Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

  • 297 Accesses


Key message

A whole genome bin map was developed for a MAGIC population. Association studies for heading date at bin level exhibited powerful QTL mapping and identified favorable alleles.


The presumed advantages of multiparent advanced generation intercross (MAGIC) population in quantitative trait locus (QTL) mapping were not fully utilized in the previous studies in which genome-wide association studies (GWAS) were conducted at only single nucleotide polymorphism level. In this study, we genotyped a rice four-way MAGIC population of 247 F7 lines and their parents by sequencing. A total of 5934 bins with an average length of 65 kb were constructed and covered 97% of the genome. The MAGIC population showed low population structure and balanced parental contributions. A bin-based GWAS for heading date identified 4 QTLs in three environments. Three major QTLs were mapped exactly to the bins where the major heading date genes DTH3, Ghd7.1 and Ghd8 were located. Multiple comparisons showed that different parental alleles had varied genetic effects. Like DTH3, the alleles of the Guichao 2/YJSM, IR34 and Cypress had larger, intermediate and no effects, respectively. Based on comparative sequencing of 8 known heading date genes undetected in this MAGIC population, only Ghd7 exhibited diverse function among parents. The failure in Ghd7 mapping was well explained by its interaction with Hd1 because Ghd7 had no effects on heading date when combined with the nonfunctional hd1 carried by all four parents. Overall, bin-based GWAS have more mapping power and higher resolution with a MAGIC population and provide favorable alleles to breeders. The use of more diversified parents is encouraged to develop a MAGIC population for detecting more QTLs for important agronomical traits.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 199

This is the net price. Taxes to be calculated in checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Kumar Singh R, Gregorio G, Redoña E, Leung H (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6:11

  2. Bian XF, Liu X, Zhao ZG, Jiang L, Gao H, Zhang YH, Zheng M, Chen LM, Liu SJ, Zhai HQ, Wan JM (2011) Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1. Plant Cell Rep 30:2243–2254

  3. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

  4. Bossa-Castro AM, Tekete C, Raghavan C, Delorean EE, Dereeper A, Dagno K, Koita O, Mosquera G, Leung H, Verdier V, Leach JE (2018) Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population. Plant Biotechnol J 16:1559–1568

  5. Brachi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232

  6. Browning BL, Zhou Y, Browning SR (2018) A one-penny imputed genome from next-generation reference panels. Am J Hum Genet 103:338–348

  7. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221

  8. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin) 6:80–92

  9. Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141:1199–1207

  10. De Mendiburu F (2014) Agricolae: statistical procedures for agricultural research. R Package Version 1

  11. Dell’Acqua M, Gatti DM, Pea G, Cattonaro F, Coppens F, Magris G, Hlaing AL, Aung HH, Nelissen H, Baute J, Frascaroli E, Churchill GA, Inzé D, Morgante M, Pè ME (2015) Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. Genome Biol 16:167

  12. Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936

  13. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5 c. Joseph Felsenstein.

  14. Fornara F, de Montaigu A, Coupland G (2010) SnapShot: Control of Flowering in Arabidopsis. Cell 141:550–550.e2

  15. Haley C, Knott S (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324

  16. Hori K, Ogiso-Tanaka E, Matsubara K, Yamanouchi U, Ebana K, Yano M (2013) Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant J 76:36–46

  17. Huang BE, George AW (2011) R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. Bioinformatics 27:727–729

  18. 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 (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076

  19. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q-F, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967

  20. Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10:826–839

  21. Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK, Gaur P, Leung H, Varshney RK, Cavanagh CR (2015) MAGIC populations in crops: current status and future prospects. Theor Appl Genet 128:999–1017

  22. Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants; where are we now? Heredity 80:137–142

  23. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43:1096–1105

  24. Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K (2008) Hd3a and RFT1 are essential for flowering in rice. Development 135:767–774

  25. Komiya R, Yokoi S, Shimamoto K (2009) A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development 136:3443–3450

  26. Kwon CT, Yoo SC, Koo BH, Cho SH, Park JW, Zhang Z, Li J, Li Z, Paek NC (2014) Natural variation in Early flowering1 contributes to early flowering in japonica rice under long days. Plant Cell Environ 37:101–112

  27. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124–1132

  28. Li XF, Liu ZX, Lu DB, Liu YZ, Mao XX, Li ZX, Li HJ (2013) Development and evaluation of multi-genotype varieties of rice derived from MAGIC lines. Euphytica 192:77–86

  29. Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8:833–835

  30. Mackay IJ, Bansept-Basler P, Barber T, Bentley AR, Cockram J, Gosman N, Greenland AJ, Horsnell R, Howells R, O’Sullivan DM, Rose GA, Howell PJ (2014) An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation. G3-Genes Genom Genet 4:1603–1610

  31. Matsubara K, Ogiso-Tanaka E, Hori K, Ebana K, Ando T, Yano M (2012) Natural variation in Hd17, a homolog of arabidopsis ELF3 that is involved in rice photoperiodic flowering. Plant Cell Physiol 53:709–716

  32. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

  33. McKinney W (2013) Python for data analysis. O’Reilly, Beijing

  34. Meng L, Zhao X, Ponce K, Ye G, Leung H (2016) QTL mapping for agronomic traits using multi-parent advanced generation inter-cross (MAGIC) populations derived from diverse elite indica rice lines. Field Crops Res 189:19–42

  35. Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci 97:12649–12654

  36. Nemoto Y, Nonoue Y, Yano M, Izawa T (2016) Hd1, a CONSTANS ortholog in rice, functions as an Ehd1 repressor through interaction with monocot-specific CCT-domain protein Ghd7. Plant J 86:221–233

  37. Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru J (2018) Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 8:4379

  38. Ogiso-Tanaka E, Matsubara K, Yamamoto S, Nonoue Y, Wu J, Fujisawa H, Ishikubo H, Tanaka T, Ando T, Matsumoto T, Yano M (2013) Natural variation of the Rice Flowering Locus T 1 contributes to flowering time divergence in rice. PLoS ONE 8:e75959

  39. Paradis E, Claude J, Strimmer K (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20:289–290

  40. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909

  41. Sakai H, Aoyama T, Oka A (2000) Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J 24:703–711

  42. Sannemann W, Huang BE, Mathew B, Léon J (2015) Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept. Mol Breed 35:86

  43. Simes RJ (1986) An improved Bonferroni procedure for multiple tests of significance. Biometrika 73:751–754

  44. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. Proc Natl Acad Sci 98:7922–7927

  45. Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K (2009) Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc Natl Acad Sci 106:4555–4560

  46. Tan C, Han Z, Yu H, Zhan W, Xie W, Chen X, Zhao H, Zhou F, Xing Y (2013) QTL scanning for rice yield using a whole genome SNP array. J Genet Genomics 40:629–638

  47. Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann J-C, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557:43

  48. Wei J, Xu S (2016) A random-model approach to QTL mapping in Multiparent Advanced Generation Intercross (MAGIC) populations. Genetics 202:471–486

  49. Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci 107:10578–10583

  50. Xu S (1996) Mapping quantitative trait loci using four-way crosses. Genet Res 68:175–181

  51. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

  52. Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4:319–330

  53. Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969–971

  54. Zhang J, Zhou X, Yan W, Zhang Z, Lu L, Han Z, Zhao H, Liu H, Song P, Hu Y, Shen G, He Q, Guo S, Gao G, Wang G, Xing Y (2015) Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice. New Phytol 208:1056–1066

  55. Zhang Z, Hu W, Shen G, Liu H, Hu Y, Zhou X, Liu T, Xing Y (2017) Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions. Sci Rep 7:5388

  56. Zhang B, Liu H, Qi F, Zhang Z, Li Q, Han Z, Xing Y (2019) Genetic Interactions Among Ghd7, Ghd8, OsPRR37 and Hd1 Contribute to Large Variation in Heading Date in Rice. Rice 12:48

  57. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467

  58. Zhao D, Zhang C, Feng G, Yang Q, Gu M, Liu Q (2013) Hd-q, a novel allele of Ef7 from a Chinese rice landrace, confers weak photoperiod sensitivity and improves local adaptability and yield potential. Mol Breed 32:651–662

  59. Zhao J, Chen H, Ren D, Tang H, Qiu R, Feng J, Long Y, Niu B, Chen D, Zhong T, Liu Y-G, Guo J (2015) Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa). New Phytol 208:936–948

Download references


We thank the field technician Mr. JB Wang for his excellent work in the field. This work is partly supported by grants National Natural Science Foundation of China (31701391 and 31821005), and National Key Research and Development Program of China (2016YFD0100301).

Author information

ZH analyzed the data and wrote the article; GH performed most of the experiments; HL and FL investigated the phenotypes; LY developed the MAGIC population; HZ provided technical assistance to ZH; QZ gathered the sequencing data; ZL supervised the phenotypic investigation; QZ helped in experimental design; YX conceived the research plans, supervised and completed the writing and agrees to serve as the author responsible for contact and ensures communication.

Correspondence to Yongzhong Xing.

Ethics declarations

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Communicated by Christine A. Hackett.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 8023 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Han, Z., Hu, G., Liu, H. et al. Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population. Theor Appl Genet 133, 59–71 (2020) doi:10.1007/s00122-019-03440-y

Download citation