Genomic and Conventional Inbreeding Coefficient Estimation Using Different Estimator Models in Korean Duroc, Landrace, and Yorkshire Breeds Using 70K Porcine SNP BeadChip

The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated an...

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Bibliographic Details
Published in:Animals (Basel) 2024-09, Vol.14 (17), p.2621
Main Authors: Mekonnen, Kefala Taye, Lee, Dong-Hui, Cho, Young-Gyu, Son, Ah-Yeong, Seo, Kang-Seok
Format: Article
Language:English
Subjects:
Animals
correlation
Genetic engineering
Genomes
genomics
Genotype & phenotype
Haplotypes
Hogs
inbreeding coefficient
Livestock
pedigree
pig breed
Quality control
run of homozygosity
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Summary:The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between F total and F , showing that short ROH were the primary contributors to overall F values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (F ) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes.
ISSN:2076-2615
2076-2615
DOI:10.3390/ani14172621