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

Salar Shaaf, Rajiv Sharma, Faheem Shehzad Baloch, Ekaterina D. Badaeva, Helmut Knüpffer, Benjamin Kilian, Hakan Özkan

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)1259-1275
Number of pages17
JournalMolecular Genetics and Genomics
Volume291
Issue number3
DOIs
Publication statusPrint publication - 1 Jun 2016
Externally publishedYes

Fingerprint

Hardness
Phylogeny
Haplotypes
Triticum
Transcaucasia
Alleles
Tetraploidy
Bread
Iran
Diploidy
Breeding
Sequence Analysis
Proteins
Chromosomes
Genes

Keywords

  • Aegilops
  • Domestication
  • Fertile Crescent
  • Genetic diversity
  • Grain softness protein
  • Hardness locus
  • Phylogeny
  • Puroindoline
  • Triticum

Cite this

Shaaf, Salar ; Sharma, Rajiv ; Baloch, Faheem Shehzad ; Badaeva, Ekaterina D. ; Knüpffer, Helmut ; Kilian, Benjamin ; Özkan, Hakan. / 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. In: Molecular Genetics and Genomics. 2016 ; Vol. 291, No. 3. pp. 1259-1275.
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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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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. / Shaaf, Salar; Sharma, Rajiv; Baloch, Faheem Shehzad; Badaeva, Ekaterina D.; Knüpffer, Helmut; Kilian, Benjamin; Özkan, Hakan.

In: Molecular Genetics and Genomics, Vol. 291, No. 3, 01.06.2016, p. 1259-1275.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - 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

AU - Shaaf, Salar

AU - Sharma, Rajiv

AU - Baloch, Faheem Shehzad

AU - Badaeva, Ekaterina D.

AU - Knüpffer, Helmut

AU - Kilian, Benjamin

AU - Özkan, Hakan

PY - 2016/6/1

Y1 - 2016/6/1

N2 - 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.

AB - 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.

KW - Aegilops

KW - Domestication

KW - Fertile Crescent

KW - Genetic diversity

KW - Grain softness protein

KW - Hardness locus

KW - Phylogeny

KW - Puroindoline

KW - Triticum

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DO - 10.1007/s00438-016-1180-5

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EP - 1275

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