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The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny

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Abstract

Wheat belongs to the most important crops domesticated in the Fertile Crescent. In this region, fortunately, locally adapted wheat landraces are still present in farmers’ fields. This material might be of immense value for future breeding programs. However, especially wheat germplasm adapted to the central part of the Fertile Crescent has been poorly characterized for allelic variation at key loci of agricultural importance. Grain hardness is an important trait influencing milling and baking quality of wheat. This trait is mainly determined by three tightly linked genes, namely, Puroindoline a (Pina), Puroindoline b (Pinb), and Grain softness protein-1 (Gsp-1), at the Hardness (Ha-D) locus on chromosome 5DS. To investigate genetic diversity and haplotype structure, we resequenced 96 diverse wheat lines at Pina-D1, Pinb-D1, Gsp-A1, Gsp-B1, and Gsp-D1. Three types of null alleles were identified using diagnostic primers: the first type was a multiple deletion of Pina-D1, Pinb-D1, and Gsp-D1 (Pina-D1k), the second was a Pina-D1 deletion (Pina-D1b); and the third type was a deletion of Gsp-D1, representing a novel null allele designated here as Gsp-D1k. Sequence analysis resulted in four allelic variants at Pinb-D1 and five at Gsp-A1, among them Gsp-A1-V was novel. Pina-D1, Gsp-B1 and Gsp-D1 sequences were monomorphic. Haplotype and phylogenetic analysis suggested that (1) bread wheat inherited its 5DS telomeric region probably from wild diploid Ae. tauschii subsp. tauschii found within an area from Transcaucasia to Caspian Iran; and that (2) the Ha-A and Ha-B homoeoloci were most closely related to sequences of wild tetraploid T. dicocco ides. This study provides a good overview of available genetic diversity at Pina-D1, Pinb-D1, and Gsp-1, which can be exploited to extend the range of grain texture traits in wheat.

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Acknowledgments

We thank Frank Blattner for discussions, Birgit Kränzlin for excellent technical support and the sequencing services at IPK Gatersleben and at Max-Planck Institute for Plant Breeding Research Cologne for their excellent job. The authors would like to acknowledge the financial support given by TÜBİTAK (The Scientific and Technological Research Council of Turkey, TOVAG-107O207) and by IPK Gatersleben.

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Author notes

  1. Rajiv Sharma

    Present address: College of Life Science, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK

  2. Benjamin Kilian

    Present address: Bayer CropScience NV, Innovation Center, BCS Breeding & Trait Development, Technologiepark 38, 9052, Zwijnaarde (Gent), Belgium

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, OT Gatersleben, Germany

    Salar Shaaf, Rajiv Sharma, Helmut Knüpffer & Benjamin Kilian

  2. Department of Agronomy and Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, P.O. Box 618, Sanandaj, Iran

    Salar Shaaf

  3. Department of Field Crops, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey

    Faheem Shehzad Baloch & Hakan Özkan

  4. N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow, 119991, Russia

    Ekaterina D. Badaeva

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  1. Salar Shaaf
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Correspondence to Benjamin Kilian or Hakan Özkan.

Additional information

Communicated by S. Hohmann.

B. Kilian and H. Özkan shared last authors.

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Sequence data have been deposited in GenBank Data library under accession numbers KC585009–KC585020 (Table 2).

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Shaaf, S., Sharma, R., Baloch, F.S. et al. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny. Mol Genet Genomics 291, 1259–1275 (2016). https://doi.org/10.1007/s00438-016-1180-5

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