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

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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.

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Authors and Affiliations

  1. Department of Genomics and Biotechnology, Plant Breeding and Genetics Institute – National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine

    Alexandr Muterko & Irina Balashova

  2. Laboratory of Plant Genomics and Bioinformatics, RSE “National Center for Biotechnology”, Sh. Valikhanov 13/1, Astana, Kazakhstan, 010000

    Ruslan Kalendar

  3. National Institute of Agricultural Botany (NIAB), Huntington Road, Cambridge, CB3 0LE, UK

    James Cockram

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  1. Alexandr Muterko
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  2. Ruslan Kalendar
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  4. Irina Balashova
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Correspondence to Alexandr Muterko.

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Muterko, A., Kalendar, R., Cockram, J. et al. Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. Plant Mol Biol 88, 149–164 (2015). https://doi.org/10.1007/s11103-015-0313-2

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  • DOI: https://doi.org/10.1007/s11103-015-0313-2

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