On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn Wheat

Abstract

Einkorn and emmer wheat together with barley were among the first cereals domesticated by humans more than 10,000 years ago, long before durum or bread wheat originated. Domesticated einkorn wheat differs from its wild progenitor in basic morphological characters such as the grain dispersal system. This study identified the Non-brittle rachis 1 (btr1) and Non-brittle rachis 2 (btr2) in einkorn as homologous to barley. Re-sequencing of the Btr1 and Btr2 in a collection of 53 lines showed that a single non-synonymous amino acid substitution (alanine to threonine) at position 119 at btr1, is responsible for the non-brittle rachis trait in domesticated einkorn. Tracing this haplotype variation back to wild einkorn samples provides further evidence that the einkorn progenitor came from the Northern Levant. We show that the geographical origin of domesticated haplotype coincides with the non-brittle domesticated barley haplotypes, which suggest the non-brittle rachis phenotypes of einkorn and barley were fixed in same geographic area in today's South-east Turkey.

Keywords: agricultural origins; domestication; einkorn; non-brittle rachis; wheat.

FIGURE 1

Wheat spike showing the brittle rachis of wild einkorn (Tb) accession KT1-1 (Left) and non-brittle rachis of domesticated einkorn (Tm) accession KT3-5 (Right).

FIGURE 2

QTL mapping for rachis brittleness in einkorn wheat. The mean (across two seasons) rachis brittleness score was used to represent the trait in the analysis. The horizontal line represents the LOD threshold. The btr1 (dCAPS), k03461, and k07581 are molecular markers linked to the QTLs.

FIGURE 3

Comparison of orthologous Btr1/Btr2 loci from wild barley OUH602 (Upper, accession KR813335, Pourkheirandish et al., 2015) and bread wheat cultivar Chinese Spring (CS) A genome (Lower, accession MG324346, this study). Btr1 and Btr1-like are marked by black arrows, Btr2 and Btr2-like by gray arrows, while Ψ is a pseudogene sharing some homology with Btr2.

FIGURE 4

BTR1 peptide alignment of wild diploid and tetraploid wheat and wild barley. The A119 residue is conserved across the species except for Tm. The two predicted transmembrane helices are indicated by boxes. Wheat 2X_BTR1-Tb stands for Tb accession KT1-1, Wheat 2X_BTR1-Tm stands for Tm accession KT3-5, Wheat 4X_BTR1-A and -B T. turgidum ssp. dicoccoides ‘Zavitan’, and Barley_BTR1-A is wild barley OUH602.

FIGURE 5

The origin of the btr1 allele found in domesticated einkorn wheat. (A) The eleven recognized Btr1 haplotypes found in Tm (three haplotypes)and Tb (eight haplotypes). Identical nucleotides are shown in the first line as dots. The A119T amino acid substitution caused non-brittle phenotype in Tm. (B) A phylogenetic analysis of Btr1 based on nucleotide sequence spanning the Btr1 coding sequence plus 750 bp upstream and 900 bp downstream of the coding sequence. Wheat 4X_Btr1-A and -B T. turgidum ssp. dicoccoides ‘Zavitan’ (A and B genome) formed the paraphyletic outgroup. Domesticated haplotypes are indicated by underline. Local bootstrap values after 1000 replicates are indicated near the branches.

FIGURE 6

The origin of the Btr2 allele found in domesticated einkorn wheat. (A) The 16distinct Btr2 haplotypes found in Tm (three haplotypes) and Tb (14 haplotypes), of which one (B2_Hap14) is represented in both genepools. Identical nucleotides are shown in the first line as dots. (B) A phylogenetic analysis of Btr2 based on nucleotide sequence spanning the Btr2 coding sequence plus 350 bp upstream and 650 bp downstream of the coding sequence. Wheat 4X_Btr1-A and -B T. turgidum ssp. dicoccoides ‘Zavitan’ (A and B genome) formed the paraphyletic outgroup. Cultivated haplotypes are indicated by underline. Local bootstrap values after 1000 replicates are indicated near the branches.

FIGURE 7

Domesticated einkorn originated in the Northern Levant. The GIS-based map of the Fertile Crescent indicates the collection sites of wild einkorn accessions analyzed in this study. Two wild einkorn lines equally closest to domesticated einkorn types at Btr1 and Btr2 are indicated by black dots. KT, Kartal–Karadaǧ; KK, Karacadaǧ mountains are indicated with stars. The archeological site of Tell Qaramel is indicated with plus sign.