Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 56-65 http://cropscipublisher.com/index.php/tgg 62 Additionally, the domestication of barley has involved changes in morphological features, such as seed size and inflorescence architecture. The identification of genes like SIX-ROWED SPIKE 1 (VRS1) and INTERMEDIUM-C (INT-C), which are involved in these morphological changes, underscores the genetic modifications that have occurred during domestication. These genes have been linked to variations in lateral spikelet fertility, further illustrating the genetic impact of domestication on barley (Ramsay et al., 2011). 4.2 Nucleotide diversity analysis of specific genes or genomic regions The impact of domestication on nucleotide diversity can be further understood by analyzing specific genes or genomic regions. For instance, the Rrs2 scald resistance gene region in barley showed more nucleotide diversity in wild barley compared to cultivated barley, with three distinct haplotype groups detected across samples from different countries and regions (Fu, 2012). This indicates that domestication has led to a reduction in genetic diversity in this specific genomic region. The analysis of single nucleotide polymorphisms (SNPs) in barley conducted by Russell et al. (2011) revealed significant chromosome-level differences in diversity around domestication genes, indicating that certain genomic regions have been more affected by domestication than others. This study also provided evidence that hybridization serves as a mechanism for the continued adaptation of landrace barley under cultivation conditions (Russell et al., 2011). Moreover, a study on the genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes found that domesticated regions on chromosomes 5H, 1H, and 7H had higher diversity ratios compared to non-domesticated regions (Yan et al., 2015). This indicates that domestication has led to a more pronounced reduction in nucleotide diversity in specific genomic regions associated with domestication traits (Yan et al., 2015). 4.3 Comparative study on the effects of domestication on nucleotide diversity in barley Domestication has led to significant genetic differentiation between wild and cultivated barley. A study using over 1 000 single nucleotide polymorphisms (SNPs) in geographically matched samples of landrace and wild barley from Jordan and Syria revealed clear genetic differentiation between the two groups, with limited secondary contact (Russell et al., 2011). This differentiation is indicative of the genetic bottleneck that occurred during domestication, which reduced nucleotide diversity in cultivated barley. The impact of domestication on nucleotide diversity varies across different chromosomal regions. Yan et al. (2015) investigated the genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes and found that chromosome 5H exhibited the highest divergence, with a 35.29% reduction in diversity, followed by chromosomes 3H, 7H, 4H, 2H, and 6H. This study emphasizes that domesticated regions generally show a higher loss of diversity compared to non-domesticated regions, with an average diversity reduction of 33.73% in domesticated regions versus 27.56% in non-domesticated regions. Domestication has also affected gene regulation and expression in barley. An investigation into the contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress conditions found that most genes have conserved regulation, with a notable absence of trans effects (Haas et al., 2020). This stability in gene regulation suggests that domestication has not drastically altered the regulatory mechanisms in barley, although the overall sequence diversity has been reduced. Comparative studies with other crops, such as common bean and wheat, provide additional insights into the effects of domestication on nucleotide diversity. For instance, domestication in common bean resulted in a 60% loss of nucleotide diversity and an 18% reduction in gene expression diversity (Bellucci et al., 2014). Similarly, wheat experienced a significant reduction in nucleotide diversity, with bread wheat losing 69% and durum wheat losing 84% of its diversity during domestication. These findings underscore the common trend of reduced genetic diversity following domestication across different crop species.
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