Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 56-65 http://cropscipublisher.com/index.php/tgg 61 correlation between adaptive genes and these traits is essential for improving crop performance and resilience (Haudry et al., 2007). The knowledge of adaptive genes and their regulation can be applied in crop breeding to enhance desirable traits. For instance, genes regulated in cis are more likely to be expressed consistently in new genetic backgrounds, making them valuable targets for crop improvement using wild relatives (Haas et al., 2020). This approach can help in developing barley varieties with improved stress tolerance and yield. Haas et al. (2020) compared the transcriptional level differences between unidirectional and bidirectional non coding RNAs using two different statistical methods, limma and binary, under both cold and hot conditions. The study revealed the expression patterns of these genes under different conditions by comparing the differences in cis regulation and possible trans regulation, as well as the data from the control group and the cold treatment group . It was found that cis regulated genes have characteristics such as stability, predictability, and direct effects. 3.3 The impact of domestication on the genome structure of barley Domestication has led to changes in the genome structure of barley, including alterations in recombination rates and genomic variation. The reduction in genetic diversity due to bottlenecks and selection has impacted the overall genomic landscape, with certain regions showing higher divergence between wild and domesticated forms (Yan et al., 2015). The domestication process has also resulted in changes in chromosome structure. Comparative studies have shown that domesticated barley exhibits different patterns of genetic diversity across chromosomes, with some regions experiencing more significant changes than others (Yan et al., 2015). These structural changes can influence gene expression and the overall adaptability of the crop. Copy number variation (CNV) and gene expression are also affected by domestication. The loss of nucleotide diversity can impact regulatory elements, leading to changes in the expression balance of gene isoforms. For example, domesticated sorghum shows less variation in isoform expression balance compared to its wild relatives, suggesting that domestication can lead to more homogenous gene expression patterns (Ranwez et al., 2017). 4 Case Analysis of the Impact of Domestication on Nucleotide Diversity in Barley 4.1 Research cases on domestication of barley at home and abroad The domestication of barley (Hordeum vulgare) has been a subject of extensive research, revealing significant insights into the genetic and evolutionary consequences of this process. Domestication has led to a marked reduction in nucleotide diversity, a phenomenon observed in various studies. The study conducted by Kilian et al. (2026) examined the haplotype structure of seven barley genes and compared them with the haplotypes at the same loci of 25 wild forms collected within and outside the Fertile Crescent. The research found a significant reduction in nucleotide diversity in domesticated barley, with the number of haplotypes dropping from 70 in wild forms to 17 in domesticated lines. This reduction was attributed to bottlenecks during domestication and subsequent breeding processes, which significantly decreased genetic diversity at most loci. The research by Smýkal et al. (2018) on genetic changes during crop domestication has highlighted the broader implications of these processes. Domestication often involves selective sweeps, where favorable haplotypes are retained around selected genes, leading to a genetic valley with extremely low genetic diversity. This phenomenon has been observed in barley, where selection for traits such as seed size and retention has resulted in reduced genetic diversity. The study also noted that genetic bottlenecks during domestication or founding events, as crops moved away from their centers of origin, further altered gene pools, contributing to the reduced nucleotide diversity observed in domesticated barley.
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