Bioscience Methods 2025, Vol.16, No.6, 299-307 http://bioscipublisher.com/index.php/bm 3 02 some results may be significantly influenced by the variety background or environment, and stability also needs to be further confirmed in combination with analytical methods such as RHM (Alvarez et al., 2019). 3.3 Candidate gene approach and gene expression analysis strategies Sometimes, rather than blindly searching for variations across the entire genome, it is better to first identify those genes that are "most suspected". This is the idea behind the candidate gene method. For genes like IL2, IL13, and IFNG, which are known to be related to immune responses, researchers often prioritize analyzing the relationship between their SNP variations and resistance traits (Selvam et al., 2023). However, relying solely on static SNP typing is not enough. To determine whether they actually work or not, the expression levels also need to be analyzed. For instance, by using transcriptome or eQTL methods to compare the genetic differences between confrontational individuals and susceptible individuals, the activity levels in regulatory pathways can be directly observed. In recent years, an increasing number of studies have also attempted to combine GWAS with expression analysis to explore regulatory networks at the system level. In this way, the identified candidate genes are not only "possibly related", but also how they function can be known (Zhang et al., 2024). 4 Key Genetic Markers Associated with Parasite Resistance Traits 4.1 Genes related to immune responses Not all goats react the same way when facing parasites. Some individuals exhibit a stronger immune response, which is closely related to the expression of certain specific genes in their bodies. Cytokines such as IL2, IL4, IL5, IL13 and IFNG are often associated with Th1/Th2 type immune pathways. Their high expression often corresponds to a lower number of fecal eggs, meaning that these goats are more resistant to insects (Mpofu et al., 2022). Of course, immunity is not just about the participation of cytokines. The DRB1 site of MHC Class II, as well as Toll-like receptors such as TLR2, TLR4, and TLR9, have long been proven indispensable in antigen recognition and initiating immunity. Genes like CD1D, ITGA9, IL12A, IL13RA1, CD86, and TGFB2 are not significantly expressed in every sheep, but they recur in individuals classified as resistant populations (Estrada-Reyes et al., 2019; Reyes et al., 2018; 2022). In addition, the activity levels of NOD-like receptors and MAPK pathways in resistant individuals also significantly increased, indicating that the participation of these pathways in overall immune regulation is not low. 4.2 Candidate genes involved in intestinal mucosal barrier function For parasites to enter the body, they first have to pass through a checkpoint - the intestinal mucosa. But not every time can the immune system intervene at the first moment. Sometimes, what actually determines whether the parasite can "enter" or not is this barrier itself. Goats with strong resistance seem to have intestines that are better at "guarding the door". Genes involved in tight junction structures such as ZO-1 and occludin were expressed significantly higher in such individuals, indicating that these genes contribute to maintaining mucosal integrity (Aboshady et al., 2019). Of course, merely locking the door is not enough. If the intestines are damaged, the speed of repair is also crucial. PROM1 is precisely such a restorative role, often "coming to patch up" after tissue damage. C-type lectins such as CLEC4E cannot be ignored either. They are mainly responsible for identifying invading parasites and are part of the early response system (Silva et al., 2018). However, these are not fighting in isolation. Behind them, there is also a relatively "invisible" regulatory network - the TGF-β pathway. In particular, TGF-β1 and TGF-β2 show different manifestations in some resistant individuals. The differences in expression levels may be related to their roles in regulating immune tolerance and maintaining tissue balance. This entire set of mechanisms, to put it bluntly, is like "blocking the door" on one side and "patching the wall" on the other. Only when both actions are carried out simultaneously can the intestines have true resistance. 4.3 Genetic loci related to inflammation regulation and antioxidant defense When goats fight parasites, many of their tissues suffer collateral damage. But not every sheep was equally intense, and there were also genetic factors behind this. Genes like NFKBIA and NFKBID, which regulate the NF-κB pathway, play a "braking" role in regulating the intensity of inflammation. NOS2 (nitric oxide synthase) will "step on the gas" when needed to help eliminate parasites (Silva et al., 2018; Wang et al., 2024). FGFBP1 is also
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