Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat

Demissew Sertse; Jemanesh K Haile; Ehsan Sari; Valentyna Klymiuk; Amidou N'Diaye; Curtis J Pozniak; Sylvie Cloutier; Sateesh Kagale

doi:10.1002/tpg2.20410

Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat

Plant Genome. 2023 Nov 16:e20410. doi: 10.1002/tpg2.20410. Online ahead of print.

Authors

Demissew Sertse^{1

2}, Jemanesh K Haile^{3

4}, Ehsan Sari⁵, Valentyna Klymiuk³, Amidou N'Diaye³, Curtis J Pozniak³, Sylvie Cloutier⁶, Sateesh Kagale¹

Affiliations

¹ Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada.
² Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
³ Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
⁴ Canola Council of Canada, Crop Production and Innovation, Saskatoon, SK, Canada.
⁵ Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA.
⁶ Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.

PMID: 37974527
DOI: 10.1002/tpg2.20410

Abstract

Tetraploid wheats (Triticum turgidum L.), including durum wheat (T. turgidum ssp. durum (Desf.) Husn.), are important crops with high nutritional and cultural values. However, their production is constrained by sensitivity to environmental conditions. In search of adaptive genetic signatures tracing historical selection and hybridization events, we performed genome scans on two datasets: (1) Durum Global Diversity Panel comprising a total of 442 tetraploid wheat and wild progenitor accessions including durum landraces (n = 286), domesticated emmer (T. turgidum ssp. dicoccum (Schrank) Thell.; n = 103) and wild emmer (T. turgidum ssp. dicoccoides (Korn. ex Asch. & Graebn.) Thell.; n = 53) wheats genotyped using the 90K single nucleotide polymorphism (SNP) array, and (2) a second dataset comprising a total 121 accessions of nine T. turgidum subspecies including wild emmer genotyped with >100 M SNPs from whole-genome resequencing. The genome scan on the first dataset detected six outlier loci on chromosomes 1A, 1B, 3A (n = 2), 6A, and 7A. These loci harbored important genes for adaptation to abiotic stresses, phenological responses, such as seed dormancy, circadian clock, flowering time, and key yield-related traits, including pleiotropic genes, such as HAT1, KUODA1, CBL1, and ZFN1. The scan on the second dataset captured a highly differentiated region on chromosome 2B that shows significant differentiation between two groups: one group consists of Georgian (T. turgidum ssp. paleocolchicum A. Love & D. Love) and Persian (T. turgidum ssp. carthlicum (Nevski) A. Love & D. Love) wheat accessions, while the other group comprises all the remaining tetraploids including wild emmer. This is consistent with a previously reported introgression in this genomic region from T. timopheevii Zhuk. which naturally cohabit in the Georgian and neighboring areas. This region harbored several adaptive genes, including the thermomorphogenesis gene PIF4, which confers temperature-resilient disease resistance and regulates other biological processes. Genome scans can be used to fast-track germplasm housed in gene banks and in situ; which helps to identify environmentally resilient accessions for breeding and/or to prioritize them for conservation.

© 2023 National Research Council Canada and The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America. Reproduced with the permission of the Minister of Innovation, Science and Industry.