Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 56-65 http://cropscipublisher.com/index.php/tgg 60 genome-scale properties of sub-populations in barley, revealing distinct genomic variations between oriental and occidental barley populations (Takahagi et al., 2016). 3 Impact of Domestication on Nucleotide Diversity in Barley 3.1 The impact of domestication on genetic diversity of barley Domestication has significantly affected the genetic diversity of barley. Research shows that compared with wild barley, the nucleotide diversity of domesticated barley has been significantly reduced. For example, the genetic diversity loss between wild barley and domesticated cultivated barley varies with different chromosomes, and the difference of 5H chromosome is the largest, which is 35.29% (Table 1) (Yan et al., 2015). This reduction in diversity is consistent with the research results of other crops such as wheat and rice, where domestication leads to a significant reduction in genetic variation (Haudry et al., 2007; Zhu et al., 2007). Table 1 Genetic diversity and diversity ratio in domesticated and non-domesticated gene regions of barley chromosomes (Adapted from Yan et al., 2015) Chromosome Domestication or not Wild types Cultivated types Diversity Ratio (%) 1H Domesticated region 0.613 0.379 38.24 Undomesticated region 0.762 0.615 19.30 2H Domesticated region 0.542 0.407 24.83 Undomesticated region 0.842 0.635 24.61 3H Domesticated region 0.515 0.611 -18.77 Undomesticated region 0.744 0.485 34.91 4H Domesticated region 0.757 0.519 31.44 Undomesticated region 0.811 0.550 32.22 5H Domesticated region 0.482 0.231 52.06 Undomesticated region 0.638 0.443 30.53 7H Domesticated region 0.464 0.277 40.27 Undomesticated region 0.815, 0.603 26.04 Average domesticated region Domesticated region 0.558 0.370 33.73 Average undomesticated Undomesticated region 0.741 0.536 27.56 Note: diversity ratio = (diversity of wild type - diversity of cultivated type)/diversity of wild typex100% (Adapted from Yan et al., 2015) The domestication process often involves genetic bottlenecks, which result in a reduced effective population size and a loss of genetic diversity. In barley, this bottleneck effect is evident, with significant reductions in genetic diversity observed in domesticated regions of the genome (Yan et al., 2015). Similar bottlenecks have been documented in other crops, such as maize and rice, where the founding populations during domestication were relatively small, leading to a severe reduction in genetic diversity (Tenaillon et al., 2004, Zhu et al., 2007). Genetic drift and selection pressure during domestication have further shaped the genetic landscape of barley. The reduction in effective population size due to bottlenecks increases the impact of genetic drift, altering genotype frequencies and reducing overall diversity (Smýkal et al., 2018). Additionally, selection for agronomically important traits has led to directional selection at specific loci, further reducing genetic diversity in domesticated barley(Tenaillon et al., 2004; Beissinger et al., 2015). 3.2 The impact of domestication on the adaptive genes of barley Domestication has also influenced the adaptive genes in barley. The process has led to changes in gene regulation and expression, particularly in response to environmental stresses. For example, studies have shown that domestication has resulted in a reduction of sequence diversity in genes and regulatory regions, impacting the expression of adaptive genes under stress conditions (Haas et al., 2020). Adaptive genes play a crucial role in determining crop yield, quality, and other important traits. The selection of favorable haplotypes around these genes during domestication has created genetic valleys with low diversity, which can affect traits such as grain softness and end-use quality (Haudry et al., 2007). Understanding the
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