Triticeae Genomics and Genetics, 2024, Vol.15, No.4, 221-233 http://cropscipublisher.com/index.php/tgg 228 Another significant advancement is the use of doubled haploid (DH) technology, which accelerates the development of homozygous lines. This technique shortens the breeding cycle and enhances the efficiency of selecting desirable traits. Additionally, recent developments in genome editing technologies, such as CRISPR/Cas9, have opened new possibilities for precisely modifying rye genomes to introduce beneficial traits or remove undesirable ones (Schlegel, 2022). 7.2 Incorporation of wild and ancestral traits The incorporation of traits from wild and ancestral relatives of rye has been a key strategy in breeding programs aimed at enhancing resilience and adaptability. Wild relatives, such as Secale vavilovii and Secale strictum, possess traits that are often lost during domestication but are critical for survival in harsh environments. These traits include enhanced disease resistance, drought tolerance, and cold hardiness. By introgressing these traits into cultivated rye, breeders have been able to produce varieties that are better suited to challenging growing conditions (Maraci et al., 2018). The process of introgression involves crossing cultivated rye with wild relatives and then backcrossing the hybrids with the cultivated parent. Through this process, beneficial alleles from the wild species are incorporated into the cultivated gene pool while retaining the desirable characteristics of the domesticated rye. This approach has been instrumental in developing varieties with improved resistance to diseases such as rusts and smuts, which are major threats to rye crops (Schreiber et al., 2018). 7.3 Marker-assisted selection and genomic selection Marker-assisted selection (MAS) and genomic selection (GS) have revolutionized rye breeding by allowing for the precise selection of desirable traits based on genetic markers. MAS involves the identification of specific genetic markers linked to traits of interest, such as disease resistance or yield. These markers are then used to select individuals that carry the desired alleles, significantly speeding up the breeding process and increasing the accuracy of selection (Sidhu et al., 2019). Genomic selection goes a step further by using genome-wide marker data to predict the breeding value of individuals. This method accounts for the cumulative effects of many small-effect alleles spread across the genome, providing a more comprehensive approach to selection. Genomic selection has been particularly effective in complex traits like yield, where multiple genes contribute to the phenotype. The use of genomic selection in rye breeding has led to the development of varieties with improved performance in various environments, as it enables the selection of individuals that are likely to perform well under a wide range of conditions (Miedaner et al., 2018). The integration of these advanced selection methods with traditional breeding techniques has significantly enhanced the efficiency and effectiveness of rye breeding programs. As a result, modern rye varieties are more resilient, productive, and capable of meeting the demands of contemporary agriculture. The advances in breeding techniques, the incorporation of wild and ancestral traits, and the application of marker-assisted and genomic selection have collectively transformed rye breeding. These innovations continue to play a crucial role in the ongoing effort to improve rye's adaptability, yield, and overall performance in diverse agricultural environments. 8 Challenges in Rye Research and Cultivation Despite the progress in rye (Secale cereale) research and breeding, several challenges remain that impact its cultivation and productivity. These challenges encompass environmental stress, disease resistance, pest management, and socio-economic and policy issues. Addressing these challenges is crucial for ensuring the sustainability and resilience of rye as a vital cereal crop. 8.1 Environmental stress and resilience One of the primary challenges in rye cultivation is managing the impact of environmental stressors, such as drought, extreme temperatures, and soil degradation. Rye is known for its resilience, particularly in poor soils and
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