An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Chen, Zongliang ^a   Wang, Baobao ^a   Dong, Xiaomei ^a   Liu, Han ^a   Ren, Longhui ^a   Chen, Jian ^a   Hauck, Andrew ^a   Song, Weibin ^a   Lai, Jinsheng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Breeding; Genotyping by sequencing; Maize; Next generation sequencer; Quantitative trait loci

Indexed keywords

VEGETABLE PROTEIN; PLANT DNA;

ARTICLE; CHROMOSOME 10; CHROMOSOME 3; CONTROLLED STUDY; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC CODE; GENETIC DISTANCE; GENOTYPE; MAIZE; NONHUMAN; PLANT GENETICS; PROGENY; PROTEIN DOMAIN; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; ANATOMY AND HISTOLOGY; CHROMOSOME MAP; DNA SEQUENCE; ECONOMICS; GENETICS; GROWTH, DEVELOPMENT AND AGING; INFLORESCENCE; PHENOTYPE; PLANT CHROMOSOME; PROCEDURES; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS;

ZEA MAYS;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; INFLORESCENCE; PHENOTYPE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

EID: 84902346968     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-433     Document Type: Article

References (57)

1. Upadyayula N, Da Silva H, Bohn M, Rocheford T. Genetic and QTL analysis of maize tassel and ear inflorescence architecture. Theor Appl Genet 2006, 112(4):592-606. 10.1007/s00122-005-0133-x, 16395569.
2. Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet 2011, 7(11):e1002383. 10.1371/journal.pgen.1002383, 3219606, 22125498.
3. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science 2005, 309(5735):741-745. 10.1126/science.1113373, 15976269.
4. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q. 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):19579-19584. 10.1073/pnas.1014419107, 2984220, 20974950.
5. Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 2007, 39(5):623-630. 10.1038/ng2014, 17417637.
6. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 2010, 42(6):541-544. 10.1038/ng.591, 20495565.
7. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E, Li B, Hainey CF, Radovic S, Zaina G, Rafalski JA, Tingey SV, Miao GH, Phillips RL, Tuberosa R. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A 2007, 104(27):11376-11381. 10.1073/pnas.0704145104, 2040906, 17595297.
8. Hung H-Y, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, McMullen MD, Ware D, Buckler ES, Doebley JF, Holland JB. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci U S A 2012, 109(28):E1913-E1921. 10.1073/pnas.1203189109, 3396540, 22711828.
9. Bommert P, Nagasawa NS, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet 2013, 45(3):334-337. 10.1038/ng.2534, 23377180.
10. Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q. 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. 10.1371/journal.pone.0017595, 3048400, 21390234.
11. Wang L, Wang A, Huang X, Zhao Q, Dong G, Qian Q, Sang T, Han B. Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 2011, 122(2):327-340. 10.1007/s00122-010-1449-8, 3021254, 20878143.
12. Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, Melchinger AE. Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 2004, 167(1):485-498. 10.1534/genetics.167.1.485, 1470842, 15166171.
13. Vales M, Schön C, Capettini F, Chen X, Corey A, Mather DE, Mundt C, Richardson K, Sandoval-Islas J, Utz H, Hayes PM. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. Theor Appl Genet 2005, 111(7):1260-1270. 10.1007/s00122-005-0043-y, 16179997.
14. Briggs WH, McMullen MD, Gaut BS, Doebley J. Linkage mapping of domestication loci in a large maize-teosinte backcross resource. Genetics 2007, 177(3):1915-1928. 10.1534/genetics.107.076497, 2147989, 17947434.
15. Schuster SC. Next-generation sequencing transforms today's biology. Nat Methods 2008, 5(1):16-18.
16. Varshney RK, Nayak SN, May GD, Jackson SA. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 2009, 27(9):522-530. 10.1016/j.tibtech.2009.05.006, 19679362.
17. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24(3):133-141. 10.1016/j.tig.2007.12.007, 18262675.
18. Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES. A first-generation haplotype map of maize. Science 2009, 326(5956):1115-1117. 10.1126/science.1177837, 19965431.
19. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326(5956):1112-1115. 10.1126/science.1178534, 19965430.
20. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 2010, 42(11):1027-1030. 10.1038/ng.684, 20972441.
21. Chia J-M, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 2012, 44(7):803-807. 10.1038/ng.2313, 22660545.
22. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one 2011, 6(5):e19379. 10.1371/journal.pone.0019379, 3087801, 21573248.
23. Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells M, Jannink JL. Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 2012, 5(3):103-113.
24. Poland JA, Brown PJ, Sorrells ME, Jannink J-L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS one 2012, 7(2):e32253. 10.1371/journal.pone.0032253, 3289635, 22389690.
25. Byrne S, Czaban A, Studer B, Panitz F, Bendixen C, Asp T. Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PloS One 2013, 8(3):e57438. 10.1371/journal.pone.0057438, 3587605, 23469194.
26. Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau T, Laroche J, Larose S, Jean M, Belzile F. An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PloS one 2013, 8(1):e54603. 10.1371/journal.pone.0054603, 3553054, 23372741.
27. Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 2013, 126(11):2699-2716. 10.1007/s00122-013-2166-x, 23918062.
28. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B, Tao Y. High-throughput genotyping by whole-genome resequencing. Genome Res 2009, 19(6):1068-1076. 10.1101/gr.089516.108, 2694477, 19420380.
29. Zou G, Zhai G, Feng Q, Yan S, Wang A, Zhao Q, Shao J, Zhang Z, Zou J, Han B. Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods. J Exp Bot 2012, 63(15):5451-5462. 10.1093/jxb/ers205, 22859680.
30. Gao Z-Y, Zhao S-C, He W-M, Guo L-B, Peng Y-L, Wang J-J, Guo X-S, Zhang X-M, Rao Y-C, Zhang C, Dong GJ, Zheng FY, Lu CX, Hu J, Zhou Q, Liu HJ, Wu HY, Xu J, Ni PX, Zeng DL, Liu DH, Tian P, Gong LH, Ye C, Zhang GH, Wang J, Tian FK, Xue DW, Liao Y, Zhu L, 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):14492-14497. 10.1073/pnas.1306579110, 3761582, 23940322.
31. Xu X, Zeng L, Tao Y, Vuong T, Wan J, Boerma R, Noe J, Li Z, Finnerty S, Pathan SM, Shannon JG, Nguyen HT. 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):13469-13474. 10.1073/pnas.1222368110, 3746920, 23898176.
32. van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, Van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JN, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RG, Bakker J, van Eck HJ. Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 2006, 173(2):1075-1087. 10.1534/genetics.106.055871, 1526527, 16582432.
33. Ludwig SR, Habera LF, Dellaporta SL, Wessler SR. Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proc Natl Acad Sci U S A 1989, 86(18):7092-7096. 10.1073/pnas.86.18.7092, 298000, 2674946.
34. Gallavotti A, Zhao Q, Kyozuka J, Meeley RB, Ritter MK, Doebley JF, Pè ME, Schmidt RJ. The role of barren stalk1 in the architecture of maize. Nature 2004, 432(7017):630-635. 10.1038/nature03148, 15577912.
35. Beavis W, Smith O, Grant D, Fincher R. Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci 1994, 34(4):882-896.
36. Austin D, Lee M. Comparative mapping in F2:3 and F6:7 generations of quantitative trait loci for grain yield and yield components in maize. Theor Appl Genet 1996, 92(7):817-826. 10.1007/BF00221893, 24166546.
37. Winter CM, Austin RS, Blanvillain-Baufume S, Reback MA, Monniaux M, Wu M-F, Sang Y, Yamaguchi A, Yamaguchi N, Parker JE, Parcy F, Jensen ST, Li H, Wagner D. LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response. Dev Cell 2011, 20(4):430-443. 10.1016/j.devcel.2011.03.019, 21497757.
38. Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D, Jackson D. Regulatory modules controlling maize inflorescence architecture. Genome Res 2014, 24(3):431-443. 10.1101/gr.166397.113, 24307553.
39. Lechner E, Leonhardt N, Eisler H, Parmentier Y, Alioua M, Jacquet H, Leung J, Genschik P. MATH/BTB CRL3 receptors target the homeodomain-leucine zipper ATHB6 to modulate abscisic acid signaling. Dev Cell 2011, 21(6):1116-1128. 10.1016/j.devcel.2011.10.018, 22172674.
40. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS one 2008, 3(10):e3376. 10.1371/journal.pone.0003376, 2557064, 18852878.
41. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC genomics 2011, 12:4. 10.1186/1471-2164-12-4, 3023751, 21205322.
42. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L, Henikoff S. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 2004, 4(1):12. 10.1186/1471-2229-4-12, 512284, 15282033.
43. Brutnell T, Conrad L. Transposon tagging using Activator (Ac) in maize. Methods Mol Biol 2003, 236:157-176.
44. McCarty DR, Mark Settles A, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier J, Avigne W, Lai J, Messing J, Koch KE, Hannah LC. Steady-state transposon mutagenesis in inbred maize. Plant J 2005, 44(1):52-61. 10.1111/j.1365-313X.2005.02509.x, 16167895.
45. Bommert P, Nardmann J, Vollbrecht E, Running M, Jackson D, Hake S, Werr W. Thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development 2005, 132(6):1235-1245. 10.1242/dev.01671, 15716347.
46. Taguchi-Shiobara F, Yuan Z, Hake S, Jackson D. The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize. Gene Dev 2001, 15(20):2755-2766. 10.1101/gad.208501, 312812, 11641280.
47. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 2011, 43(2):159-162. 10.1038/ng.746, 21217756.
48. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 2013, 74(1):174-183. 10.1111/tpj.12105, 23289725.
49. Bruce W, Folkerts O, Garnaat C, Crasta O, Roth B, Bowen B. Expression profiling of the maize flavonoid pathway genes controlled by estradiol-inducible transcription factors CRC and P. Plant Cell 2000, 12(1):65-80. 10.1105/tpc.12.1.65, 140215, 10634908.
50. Hernandez JM, Feller A, Morohashi K, Frame K, Grotewold E. The basic helix-loop-helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor. Proc Natl Acad Sci U S A 2007, 104(43):17222-17227. 10.1073/pnas.0705629104, 2040437, 17940002.
51. Vollbrecht E, Springer PS, Goh L, Buckler ES, Martienssen R. Architecture of floral branch systems in maize and related grasses. Nature 2005, 436(7054):1119-1126. 10.1038/nature03892, 16041362.
52. Barazesh S, McSteen P. Hormonal control of grass inflorescence development. Trends Plant Sci 2008, 13(12):656-662. 10.1016/j.tplants.2008.09.007, 18986827.
53. Tan B-C, Chen Z, Shen Y, Zhang Y, Lai J, Sun SS. Identification of an active new mutator transposable element in maize. G3 (Bethesda) 2011, 1(4):293-302. 2011, 3276141, 22384340.
54. Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W, Zhang M, Xie S, Lai J. Genome-wide genetic changes during modern breeding of maize. Nat Genet 2012, 44(7):812-815. 10.1038/ng.2312, 22660547.
55. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
56. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
57. Broman KW, Wu H, Sen T, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003, 19(7):889-890. 10.1093/bioinformatics/btg112, 12724300.