Jin, and M. D. Shriver, 2002 Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12: 1805–1814.
3. Argyros, R. D., D. E. Mathews, Y. H. Chiang, C. M. Palmer, D. M. Thibault et al., 2008 Type B response regulators of Arabidopsis play key roles in cytokinin signaling and plant development. Plant Cell 20: 2102–2116.
4. Austin, D. F., and M. Lee, 1998 Detection of quantitative trait loci for grain yield and yield components in maize across generations in stress and nonstress environments. Crop Sci. 38: 1296–1308.
5. Beissinger, T. M., C. N. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry et al., 2014 A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics 196: 829–840.
6. Bhave, M. R., S. Lawrence, C. Barton, and L. C. Hannah, 1990 Identification and molecular characterization of shrunken-2 cDNA clones of maize. Plant Cell 2: 581–588.
7. Buckler, E. S., J. B. Holland, P. J. Bradbury, C. B. Acharya, P. J. Brown et al., 2009 The genetic architecture of maize flowering time. Science 325: 714–718.
8. Cheng, W. H., E. W. Taliercio, and P. S. Chourey, 1996 The Miniature1 seed locus of maize encodes a cell wall invertase required for normal development of endosperm and maternal cells in the pedicel. Plant Cell 8: 971–983.
9. Chia, J. M., C. Song, P. J. Bradbury, D. Costich, N. de Leon et al., 2012 Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44: 803–807.
10. Cook, D. E., T. G. Lee, X. Guo, S. Melito, K. Wang et al., 2012a Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338: 1206–1209.
11. Cook, J. P., M. D. McMullen, J. B. Holland, F. Tian, P. Bradbury et al., 2012b Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol. 158: 824–834.
12. Crow, J. F., and M. Kimura, 1970 An Introduction to Population Genetic Theory. Harper & Row, New York.
13. Ducrocq, S., D. Madur, J. B. Veyrieras, L. Camus-Kulandaivelu, M. Kloiber-Maitz et al., 2008 Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information. Genetics 178: 2433–2437.
14. Eichten, S. R., M. W. Vaughn, P. J. Hermanson, and N. M. Springer, 2013 Variation in DNA methylation patterns is more common among maize inbreds than among tissues. Plant Gen. 6: 1–10.
15. Flint-Garcia, S. A., A. C. Thuillet, J. Yu, G. Pressoir, S. M. Romero et al., 2005 Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J. 44: 1054–1064.
16. Fu, J., Y. Cheng, J. Linghu, X. Yang, L. Kang et al., 2013 RNA sequencing reveals the complex regulatory network in the maize kernel. Nat. Commun. 4: 2832.
17. Gilmour, A., B. Gogel, B. Cullis, and R. Thompson, 2006 ASReml User Guide Release 2.0. VSN Intl., Hemel, Hempstead, UK.
18. Gore, M. A., J. M. Chia, R. J. Elshire, Q. Sun, E. S. Ersoz et al., 2009 A first-generation haplotype map of maize. Science 326: 1115–1117.
19. Hansey, C. N., B. Vaillancourt, R. S. Sekhon, N. de Leon, S. M. Kaeppler et al., 2012 Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS ONE 7: e33071.
20. Hermisson, J., and P. S. Pennings, 2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335–2352.
21. Hirsch, C. N., J. M. Foerster, J. M. Johnson, R. S. Sekhon, G. Muttoni et al., 2014 Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26: 121–135.
22. Huber, W., A. von Heydebreck, H. Sultmann, A. Poustka, and M. Vingron, 2002 Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18(Suppl. 1): S96–S104.
23. Hung, H. Y., C. Browne, K. Guill, N. Coles, M. Eller et al., 2012 The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity 108: 490–499.
24. Hunter, C. T., M. Suzuki, J. Saunders, S. Wu, A. Tasi et al., 2014 Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants. Front. Plant Sci. 4: 545.
25. Johansson, A. M., M. E. Pettersson, P. B. Siegel, and O. Carlborg, 2010 Genome-wide effects of long-term divergent selection. PLoS Genet. 6: e1001188.
26. Jones, E., W.-C. Chu, M. Ayele, J. Ho, E. Bruggeman et al., 2009 Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm. Mol. Breed. 24: 165–176.
27. Kesavan, M., J. T. Song, and H. S. Seo, 2013 Seed size: a priority trait in cereal crops. Physiol. Plant. 147: 113–120.
28. Khaled, A. S., V. Vernoud, G. C. Ingram, P. Perez, X. Sarda et al., 2005 Engrailed-ZmOCL1 fusions cause a transient reduction of kernel size in maize. Plant Mol. Biol. 58: 123–139.
29. Kiesselbach, T. A., 1999 The Structure and Reproduction of Corn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
30. Kowles, R. V., F. Srienc, and R. L. Phillips, 1990 Endoreduplication of nuclear DNA in the developing maize endosperm. Dev. Genet. 11: 125–132.
31. Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne et al., 2009 Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639–1645.
32. Lai, J., R. Li, X. Xu, W. Jin, M. Xu et al., 2010 Genome-wide patterns of genetic variation among elite maize inbred lines. Nat. Genet. 42: 1027–1030.
33. Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
34. Lee, M., N. Sharopova, W. D. Beavis, D. Grant, M. Katt et al., 2002 Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol. Biol. 48: 453–461.
35. Lewontin, R. C., 1962 Interdeme selection controlling a polymorphism in the house mouse. Am. Nat. 96: 65–78.
36. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079.
37. Liu, K., M. Goodman, S. Muse, J. S. Smith, E. Buckler et al., 2003 Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117–2128.
38. Liu, S., C. T. Yeh, T. Ji, K. Ying, H. Wu et al., 2009 Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet. 5: e1000733.
39. Maron, L. G., C. T. Guimaraes, M. Kirst, P. S. Albert, J. A. Birchler et al., 2013 Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc. Natl. Acad. Sci. USA 110: 5241–5246.
40. Maynard Smith, J., and J. Haigh, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23–35.
41. McCarty, D. R., A. M. Settles, M. Suzuki, B. C. Tan, S. Latshaw et al., 2005 Steady-state transposon mutagenesis in inbred maize. Plant J. 44: 52–61.
42. McMullen, M. D., S. Kresovich, H. S. Villeda, P. Bradbury, H. Li et al., 2009 Genetic properties of the maize nested association mapping population. Science 325: 737–740.
43. Neuffer, M. G., E. H. Coe, and S. R. Wessler, 1997 Mutants of Maize. Cold Spring Harbor Laboratory Press, Plainview, NY.
44. Odhiambo, M. O., and W. A. Compton, 1987 Twenty cycles of divergent mass selection for seed size in Corn1. Crop Sci. 27: 1113–1116.
45. Oleksyk, T. K., K. Zhao, F. M. De La Vega, D. A. Gilbert, S. J. O’Brien et al., 2008 Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS One 3: e1712.
46. Pan, D., S. Zhang, J. Jiang, L. Jiang, Q. Zhang et al., 2013 Genomewide detection of selective signature in Chinese Holstein. PLoS ONE 8: e60440.
47. Parts, L., F. A. Cubillos, J. Warringer, K. Jain, F. Salinas et al., 2011 Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res. 21: 1131–1138.
48. Paulis, J. W., and J. S. Wall, 1977 Comparison of the protein compositions of selected corns and their wild relatives, teosinte and Tripsacum. J. Agric. Food Chem. 25: 265–270.
49. Peng, B., Y. Li, Y. Wang, C. Liu, Z. Liu et al., 2011 QTL analysis for yield components and kernel-related traits in maize across multi-environments. Theor. Appl. Genet. 122: 1305–1320.
50. Phillips, A. R., and M. M. Evans, 2011 Analysis of stunter1, a maize mutant with reduced gametophyte size and maternal effects on seed development. Genetics 187: 1085–1097.
51. R Development Core Team, 2014 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
52. Russell, W. K., 2006 Registration of KLS_30 and KSS_30 populations of maize. Crop Sci. 46: 1405–1406.
53. Sabelli, P., and B. Larkins, 2009 The contribution of cell cycle regulation to endosperm development. Sex. Plant Reprod. 22: 207–219.
54. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832–837.
55. Saghai-Maroof, M. A., K. M. Soliman, R. A. Jorgensen, and R. W. Allard, 1984 Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81: 8014–8018.
56. Salvi, S., G. Sponza, M. Morgante, D. Tomes, X. Niu et al., 2007 Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl. Acad. Sci. USA 104: 11376–11381.
57. Schmidt, R. J., F. A. Burr, M. J. Aukerman, and B. Burr, 1990 Maize regulatory gene opaque-2 encodes a protein with a “leucine-zipper” motif that binds to zein DNA. Proc. Natl. Acad. Sci. USA 87: 46–50.
58. Schmidt, R. J., M. Ketudat, M. J. Aukerman, and G. Hoschek, 1992 Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. Plant Cell 4: 689–700.
59. Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei et al., 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–1115.
60. Sekhon, R. S., H. Lin, K. L. Childs, C. N. Hansey, C. R. Buell et al., 2011 Genome-wide atlas of transcription during maize development. Plant J. 66: 553–563.
61. Sekhon, R. S., C. N. Hirsch, K. L. Childs, M. W. Breitzman, P. Kell et al., 2014 Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination. Plant Physiol. 165: 658–669.
62. Springer, N. M., K. Ying, Y. Fu, T. Ji, C. T. Yeh et al., 2009 Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5: e1000734.
63. Swanson-Wagner, R. A., S. R. Eichten, S. Kumari, P. Tiffin, J. C. Stein et al., 2010 Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20: 1689–1699.
64. Tian, F., P. J. Bradbury, P. J. Brown, H. Hung, Q. Sun et al., 2011 Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43: 159–162.
65. Turner, T. L., A. D. Stewart, A. T. Fields, W. R. Rice, and A. M. Tarone, 2011 Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7: e1001336.
66. Venkatraman, E. S., and A. B. Olshen, 2007 A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657–663.
67. Waples, R. S., and C. Do, 2008 ldne: a program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8: 753–756.
68. Weir, B. S., and C. C. Cockerham, 1984 Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
69. Wisser, R. J., S. C. Murray, J. M. Kolkman, H. Ceballos, and R. J. Nelson, 2008 Selection mapping of loci for quantitative disease resistance in a diverse maize population. Genetics 180: 583–599.
70. Wright, S., 1951 The genetical structure of populations. Ann. Eugen. 15: 323–354.
71. Yang, Z., E. J. van Oosterom, D. R. Jordan, A. Doherty, and G. L. Hammer, 2010 Genetic variation in potential kernel size affects kernel growth and yield of sorghum Crop Sci. 50: 685–695.
72. Yu, J., J. B. Holland, M. D. McMullen, and E. S. Buckler, 2008 Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539–551.