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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

Abstract

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.

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.

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

Notes

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.

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)

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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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