Triticeae Genomics and Genetics, 2024, Vol.15, No.4, 221-233 http://cropscipublisher.com/index.php/tgg 223 3.3 Comparison with domestication of other cereals The domestication of rye presents some interesting contrasts when compared to the domestication of other major cereals such as wheat and barley. While wheat and barley were among the founder crops of early Neolithic agriculture, domesticated rye emerged later as a secondary crop. This is largely due to its initial status as a weed rather than a primary food source (Schreiber et al., 2022). In contrast to the complex hybridization and polyploidy that characterized wheat domestication, rye’s domestication involved more straightforward selection processes focused on enhancing traits that improved its survival in marginal environments (Matei et al., 2020). Another notable difference is the genetic diversity retained in rye compared to other cereals. Due to the gene flow between wild and domesticated populations, rye has maintained a higher level of genetic diversity, which continues to be a valuable resource for breeding programs aimed at improving crop resilience and productivity (Maraci et al., 2018). This contrasts with crops like wheat, where domestication and intensive breeding have led to a significant reduction in genetic diversity. The domestication of rye, therefore, highlights a unique evolutionary path characterized by gradual adaptation to environmental pressures and human agricultural practices, making it one of the most resilient cereals cultivated today. 4 Genetic and Genomic Insights The field of rye (Secale cereale) research has advanced significantly with the development of genomic tools and resources, allowing for a deeper understanding of the genetic mechanisms underlying its domestication and adaptation. These insights are critical for improving rye's agricultural performance and for breeding programs aimed at enhancing its resilience. 4.1 Genomic tools and resources in rye research The advent of high-throughput sequencing technologies has revolutionized rye research, enabling the assembly of comprehensive genome maps and the identification of key genetic regions associated with important traits. One of the most significant milestones in rye genomics was the assembly of a chromosome-scale genome, which provides a detailed blueprint of rye's genetic architecture. This resource has been instrumental in understanding rye's complex genome, which is characterized by large amounts of repetitive DNA and structural variations (Rabanus-Wallace et al., 2019). Additionally, the development of genotyping-by-sequencing (GBS) techniques has facilitated large-scale genetic studies, allowing researchers to analyze genetic diversity and population structure across different rye varieties and wild relatives (Schreiber et al., 2018). Rabanus-Wallace et al. (2021) annotated and validated the 790-million-base-pair rye genome (Figure 1), demonstrating its applicability across various research fields such as the mechanisms of incomplete genetic isolation between rye and its wild relatives, genome structure evolution, pathogen resistance, cold tolerance, and fertility control systems in hybrid breeding. The study's findings not only highlight rye's potential as a climate-resilient crop in agricultural improvement but also provide essential genetic resources and data to support future rye breeding and its hybridization with wheat. 4.2 Genetic markers and domestication traits Genetic markers have played a crucial role in identifying and understanding the traits that were selected during rye’s domestication. Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are among the most commonly used markers in rye research (Targonska-Karasek et al., 2020). These markers have been used to map quantitative trait loci (QTL) associated with key domestication traits such as seed size, shattering resistance, and cold tolerance (Miedaner et al., 2018). For example, QTL mapping has identified genomic regions linked to traits like drought tolerance and disease resistance, which are vital for rye’s adaptation to different environmental conditions (Sidhu et al., 2019). These markers not only enhance our understanding of rye domestication but also provide valuable tools for marker-assisted selection in breeding programs.
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