Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool

Behailu Mulugeta; Rodomiro Ortiz; Mulatu Geleta; Teklehaimanot Hailesilassie; Cecilia Hammenhag; Faris Hailu; Kassahun Tesfaye

doi:10.3389/fpls.2023.1192356

Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool

Front Plant Sci. 2023 Jul 20:14:1192356. doi: 10.3389/fpls.2023.1192356. eCollection 2023.

Authors

Behailu Mulugeta^{1

2

3}, Rodomiro Ortiz², Mulatu Geleta², Teklehaimanot Hailesilassie¹, Cecilia Hammenhag², Faris Hailu⁴, Kassahun Tesfaye^{1

5}

Affiliations

¹ Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
² Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
³ Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia.
⁴ Bio and Emerging Technology Institute, Addis Ababa, Ethiopia.
⁵ Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia.

Abstract

Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r² > 0.20, P < 0.01), with an average r² of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the F_st outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.

Keywords: domestication; durum wheat; landraces; nucleotide diversity; polymorphic information content; selection signature; single nucleotide polymorphisms.

Grants and funding

The study was funded by the Swedish International Development Cooperation Agency (Sida) grant awarded to Addis Ababa University and the Swedish University of Agricultural Sciences for a bilateral capacity-building program in biotechnology. The funding information is available on “https://sida.aau.edu.et/index.php/biotechnology-phdprogram/; accessed on May 21, 2022”. The funders played no role in the design of the study, data collection, analysis, decision to publish, or preparation of the manuscript.