An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Liu, Hongjun ^a   Niu, Yongchao ^b   Gonzalez Portilla, Pedro J ^c   Zhou, Huangkai ^b   Wang, Liya ^d   Zuo, Tao ^c   Qin, Cheng ^a   Tai, Shuaishuai ^b   Jansen, Constantin ^c   Shen, Yaou ^a   Lin, Haijian ^a   Lee, Michael ^c   Ware, Doreen ^d   Zhang, Zhiming ^a   Lübberstedt, Thomas ^c   Pan, Guangtang ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b BGI SHENZHEN   (China)

^c IOWA STATE UNIVERSITY   (United States)

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

Author keywords

IBM Syn10, Resequencing; Inadvertent selection; IPlant Discovery Environment; Quantitative trait locus mapping

Indexed keywords

BREEDING; DATA BASE; FLOWER DEVELOPMENT; GENETIC LINKAGE; GENETIC MARKER; MAIZE; PLANT HEIGHT; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; SEGREGATION DISTORTION; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENETICS; PHYSIOLOGY; PLANT GENOME; PROCEDURES;

CHROMOSOME MAPPING; GENETIC LINKAGE; GENOME, PLANT; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

EID: 84953392490     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2242-5     Document Type: Article

References (68)

1. Tester M, Langridge P. Breeding technologies to increase crop production in a changing world. Science. 2010;327(5967):818-22.
2. Teng F, Zhai L, Liu R, Bai W, Wang L, Huo D, Tao Y, Zheng Y, Zhang Z: ZmGA3ox2, a candidate gene for a major QTL, qPH3.1, for plant height in maize. The Plant journal: for cell and molecular biology 2012.
3. Lu Y, Shah T, Hao Z, Taba S, Zhang S, Gao S, et al. Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize. PLoS One. 2011;6(9):e24861.
4. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, et al. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci U S A. 2010;107(45):19579-84.
5. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, et al. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet. 2008;40(6):761-7.
6. Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet. 2008;40(11):1370-4.
7. Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, et al. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet. 2008;40(11):1360-4.
8. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet. 2007;39(5):623-30.
9. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A. 2007;104(27):11376-81.
10. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, et al. Cytokinin Oxidase Regulates Rice Grain Production. Science. 2005;309(5735):741-5.
11. Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S, van Beuningen L, et al. Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol Biol. 2002;48(5-6):601-13.
12. Penning BW, Sykes RW, Babcock NC, Dugard CK, Held MA, Klimek JF, et al. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. Plant Physiol. 2014;165(4):1475-87.
13. Burton AL, Johnson J, Foerster J, Hanlon MT, Kaeppler SM, Lynch JP, Brown KM: QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.). TAG Theoretical and applied genetics Theoretische und angewandte Genetik 2014.
14. Xin M, Yang R, Li G, Chen H, Laurie J, Ma C, et al. Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. Plant Cell. 2013;25(9):3212-27.
15. Morrell PL, Buckler ES, Ross-Ibarra J. Crop genomics: advances and applications. Nat Rev Genet. 2011;13(2):85-96.
16. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326(5956):1112-5.
17. Zhang N, Gibon Y, Gur A, Chen C, Lepak N, Hohne M, et al. Fine quantitative trait loci mapping of carbon and nitrogen metabolism enzyme activities and seedling biomass in the maize IBM mapping population. Plant Physiol. 2010;154(4):1753-65.
18. Lung'aho MG, Mwaniki AM, Szalma SJ, Hart JJ, Rutzke MA, Kochian LV, et al. Genetic and physiological analysis of iron biofortification in maize kernels. PLoS One. 2011;6(6):e20429.
19. Holloway B, Luck S, Beatty M, Rafalski JA, Li B. Genome-wide expression quantitative trait loci (eQTL) analysis in maize. BMC Genomics. 2011;12:336.
20. Li L, Petsch K, Shimizu R, Liu S, Xu WW, Ying K, et al. Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genet. 2013;9(1):e1003202.
21. Alvarez Prado S, López CG, Senior ML, Borrás L. The Genetic Architecture of Maize (Zea mays L.) Kernel Weight Determination. G3. 2014;4(9):1611-21.
22. Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, et al. Access to the maize genome: an integrated physical and genetic map. Plant Physiol. 2002;128(1):9-12.
23. Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, et al. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet. 2009;5(11):e1000733.
24. Balint-Kurti PJ, Wisser R, Zwonitzer JC. Use of an Advanced Intercross Line Population for Precise Mapping of Quantitative Trait Loci for Gray Leaf Spot Resistance in Maize All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Crop Sci. 2008;48(5):1696-704.
25. Hussain T, Tausend P, Graham G, Ho J. ing Population of Maize All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. J Plant Reg. 2007;1(1):81-1.
26. Zdunic Z, Grljusic S, Ledencan T, Duvnjak T, Simic D. Quantitative trait loci mapping of metal concentrations in leaves of the maize IBM population. Hereditas. 2014;151(2-3):55-60.
27. Benke A, Urbany C, Marsian J, Shi R, Wiren N, Stich B. The genetic basis of natural variation for iron homeostasis in the maize IBM population. BMC Plant Biol. 2014;14:12.
28. Ordas B, Malvar RA, Santiago R, Sandoya G, Romay MC, Butron A. Mapping of QTL for resistance to the Mediterranean corn borer attack using the intermated B73 x Mo17 (IBM) population of maize. Theor Appl Gen. 2009;119(8):1451-9.
29. Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, et al. Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol. 2002;48(5-6):453-61.
30. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, et al. High-throughput genotyping by whole-genome resequencing. Genome Res. 2009;19(6):1068-76.
31. Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, et al. Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers. PLoS One. 2011;6(3):e17595.
32. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 2011;12(11):R114.
33. Chen Z, Wang B, Dong X, Liu H, Ren L, Chen J, et al. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F(2) maize population. BMC Genomics. 2014;15:433.
34. Huang X, Kurata N, Wei X, Wang Z-X, Wang A, Zhao Q, et al. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490(7421):497-501.
35. Zhou G, Chen Y, Yao W, Zhang C, Xie W, Hua J, et al. Genetic composition of yield heterosis in an elite rice hybrid. Proc Natl Acad Sci U S A. 2012;109(39):15847-52.
36. Gao ZY, Zhao SC, He WM, Guo LB, Peng YL, Wang JJ, et al. Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci U S A. 2013;110(35):14492-7.
37. Xu X, Zeng L, Tao Y, Vuong T, Wan J, Boerma R, et al. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. Proc Natl Acad Sci U S A. 2013;110(33):13469-74.
38. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers Plant Sci. 2011;2:34.
39. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, et al. High-throughput genotyping by whole-genome resequencing. Genome Res. 2009;19(6):1068-76.
40. Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, Charcosset A, et al. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One. 2011;6(12):e28334.
41. Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet. 2012;44(7):803-7.
42. Liu S-C, Kowalski SP, Lan T-H, Feldmann KA, Paterson AH. Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics. 1996;142(1):247-58.
43. Williams RW, Gu J, Qi S, Lu L. The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol. 2001;2(11):RESEARCH0046.
44. Winkler CR, Jensen NM, Cooper M, Podlich DW, Smith OS. On the determination of recombination rates in intermated recombinant inbred populations. Genetics. 2003;164(2):741-5.
45. Teuscher F, Guiard V, Rudolph PE, Brockmann GA. The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs. Genetics. 2005;170(2):875-9.
46. Li H, Kilian A, Zhou M, Wenzl P, Huttner E, Mendham N, et al. Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Mol Gen Genom. 2010;284(5):319-31.
47. Lu H, Romero-Severson J, Bernardo R. Chromosomal regions associated with segregation distortion in maize. Theor Appl Gen. 2002;105(4):622-8.
48. Buckler ES, Phelps-Durr TL, Buckler CS, Dawe RK, Doebley JF, Holtsford TP. Meiotic drive of chromosomal knobs reshaped the maize genome. Genetics. 1999;153(1):415-26.
49. Xu S. Quantitative trait locus mapping can benefit from segregation distortion. Genetics. 2008;180(4):2201-8.
50. Zhang L, Wang S, Li H, Deng Q, Zheng A, Li S, et al. Effects of missing marker and segregation distortion on QTL mapping in F2 populations. Theor Appl Gen. 2010;121(6):1071-82.
51. Harushima Y, Kurata N, Yano M, Nagamura Y, Sasaki T, Minobe Y, et al. Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map. Theor Appl Gen. 1996;92(2):145-50.
52. Yamanaka N, Ninomiya S, Hoshi M, Tsubokura Y, Yano M, Nagamura Y, et al. An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion. DNA Res. 2001;8(2):61-72.
53. Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, et al. B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize. Plant Physiol. 2011;156(4):1679-90.
54. Fu Y, Wen T-J, Ronin YI, Chen HD, Guo L, Mester DI, et al. Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics. 2006;174(3):1671-83.
55. Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, Shi J, et al. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons. PLoS Genet. 2009;5(11):e1000743.
56. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestication of Rice. Mol Biol Evol. 2007;24(3):875-88.
57. Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinform. 2009;25(15):1966-7.
58. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456(7218):60-5.
59. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet. 2010;42(11):1027-30.
60. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science. 2009;326(5951):433-6.
61. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, et al. Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx). Science. 2009;326(5951):433-6.
62. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K. SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009;19(6):1124-32.
63. Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J: SOAPindel: Efficient identification of indels from short paired reads. Genome research 2012
64. Zhao Q, Huang X, Lin Z, Han B. SEG-Map: A Novel Software for Genotype Calling and Genetic Map Construction from Next-generation Sequencing. Rice. 2010;3(2):98-102.
65. JW VANO: Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res (Camb) 2011, 93(5):343-349.
66. Wu Y, Bhat PR, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 2008;4(10):e1000212.
67. Wang SBC, Zeng ZB. QTL Cartographer 1.7 (linux version). Raleigh: Department of Statistics, North Carolina State University; 2005.
68. Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, et al. High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics. 2010;184(1):19-26.