Molecular Pathogens 2024, Vol.15, No.3, 142-154 http://microbescipublisher.com/index.php/mp 144 pathogens like Sphaeropsis sapinea, which causes Diplodia tip blight. This disease leads to significant shoot dieback, reducing tree vigor and growth. Managing these impacts requires a comprehensive approach, integrating disease monitoring, genetic resistance breeding, and sustainable forest management practices to maintain forest health and resilience (Pandit et al., 2020). 3 Identification and Collection of Disease Resistance Genes 3.1 Sources of resistance genes Resistance genes in pine species are primarily sourced from natural populations that exhibit varying levels of disease resistance. These genes often originate from individuals or populations that have survived severe disease outbreaks, suggesting an inherent genetic resistance. For instance, in sugar pine (Pinus lambertiana), the Cr1 gene has been identified as providing significant resistance to white pine blister rust (WPBR) caused by Cronartium ribicola (Wright et al., 2022). Similarly, in Masson pine (Pinus massoniana), genes associated with resistance to pine wilt disease (PWD) caused by the pine wood nematode (Bursaphelenchus xylophilus) have been identified through transcriptomic analyses, which highlight differentially expressed genes linked to resistance mechanisms (Liu et al., 2017). Wild populations of limber pine (Pinus flexilis) and southwestern white pine (Pinus strobiformis) have also been valuable sources of resistance genes. Studies have shown that these species harbor major resistance genes (Cr3 and Cr4) that confer resistance to WPBR. These genes have been found to be conserved across species, indicating a shared evolutionary response to the pathogen (Liu et al., 2021). Additionally, loblolly pine (Pinus taeda) has been a critical source of resistance genes for fusiform rust, with nine identified pathotype-specific resistance genes (Fr genes) mapped to its genome (Amerson et al., 2015). 3.2 Techniques for gene identification The identification of disease resistance genes in pines involves a combination of classical genetics, molecular biology, and advanced genomic techniques. One common approach is Quantitative Trait Loci (QTL) mapping, which helps identify regions of the genome associated with disease resistance traits. This technique was effectively used to identify SNPs linked to WPBR resistance in sugar pine and southwestern white pine (Weiss et al., 2020). Another powerful method is Genome-Wide Association Studies (GWAS), which analyze the entire genome to find genetic variations linked to resistance traits. This method has been instrumental in identifying NLR genes associated with resistance in limber pine (Liu et al., 2019). Transcriptomic analyses are also widely used to identify genes differentially expressed in response to pathogen infection. For instance, RNA sequencing (RNA-seq) has been employed to profile gene expression in resistant and susceptible pine species, revealing key regulatory genes and pathways involved in disease resistance. In Masson pine, transcriptomic profiling identified genes involved in oleoresin biosynthesis and reactive oxygen species (ROS) scavenging as crucial for resistance to PWD (Liu et al., 2017). In addition, targeted sequencing of specific gene families, such as the NLR gene family, has been utilized to pinpoint resistance genes. This approach has led to the identification of multiple NLR genes in limber pine that co-segregate with resistance traits (Liu et al., 2021). Furthermore, bioinformatic mining of transcriptomic data has identified pathogenesis-related (PR) genes in western white pine that play roles in quantitative disease resistance (Liu et al., 2021). 3.3 Gene collection and storage The collection and storage of resistance genes involve several steps to ensure the preservation and availability of genetic resources for breeding programs. Initially, resistance genes are identified and validated through field trials and molecular assays. Once confirmed, seeds or tissues from resistant individuals are collected. For instance, seeds from sugar pine trees carrying the Cr1 gene are collected and used in breeding programs to propagate resistant trees (Wright et al., 2022).
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