Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

Abstract

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes

“…Therefore, the A and B subgenomes between bread wheat and European spelt had higher sequence divergence, while the D subgenome showed greater sequence similarity (Blatter et al, 2004;Dvorak et al, 2012). Our observation of the separation of α-gliadin sequences in PI190962 from those of other bread wheats in Gli-A2 and Gli-B2-1 supports that this Central European spelt accession had an introgressed origin with a tetraploid emmer wheat, which was recently shown to be distinct from the origins of Iberian spelt (Abrouk et al, 2021). This result also indicates that the introgressed loci from chromosome 6B of emmer wheat may be confined to the region encoding Gli-B2-1, further supporting a different evolutionary history for the two Gli-B2 loci identified in this study.…”

Induction of useful mutations in Triticum aestivum in the conditions of the radionuclide-contaminated alienation zone of the Chornobyl Power Plant

“…Detection of anthocyanin colour on various organs of the plants in the process of ontogenesis is a reaction of plants to unfavourable abiotic and biotic environmental factors, which may correlate with the level of radionuclide contamination and degree of adaptation to ionizing radiation (Guscha et al, 2002;Shoeva et al, 2017;Shoeva & Khlestkina, 2018). The red colour of organs of plants is controlled by a number of genes: R c -determines the colour of coleoptile, R a -colour of the leaf base and the "ears" of the leaf axil, P an -anthers in blossom phase, P c -colour of the stem in the early period of ripening of seeds, R g and R -colours of ear scales and grains (Hlestkina, 2012;Jiang et al, 2018;Jia et al, 2020;Abrouk et al, 2021). Emergence of distinct mutants with squareheaded, speltoid and erectoid ears is related to deletion, deletion-duplication, translocation, microabberations in the fifth chromosome of А genome, which contains locus Q (Konopatskaia et al, 2016;Simonov et al, 2017).…”

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

“…However, the large (approximately 16 gigabase (Gb)), repeat-rich genome of polyploid bread wheat remains a challenge for genome sequencing and gene cloning projects. A comparison of the genomes of various bread wheat cultivars demonstrated their high tolerance for extensive structural rearrangements, introgressions from wild wheat relatives and differences in gene content 7 , 8 , highlighting the need to generate genomic resources from specific donor wheat lines to guide the cloning of agronomically important genes. Stripe rust (or yellow rust), caused by the fungal pathogen Puccinia striiformis f. sp.…”