Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL

Abstract

Key message

Three novel QTL for peroxidase activity were mapped, and gene-specific markers for TaPod-A1 were developed and validated using RILs derived from the Doumai/Shi 4185 cross and 281 wheat cultivars. TaPod-A1 is within one of the three QTL.

Abstract

Peroxidase (POD) activity in grain is an important factor determining the color of flour and end-use products of wheat, such as noodles and steamed bread. Mapping QTL for POD activity, characterization of POD genes and development of gene-specific markers are important for molecular marker-assisted selection in wheat breeding. Quantitative trait loci (QTL) for POD activity in common wheat were mapped using a recombinant inbred line (RIL) population derived from a Doumai/Shi 4185 cross grown in four environments and genotyped using the wheat 90 K iSelect assay. Three novel QTL for POD activity, QPod.caas-3AL, QPod.caas-4BS and QPod.caas-5AS, were identified on chromosomes 3AL, 4BS and 5AS, explaining 5.3–21.2 % of phenotypic variance across environments. The full-length genomic DNA (gDNA) sequence of a POD gene, designated TaPod-A1, on chromosome 3A was characterized by homolog cloning and PCR verification. Two complementary dominant sequence-tagged site (STS) markers, POD-3A1 and POD-3A2, were developed based on single nucleotide polymorphisms (SNPs) between two alleles at the TaPod-A1 locus, amplifying 291- and 766-bp fragments in cultivars with lower and higher POD activities, respectively. The two gene-specific markers were mapped on chromosome 3AL using a set of Chinese Spring (CS) nulli-tetrasomic lines, and ditelosomic lines 3AL and 3AS. QTL analysis indicated that QPod.caas-3AL co-segregated with the gene-specific markers POD-3A1 and POD-3A2. POD-3A1 and POD-3A2 were verified on 281 wheat cultivars and advanced lines, and showed significant (P < 0.05) associations with POD activities. POD-3A1 and POD-3A2 may be useful as markers for improving color attributes in wheat breeding programs.

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Fig. 1

Abbreviations

ANOVA:

Analysis of variance

cDNA:

Complementary DNA

CDS:

Coding sequence

CS:

Chinese Spring

gDNA:

Genomic DNA

LOD:

Logarithm of odds

mRNA:

Message RNA

ORF:

Open reading frame

PCR:

Polymerase chain reaction

POD:

Peroxidase

QTL:

Quantitative trait loci/locus

RIL:

Recombinant inbred line

SNP:

Single nucleotide polymorphism

STS:

Sequence-tagged site

UTR:

Untranslated region

UV:

Ultraviolet

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Acknowledgments

The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This study was supported by the National Natural Science Foundation of China (31260327, 31461143021), the National 863 Project (2012AA10A308), the Gene Transformation Projects (2011ZX08009-003, 2011ZX08002004-008), International Science & Technology Cooperation Program of China (2014DFG31690), and China Agriculture Research System (CARS-3-1-3).

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Correspondence to Xianchun Xia.

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We declare that these experiments comply with the ethical standards in China, where they were performed.

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Communicated by B. Hulke.

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Wei, J., Geng, H., Zhang, Y. et al. Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL. Theor Appl Genet 128, 2067–2076 (2015). https://doi.org/10.1007/s00122-015-2567-0

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Keywords

  • Quantitative Trait Locus
  • Common Wheat
  • Quantitative Trait Locus Analysis
  • Chinese Spring
  • Recombinant Inbred Line Population