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

Autor: Mulugeta B; Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.; Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.; Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia., Ortiz R; Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden., Geleta M; Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden., Hailesilassie T; Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia., Hammenhag C; Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden., Hailu F; Bio and Emerging Technology Institute, Addis Ababa, Ethiopia., Tesfaye K; Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.; Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia.
Jazyk: angličtina
Zdroj: Frontiers in plant science [Front Plant Sci] 2023 Jul 20; Vol. 14, pp. 1192356. Date of Electronic Publication: 2023 Jul 20 (Print Publication: 2023).
DOI: 10.3389/fpls.2023.1192356
Abstrakt: 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 ( r 2 > 0.20, P < 0.01), with an average r 2 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.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Mulugeta, Ortiz, Geleta, Hailesilassie, Hammenhag, Hailu and Tesfaye.)
Databáze: MEDLINE
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