Triticeae Genomics and Genetics, 2024, Vol.15, No.4, 221-233 http://cropscipublisher.com/index.php/tgg 224 Figure 1 Composition and Structure of the Rye 'Lo7' GenomeAcross Its 7 Chromosomes (Adapted from Rabanus-Wallace et al., 2021) Image caption: The figure includes the distribution of genetic markers, gene density, synteny with the barley genome, and the distribution and activity timeline of LTR retrotransposon families. More than 50% of the chromosome regions lack recombination, with gene density significantly increasing as it approaches the telomeric regions. The synteny map shows that, apart from the genesparse areas around the centromeres, the rye, barley, and wheat genomes maintain high synteny across most regions, indicating that genome expansion is primarily concentrated in the distal regions of the chromosome arms (Adapted from Rabanus-Wallace et al., 2021) 4.3 Population genetics and gene flow studies Population genetics studies have been crucial in unraveling the evolutionary history of rye and its domestication (Sun et al., 2022). These studies have shown that rye maintains a high level of genetic diversity, which is partly due to the continuous gene flow between wild and domesticated populations. This gene flow has allowed rye to retain adaptive traits from its wild relatives, contributing to its resilience in diverse environments (Maraci et al., 2018). Additionally, population structure analyses have revealed distinct genetic clusters within the rye gene pool, corresponding to different geographical regions and cultivation practices. These findings underscore the importance of preserving genetic diversity in rye for future breeding and conservation efforts (Larsson et al., 2019). Maraci et al. (2018) conducted a study analyzing 726 samples from different geographic regions, including cultivated varieties, landraces, wild species, and weedy types. Using SSR markers and sequence diversity analysis of nuclear EST regions, the study revealed the genetic diversity among and within species of the genus Secale and its association with geographic distribution and climatic zones (Figure 2). The research found that the perennial subspecies S. strictum is genetically distinct from other annual species, and there are two significantly different genetic groups between the Asian samples and those from other regions. Gene flow studies have also highlighted the complex interactions between domesticated rye and its wild relatives. The exchange of genetic material between these groups has been a double-edged sword, providing both beneficial traits and potential challenges for rye breeding. For instance, while gene flow has introduced traits that enhance cold tolerance and disease resistance, it has also introduced undesirable traits that complicate breeding efforts
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