Abstract
<jats:p>Knowledge of linkage disequilibrium (LD) decay is a prerequisite for designing genomic selection and genome-wide association panels, yet no such characterisation exists for the indigenous goat breeds of Punjab, Pakistan. Using Illumina Caprine 50K SNP Bead Chip genotypes generated from the Punjab goat population previously used for growth and conformation GWAS (Beetal, Barbari, Daira Din Panah, Nachi, Pahari/Kajli, Local Pothwari and Teddi; N = 827 raw, 817 retained after breed-wise quality control), we estimated pairwise composite LD (r²) between SNPs up to 1 Mb apart and characterised its decay across physical distance, chromosome and breed, and summarised overall LD magnitude using the area under the LD-decay curve (AUC, r²×kb, 0–1000 kb). Mean genome-wide LD differed more than ten-fold among breeds, from r² = 0.020 (AUC = 24.5) in Beetal the largest, most numerous commercial breed (N = 588) to r² = 0.208 (AUC = 212.1) in Barbari (N = 23), with Nachi and Daira Din Panah forming a near-identical intermediate high tier (AUC = 134.2 and 134.1) and Local Pothwari, Pahari and Teddi forming a lower tier (AUC = 110.8, 96.2 and 83.5). LD decayed below r² = 0.2 within 20–30 kb in six of the seven breeds but only beyond 500 kb in Barbari; between-breed differences in LD (max r² − min r² at a given distance) were largest approximately 0.20 in the 50–300 kb range and persisted, undiminished, out to 1 Mb. This ranking was reproduced independently on every one of the 30 goat autosomes, and was not attributable to uneven marker coverage: genome-wide SNP density was closely uniform across chromosomes (14.2–17.4 SNPs/Mb, genome mean 16.2 SNPs/Mb), ruling out density as a confound. These results indicate that useful marker density for genomic prediction differs substantially by breed a sparse panel may be adequate for Barbari, whereas Beetal will require a considerably denser panel to capture equivalent haplotype information and that the small sample sizes available for five of the seven breeds should be treated as a caveat when interpreting the absolute, though not the relative, magnitude of LD. This is, to our knowledge, the first genome-wide LD decay analysis reported for Pakistani goat breeds and provides a quantitative baseline for future genomic selection and conservation-genetics work in this population.</jats:p>