International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.5, 241-251 http://ecoevopublisher.com/index.php/ijmeb 245 5 Molecular Markers and Breeding Techniques 5.1 Description of molecular markers used in fig research Molecular markers are essential tools in plant genetics and breeding, providing insights into genetic diversity, trait inheritance, and the domestication process. In fig research, several types of molecular markers have been employed, including restriction fragment length polymorphisms (RFLPs), microsatellites, and single nucleotide polymorphisms (SNPs). These markers are polymorphic, meaning they exhibit variation at specific loci within the genome, which can be used to distinguish between different genotypes (Beuzen et al., 2000). Recent advancements in next-generation sequencing (NGS) technologies have significantly enhanced the development and application of molecular markers. Techniques such as genotype-by-sequencing (GBS) and whole genome resequencing allow for the identification of thousands to millions of SNPs across the genome, providing a comprehensive view of genetic variation (García and Piñero, 2017; Ramesh et al., 2020). These high-throughput methods facilitate the discovery of functional markers (FMMs) that are directly associated with traits of interest, thereby improving the efficiency of breeding programs (Ramesh et al., 2020). 5.2 Breeding markers that promote ideal traits Molecular markers play a crucial role in breeding programs by enabling marker-assisted selection (MAS). MAS involves using DNA markers to select plants with desirable traits, thereby accelerating the breeding process and increasing the precision of selection. For instance, SNP markers identified through GBS can be used to map quantitative trait loci (QTL) associated with important agronomic traits such as yield, disease resistance, and stress tolerance (Li et al., 2022). The integration of molecular markers with traditional breeding techniques allows for the efficient exploitation of genetic diversity. By identifying and selecting for specific alleles associated with desirable traits, breeders can develop new cultivars with improved performance and adaptability (Charcosset and Moreau, 2004). This approach has been particularly effective in addressing complex traits that are controlled by multiple genes, as it allows for the simultaneous selection of multiple loci (Eathington et al., 2007). Moreover, molecular markers facilitate the study of domestication and evolutionary history by revealing patterns of genetic diversity and selection. For example, genomic regions with signatures of selection can be identified, providing insights into the genetic changes that occurred during domestication (Geleta and Ortiz, 2016). This information is valuable for understanding the genetic basis of domestication syndrome traits and for guiding future breeding efforts to enhance crop performance and resilience. 6 Role of Epigenetics in Fig Domestication 6.1 Overview of epigenetic factors influencing fig characteristics Epigenetics, the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence, plays a crucial role in the domestication of figs (Ficus carica L.). Epigenetic mechanisms such as DNA methylation and histone modifications can significantly influence phenotypic traits by regulating gene expression. In figs, genome-wide analysis has revealed high levels of DNA methylation in both genes and transposable elements, indicating that epigenetic modifications are prevalent and potentially influential in fig domestication (Usai et al., 2019). Epigenetic diversity can compensate for the loss of genetic diversity, which is particularly important in domesticated species that often undergo bottlenecks and reduced genetic variation due to selective breeding (Dar et al., 2022). This diversity can influence various traits, including growth, stress tolerance, and reproductive success, by modulating gene expression in response to environmental cues (Jensen, 2015; Shi and Lai, 2015). 6.2 Case studies demonstrating the impact of epigenetics Several studies have highlighted the impact of epigenetics on the domestication of various species, providing insights that are applicable to figs. For instance, in soybean domestication, differentially methylated regions (DMRs) were identified, which exhibited higher genetic diversity and were associated with important metabolic pathways (Shen et al., 2018). In figs, the high-quality genome reference and methylation profiles
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