Genomic Identification of Markers Associated with Gastrointestinal Nematode Resistance in Black Bengal Goats of West Bengal for Marker-Assisted Selection and Sustainable Breed Improvement

Gastrointestinal nematode (GIN) infections constitute one of the most important constraints to sustainable goat production in tropical and subtropical regions, causing substantial economic losses through reduced growth, impaired reproduction, anemia, and increased mortality. The Black Bengal goat, the predominant indigenous goat breed of West Bengal, India, is renowned for its prolificacy, adaptability, meat quality, and disease tolerance; however, the genetic basis of resistance to GIN infections remains poorly understood. The present study aimed to identify genomic regions and candidate genes associated with GIN resistance in Black Bengal goats using a genome-wide association study (GWAS) approach.A total of 150 Black Bengal goats aged 6–12 months were sampled from major agro-climatic zones of West Bengal, India. Phenotypic evaluation included fecal egg count (FEC), packed cell volume (PCV), FAMACHA© score, and body condition score (BCS). Animals were genotyped using the Illumina GoatSNP50 BeadChip. Following quality control, 41,752 SNPs and 142 animals were retained for analysis. GWAS was performed using a mixed linear model accounting for age, sex, location, season, and population structure.Substantial phenotypic variation in parasite resistance was observed, with FEC ranging from 0 to 7,200 eggs per gram (EPG). Resistant goats (n = 46) exhibited significantly lower FEC (320 ± 145 EPG) and higher PCV (30.2 ± 3.1%) compared with susceptible animals (2,980 ± 520 EPG and 19.3 ± 3.5%, respectively; p < 0.001). Genome-wide analysis identified 17 significant SNPs associated with FEC, with major loci located on chromosomes 2, 4, 7, 11, and 18. Candidate genes included TLR4, MUC13, IL4/IL13, SOCS3, and IFNGR1 , which are involved in innate immunity, Th2-mediated immune responses, cytokine regulation, macrophage activation, and mucosal barrier integrity. Functional enrichment analysis revealed significant overrepresentation of immune system processes, inflammatory responses, defense against parasites, and epithelial differentiation pathways. KEGG pathway analysis highlighted Toll-like receptor signaling, cytokine–cytokine receptor interaction, and JAK–STAT signaling as key mechanisms underlying host resistance. Validation of the top SNPs in an independent population confirmed seven markers significantly associated with resistance traits. Goats carrying three or more favorable alleles exhibited a 70% lower risk of high parasite burden (OR = 0.30; 95% CI: 0.15–0.61).The strong correlations between favorable alleles, reduced FEC (r = − 0.65; p < 0.001), and improved PCV (r = 0.61; p < 0.001) demonstrate the practical utility of these markers for selection programs. The identified genomic regions provide the first comprehensive evidence of genetic resistance to GIN infections in Black Bengal goats of West Bengal and offer valuable tools for marker-assisted selection, reduced anthelmintic dependence, and the development of climate-resilient, sustainable goat production systems.