Genetic dissection of a major QTL for kernel weight spanning the Rht-B1 locus in bread wheat

  • Dengan Xu
  • Weie Wen
  • Luping Fu
  • Faji Li
  • Jihu Li
  • Li Xie
  • Xianchun Xia
  • Zhongfu Ni
  • Zhonghu HeEmail author
  • Shuanghe CaoEmail author
Original Article


Key message

Genetic dissection uncovered a major QTL QTKW.caas-4BS corresponding with a 483 kb deletion that included genes ZnF, EamA and Rht-B1. This deletion was associated with increased grain weight and semi-dwarf phenotype.


Previous studies identified quantitative trait loci (QTL) for thousand kernel weight (TKW) in the region spanning the Rht-B1 locus in wheat (Triticum aestivum L.). We recently mapped a major QTL QTKW.caas-4BS for TKW spanning the Rht-B1 locus in a recombinant inbred line (RIL) population derived from Doumai/Shi 4185 using the wheat 90K array. The allele from Doumai at QTKW.caas-4BS significantly increased TKW and kernel number per spike, and conferred semi-dwarf trait, which was beneficial to improve grain yield without a penalty to lodging. To further dissect QTKW.caas-4BS, we firstly re-investigated the genotypes and phenotypes of the RILs and confirmed the QTL using cleaved amplified polymorphic sequence (CAPS) markers developed from flanking SNP markers IWA102 and IWB54814. The target sequences of the CAPS markers were used as queries to BLAST the wheat reference genome RefSeq v1.0 and hit an approximate 10.4 Mb genomic region. Based on genomic mining and SNP loci from the wheat 660K SNP array in the above genomic region, we developed eight new markers and narrowed QTKW.caas-4BS to a genetic interval of 1.5 cM. A 483 kb deletion in Doumai corresponded with QTKW.caas-4BS genetically, including three genes ZnF, EamA and Rht-B1. The other 15 genes with either differential expressions and/or sequence variations between parents were also potential candidate genes for QTKW.caas-4BS. The findings not only provide a toolkit for marker-assisted selection of QTKW.caas-4BS but also defined candidate genes for further functional analysis.



Cleaved amplified polymorphic sequence


Coding sequence


Derived cleaved amplified polymorphic sequence


Gibberellin acid


Genome-wide association study


Inclusive composite interval mapping


Kompetitive allele-specific PCR


Kernel number per spike


Logarithm of odds


Open reading frame


Plant height


Quantitative PCR


Quantitative trait locus


Recombinant inbred line


Spike number per square meter


Single nucleotide polymorphism


Simple sequence repeat


Sequence-tagged site


Thousand kernel weight



The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for review of this manuscript. This work was funded by the National Key Research and Development Programs of China (2016YFD0101802), National Key Technology R & D Program of China (2014BAD01B05) and CAAS Science and Technology Innovation Program.

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest in regard to this manuscript.

Ethical standards

We declare that these experiments comply with the ethical standards in China.

Supplementary material

122_2019_3418_MOESM1_ESM.docx (706 kb)
Supplementary file1 (DOCX 706 kb)
122_2019_3418_MOESM2_ESM.docx (33 kb)
Supplementary file2 (DOCX 33 kb)
122_2019_3418_MOESM3_ESM.xlsx (13 kb)
Supplementary file3 (XLSX 12 kb)
122_2019_3418_MOESM4_ESM.xlsx (7.9 mb)
Supplementary file4 (XLSX 8118 kb)


  1. Araki E, Miura H, Sawada S (1999) Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat. Theor Appl Genet 98:977–984CrossRefGoogle Scholar
  2. Bevan MW, Uauy C (2013) Genomics reveals new landscapes for crop improvement. Genome Biol 14:206CrossRefGoogle Scholar
  3. Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder S, Weber E (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936CrossRefGoogle Scholar
  4. Cui F, Zhao CH, Ding AM, Li J, Wang L, Li XF, Bao YG, Li JM, Wang HG (2014) Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations. Theor Appl Genet 127:659–675CrossRefGoogle Scholar
  5. Cui F, Zhang N, Fan XL, Zhang W, Zhao CH, Yang LJ, Pan RQ, Chen M, Han J, Zhao XQ, Ji J, Tong YP, Zhang HX, Jia JZ, Zhao GY, Li JM (2017) Utilization of a Wheat 660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 7:3788CrossRefGoogle Scholar
  6. Curtis T, Halford NG (2014) Food security: the challenge of increasing wheat yield and the importance of not compromising food safety. Ann Appl Biol 164:354–372CrossRefGoogle Scholar
  7. Cuthbert JL, Somers DJ, Brûlé-Babel AL, Brown PD, Crow GH (2008) Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor Appl Genet 117:595–608CrossRefGoogle Scholar
  8. de Lucas M, Daviere JM, Rodriguez-Falcon M, Pontin M, Iglesias-Pedraz JM, Lorrain S, Fankhauser C, Blazquez MA, Titarenko E, Prat S (2008) A molecular framework for light and gibberellin control of cell elongation. Nature 451:480–484CrossRefGoogle Scholar
  9. Dixon LE, Greenwood JR, Bencivenga S, Zhang P, Cockram J, Mellers G, Ramm K, Cavanagh C, Swain SM, Boden SA (2018) TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat (Triticum aestivum). Plant Cell 30:563–581CrossRefGoogle Scholar
  10. Feng SH, Martinez C, Gusmaroli G, Wang Y, Zhou JL, Wang F, Chen LY, Yu L, Iglesias-Pedraz JM, Kircher S, Schaefer E, Fu XD, Fan LM, Deng XW (2008) Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451:475–479CrossRefGoogle Scholar
  11. Guan PF, Lu LH, Jia LJ, Kabir MR, Zhang JB, Lan TY, Zhao Y, Xin MM, Hu ZR, Yao YY, Ni ZF, Sun QX, Peng HR (2018) Global QTL analysis identifies genomic regions on chromosomes 4A and 4B harboring stable loci for yield-related traits across different environments in wheat (Triticum aestivum L.). Front Plant Sci 9:529CrossRefGoogle Scholar
  12. Gupta PK, Rustgi S, Kumar N (2017) Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants. Genome 49:565–571CrossRefGoogle Scholar
  13. Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, Noll JS, Somers DJ, Brown PD (2006) Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet 113:753–766CrossRefGoogle Scholar
  14. International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191CrossRefGoogle Scholar
  15. Kumar N, Kulwal PL, Gaur A, Tyagi AK, Khurana JP, Khurana P, Balyan HS, Gupta BP (2006) QTL analysis for grain weight in common wheat. Euphytica 151:135–144CrossRefGoogle Scholar
  16. Kumar A, Mantovani EE, Seetan R, Soltani A, Echeverry-Solarte M, Jain S, Simsek S, Doehlert D, Alamri MS, Elias EM, Kianian SF, Mergoum M (2016) Dissection of genetic factors underlying wheat kernel shape and size in an Elite × Nonadapted cross using a high density SNP linkage map. Plant Genome 9:1–22Google Scholar
  17. Lewis JM, Mackintosh CA, Shin S, Gilding E, Kravchenko S, Baldridge G, Zeyen R, Muehlbauer GJ (2008) Overexpression of the maize Teosinte Branched1 gene in wheat suppresses tiller development. Plant Cell Rep 27:1217–1225CrossRefGoogle Scholar
  18. Li FJ, Wen WE, He ZH, Liu JD, Jin H, Cao SH, Geng HW, Yan J, Zhang PZ, Wan YX, Xia XC (2018) Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers. Theor Appl Genet 131:1903–1924CrossRefGoogle Scholar
  19. Liu G, Jia L, Lu L, Qin D, Zhang J, Guan P, Ni Z, Yao Y, Sun Q, Peng H (2014) Mapping QTLs of yield-related traits using RIL population derived from common wheat and Tibetan semi-wild wheat. Theor Appl Genet 127:2415–2432CrossRefGoogle Scholar
  20. McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, Cloutier S, McCallum BD (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452x'AC Domain'. Genome 48:870–883CrossRefGoogle Scholar
  21. Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012) Genetic dissection of grain weight in bread wheat through quantitative trait locus interval and association mapping. Mol Breed 29:963–972CrossRefGoogle Scholar
  22. Miraghazadeh A, Zhang P, Harding C, Hossain S, Hayden M, Wong D, Spielmeyer W, Chandler PM (2016) The use of SNP hybridisation arrays and cytogenetics to characterise deletions of chromosome 4B in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 129:2151–2160CrossRefGoogle Scholar
  23. Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S (2018) Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genom 293:463–477CrossRefGoogle Scholar
  24. Pearce S, Saville R, Vaughan SP, Chandler PM, Wilhelm EP, Sparks CA, Al-Kaff N, Korolev A, Boulton MI, Phillips AL, Hedden P, Nicholson P, Thomas SG (2011) Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat. Plant Physiol 157:1820–1831CrossRefGoogle Scholar
  25. Peng JR, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400:256–261CrossRefGoogle Scholar
  26. Ramirez-Gonzalez RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer K, Benhamed M, Latrasse D, Bendahmane A, Wulff B, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Brautigam A, Uauy C (2018) The transcriptional landscape of polyploid wheat. Science 361:eaar6089CrossRefGoogle Scholar
  27. Ramirez-Gonzalez RH, Uauy C, Caccamo M (2015) PolyMarker: a fast polyploid primer design pipeline. Bioinformatics 31:2038–2039CrossRefGoogle Scholar
  28. Rasheed A, Wen WE, Gao FM, Zhai SN, Jin H, Liu JD, Guo Q, Zhang Y, Dreisigacker S, Xia XC, He ZH (2016) Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theor Appl Genet 129:1843–1860CrossRefGoogle Scholar
  29. Ravel C, Martre P, Romeuf I, Dardevet M, El-Malki R, Bordes J, Duchateau N, Brunel D, Balfourier F, Charmet G (2009) Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. Plant Physiol 151:2133–2144CrossRefGoogle Scholar
  30. Shaw MA, Chiurazzi P, Romain DR, Neri G, Gécz J (2002) A novel gene, FAM11A, associated with the FRAXF CpG island is transcriptionally silent in FRAXF full mutation. Eur J Hum Genet 10:767–772CrossRefGoogle Scholar
  31. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 5:739–744CrossRefGoogle Scholar
  32. Tian XL, Wen WE, Xie L, Fu LP, Xu DA, Fu C, Wang DS, Chen XM, Xia XC, Chen QJ, He ZH, Cao SH (2017) Molecular mapping of reduced plant height gene Rht24 in bread wheat. Front Plant Sci 8:1379CrossRefGoogle Scholar
  33. van De Velde K, Ruelens P, Geuten K, Rohde A, van Der Straeten D (2017) Exploiting DELLA signaling in cereals. Trends Plant Sci 22:880–893CrossRefGoogle Scholar
  34. Varshney RK, Prasad M, Roy JK, Harjit-Singh NK, Dhaliwal HS, Balyan HS, Gupta PK (2000) Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTL for grain weight in bread wheat. Theor Appl Genet 100:1290–1294CrossRefGoogle Scholar
  35. Wen WE, He ZH, Gao FM, Liu JD, Jin H, Zhai SN, Qu YY, Xia XC (2017) A high-density consensus map of common wheat integrating four mapping populations scanned by the 90K SNP array. Front Plant Sci 8:1389CrossRefGoogle Scholar
  36. Wilhelm EP, Howells RM, Al-Kaff N, Jia J, Baker C, Leverington-Waite MA, Griffiths S, Greenland AJ, Boulton MI, Powell W (2013) Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat. Theor Appl Genet 126:1321–1336CrossRefGoogle Scholar
  37. Wilhelm EP, Mackay IJ, Saville RJ, Korolev AV, Balfourier F, Greenland AJ, Boulton MI, Powell W (2013) Haplotype dictionary for the Rht-1 loci in wheat. Theor Appl Genet 126:1733–1747CrossRefGoogle Scholar
  38. Wu J, Kong XY, Wan JM, Liu XY, Zhang X, Guo XP, Zhou RH, Zhao GY, Jing RL, Fu XD, Jia JZ (2011) Dominant and pleiotropic effects of a GAI gene in wheat results from a lack of interaction between DELLA and GID1. Plant Physiol 157:2120–2130CrossRefGoogle Scholar
  39. Wu WX, Cheng ZW, Liu MJ, Yang XF, Qiu DW (2014) C3HC4-type RING finger protein NbZFP1 is involved in growth and fruit development in Nicotiana benthamiana. PLoS One 9:e99352CrossRefGoogle Scholar
  40. Xu H, Liu Q, Yao T, Fu XD (2014) Shedding light on integrative GA signaling. Curr Opin Plant Biol 21:89–95CrossRefGoogle Scholar
  41. Yang L, Liu Q, Liu Z, Yang H, Wang J, Li X, Yang Y (2016) Arabidopsis C3HC4-RING finger E3 ubiquitin ligase AtAIRP4 positively regulates stress-responsive abscisic acid signaling. J Integr Plant Biol 58:67–80CrossRefGoogle Scholar
  42. Yang Y, Fu DB, Zhu CM, He YZ, Zhang HJ, Liu T, Li XH, Wu CY (2015) The RING-finger ubiquitin ligase HAF1 mediates heading date 1 degradation during photoperiodic flowering in rice. Plant Cell 27:2455–2468CrossRefGoogle Scholar
  43. Zhang JJ, Dell B, Biddulph B, Drake-Brockman F, Walker E, Khan N, Wong D, Hayden M, Appels R (2013) Wild-type alleles of Rht-B1 and Rht-D1 as independent determinants of thousand-grain weight and kernel number per spike in wheat. Mol Breed 32:771–783CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Crop Science, National Wheat Improvement CenterChinese Academy of Agricultural Sciences (CAAS)BeijingChina
  2. 2.Department of Plant Genetics & Breeding/State Key Laboratory for AgrobiotechnologyChina Agricultural UniversityBeijingChina

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