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In higher plants, seed storage proteins (SSPs) are frequently expressed from complex gene families, and allelic variation of SSP genes often affects the quality traits of crops. In common wheat, the  Glu-D1  locus, encoding 1Dx and 1Dy SSPs, has multiple alleles. The  Glu-D1d  allele frequently confers superior end-use qualities to commercial wheat varieties. Here, we studied the haplotype structure of  Glu-D1  genomic region and the origin of  Glu-D1d . Using seven diagnostic DNA markers, 12  Glu-D1  haplotypes were detected among common wheat, European spelt wheat ( T. spelta , a primitive hexaploid relative of common wheat), and  Aegilops tauschii  (the D genome donor of hexaploid wheat). By comparatively analyzing  Glu-D1  haplotypes and their associated  1Dx  and  1Dy  genes, we deduce that the haplotype carrying  Glu-D1d  was likely differentiated in the ancestral hexaploid wheat around 10,000 years ago, and was subsequently transmitted to domesticated common wheat and  T. spelta . A group of relatively ancient  Glu-D1  haplotypes was discovered in  Ae. tauschii , which may serve for the evolution of other haplotypes. Moreover, a number of new  Glu-D1d  variants were found in  T. spelta . The main steps in  Glu-D1d  differentiation are proposed. The implications of our work for enhancing the utility of  Glu-D1d  in wheat quality improvement and studying the SSP alleles in other crop species are discussed.

Haplotype Variation of Glu-D1 Locus and the Origin of Glu-D1d Allele Conferring Superior End-Use Qualities in Common Wheat