Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat

Alexandr Muterko, Ruslan Kalendar, James Cockram, Irina Balashova

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)

Abstract

Photoperiod response in wheat is determined to a large extent by the homoeologous series of Photoperiod 1 (Ppd1) genes. In this study, Ppd-A1 genomic sequences from the 5′ UTR and promoter region were analysed in 104 accessions of six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and 102 accessions of six hexaploid wheat species (T. aestivum, T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). This data was supplemented with in silico analysis of publicly available sequences from 46 to 193 accessions of diploid and tetraploid wheat, respectively. Analysis of a region of the Ppd-A1 promoter identified thirteen haplotypes, which were divided in two haplogroups. Distribution of the Ppd-A1 haplogroups and haplotypes in wheat species, and their geographical distributions were analysed. Polymerase chain reaction combined with a heteroduplex mobility assay was subsequently used to efficiently discriminate between Ppd-A1 alleles, allowing identification of the Ppd-A1b haplotypes and haplogroups. The causes of anomalous migration of Ppd-A1 heteroduplexes in gels were found to be the localization of mismatches relative to the center of fragment, the cumulative effect of neighbouring polymorphic sites, and the location of mismatches within A/T-tracts. Analysis of the Ppd-A1 5′ UTR in hexaploid wheat revealed a novel mutation within the “photoperiod critical” region in a subset of T. compactum accessions. This putative photoperiod insensitive allele (designated Ppd-A1a.4) includes a 684 bp deletion which spans region in common with deletions previously identified in other photoperiod insensitive Ppd1 alleles.

Original languageEnglish
Pages (from-to)149-164
Number of pages16
JournalPlant Molecular Biology
Volume88
Issue number1-2
DOIs
Publication statusPublished - May 1 2015
Externally publishedYes

Keywords

  • Cereal
  • Flowering time
  • Genetic variation
  • Heteroduplex mobility assay
  • Molecular evolution
  • Photoperiod response
  • Ppd-A1 haplotype
  • Wheat

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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