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

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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.

Abstract

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.

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Abbreviations

CAPS:

Cleaved amplified polymorphic sequence

CDS:

Coding sequence

dCAPS:

Derived cleaved amplified polymorphic sequence

GA:

Gibberellin acid

GWAS:

Genome-wide association study

ICIM:

Inclusive composite interval mapping

KASP:

Kompetitive allele-specific PCR

KNS:

Kernel number per spike

LOD:

Logarithm of odds

ORF:

Open reading frame

PH:

Plant height

qPCR:

Quantitative PCR

QTL:

Quantitative trait locus

RIL:

Recombinant inbred line

SN:

Spike number per square meter

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

STS:

Sequence-tagged site

TKW:

Thousand kernel weight

References

  • 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 98:977–984

    Article  CAS  Google Scholar 

  • Bevan MW, Uauy C (2013) Genomics reveals new landscapes for crop improvement. Genome Biol 14:206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 105:921–936

    Article  PubMed  Google Scholar 

  • 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 127:659–675

    Article  PubMed  Google Scholar 

  • 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 7:3788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Curtis T, Halford NG (2014) Food security: the challenge of increasing wheat yield and the importance of not compromising food safety. Ann Appl Biol 164:354–372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 117:595–608

    Article  CAS  PubMed  Google Scholar 

  • 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 451:480–484

    Article  CAS  PubMed  Google Scholar 

  • 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 30:563–581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 451:475–479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 9:529

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 49:565–571

    Article  Google Scholar 

  • 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 113:753–766

    Article  CAS  PubMed  Google Scholar 

  • International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191

    Article  CAS  PubMed  Google Scholar 

  • 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 151:135–144

    Article  CAS  Google Scholar 

  • 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 9:1–22

    Google Scholar 

  • 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 27:1217–1225

    Article  CAS  PubMed  Google Scholar 

  • 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 131:1903–1924

    Article  PubMed  Google Scholar 

  • 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 127:2415–2432

    Article  CAS  PubMed  Google Scholar 

  • 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 48:870–883

    Article  CAS  PubMed  Google Scholar 

  • 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 29:963–972

    Article  Google Scholar 

  • 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 129:2151–2160

    Article  CAS  PubMed  Google Scholar 

  • 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 293:463–477

    Article  CAS  Google Scholar 

  • 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 157:1820–1831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 400:256–261

    Article  CAS  PubMed  Google Scholar 

  • 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:eaar6089

    Article  CAS  PubMed  Google Scholar 

  • Ramirez-Gonzalez RH, Uauy C, Caccamo M (2015) PolyMarker: a fast polyploid primer design pipeline. Bioinformatics 31:2038–2039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 129:1843–1860

    Article  CAS  PubMed  Google Scholar 

  • 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 151:2133–2144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 10:767–772

    Article  CAS  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 5:739–744

    Article  Google Scholar 

  • 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 8:1379

    Article  PubMed  PubMed Central  Google Scholar 

  • van De Velde K, Ruelens P, Geuten K, Rohde A, van Der Straeten D (2017) Exploiting DELLA signaling in cereals. Trends Plant Sci 22:880–893

    Article  CAS  Google Scholar 

  • 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 100:1290–1294

    Article  CAS  Google Scholar 

  • 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 8:1389

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 126:1321–1336

    Article  CAS  PubMed  Google Scholar 

  • 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 126:1733–1747

    Article  CAS  PubMed  Google Scholar 

  • 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 157:2120–2130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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:e99352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu H, Liu Q, Yao T, Fu XD (2014) Shedding light on integrative GA signaling. Curr Opin Plant Biol 21:89–95

    Article  CAS  PubMed  Google Scholar 

  • 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 58:67–80

    Article  CAS  PubMed  Google Scholar 

  • 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 27:2455–2468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 32:771–783

    Article  Google Scholar 

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Acknowledgements

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.

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Authors and Affiliations

  1. Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China

    Dengan Xu, Weie Wen, Luping Fu, Faji Li, Jihu Li, Li Xie, Xianchun Xia, Zhonghu He & Shuanghe Cao

  2. Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100094, China

    Dengan Xu & Zhongfu Ni

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  1. Dengan Xu
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Correspondence to Zhonghu He or Shuanghe Cao.

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Xu, D., Wen, W., Fu, L. et al. Genetic dissection of a major QTL for kernel weight spanning the Rht-B1 locus in bread wheat. Theor Appl Genet 132, 3191–3200 (2019). https://doi.org/10.1007/s00122-019-03418-w

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