Molecular Breeding

, Volume 31, Issue 3, pp 517–528 | Cite as

Functional molecular markers and high-resolution melting curve analysis of low phytic acid mutations for marker-assisted selection in rice

  • Yuan-Yuan Tan
  • Hao-Wei Fu
  • Hai-Jun Zhao
  • Sha Lu
  • Jun-Jie Fu
  • You-Fa Li
  • Hai-Rui Cui
  • Qing-Yao ShuEmail author


Phytic acid (PA, myo-inositol-1,2,3,4,5,6-hexakis-phosphate) and its salt form (phytate) are the principal storage forms of phosphorus in cereal grains. Since PA and phytates cannot be efficiently digested by monogastric animals, the abundance of PA in cereal and legume grains causes nutritional and environmental problems. The present study aimed at developing breeder-friendly functional molecular markers of five low phytic acid (LPA) mutant alleles of three rice (Oryza sativa L.) genes: viz., XQZ-lpa (a 1,475-bp deletion) and KBNT-lpa (a C→T single nucleotide polymorphism [SNP]) of LOC_Os02g57400, Z9B-lpa (a 6-bp deletion) and MH-lpa (a 1-bp deletion) of LOC_Os04g55800, and XS-lpa (a C→T SNP) of LOC_Os03g04920. First, markers for gel-based length polymorphism analysis were developed: viz., two insertion–deletion markers for XQZ-lpa and Z9B-lpa, two cleaved amplified polymorphic sequence (CAPS) markers for KBNT-lpa and XS-lpa, and one derived CAPS marker for MH-lpa. Second, the high-resolution melting (HRM) curve analysis method was explored for distinguishing plants with wild-type (WT) and LPA alleles (except XQZ-lpa). Plants of genotypes with homozygous mutant allele and WT, and with heterozygous alleles, could be directly differentiated by HRM for KBNT-lpa, XS-lpa and MH-lpa; only heterozygous individuals could be directly distinguished from homozygous WT and mutant plants for Z9B-lpa. However, by adding 15 % WT DNA templates to test samples before PCR, amplicons of three genotypes of the Z9B-lpa allele could also be differentiated by HRM analysis. Third, it was demonstrated that these markers could be effectively used for marker-assisted selection of LPA rice, and breeding lines with two non-allelic LPA mutations were developed with PA contents significantly lower than their respective parental LPA lines. Taken together, the present study developed functional molecular markers for efficient selection of LPA plants and demonstrated that double mutant LPA lines with significantly lower PA levels than primary LPA mutants (with single mutations) could be developed by pyramiding two non-allelic LPA mutations.


Low phytic acid Functional marker High-resolution melting curve analysis Marker-assisted selection Oryza sativa L. 



This research was financially supported by the Sino-Swiss Joint Research Project (2009 DFA32040) and the Natural Science Foundation of China through research contracts No. 31071481 and No. 30900887, and in part supported by the Fundamental Research Funds for Central Universities, the Special Fund for Agro-scientific Research in the Public Interest (201103007). The technical assistance of Ms Liquan Mao for determination of phytic acid content is highly appreciated.

Supplementary material

11032_2012_9809_MOESM1_ESM.pdf (444 kb)
Supplementary material 1 (PDF 444 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Yuan-Yuan Tan
    • 1
    • 2
  • Hao-Wei Fu
    • 3
  • Hai-Jun Zhao
    • 1
    • 2
  • Sha Lu
    • 1
    • 2
  • Jun-Jie Fu
    • 2
  • You-Fa Li
    • 3
  • Hai-Rui Cui
    • 1
    • 2
  • Qing-Yao Shu
    • 1
    • 2
    Email author
  1. 1.National Key Laboratory of Rice BiologyZhejiang UniversityHangzhouChina
  2. 2.Key Laboratory of Nuclear-Agricultural Sciences of the Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural SciencesZhejiang UniversityHangzhouChina
  3. 3.Jiaxing Academy of Agricultural SciencesJiaxingChina

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