Contribution of All Single Nucleotide Polymorphisms (SNPs) and Minor Allele Frequency Groups to Genetic Variation of Quantitative Traits in Suffolk Sheep

Subject Areas : Camel

A. Taheri Yeganeh ¹ , M.R. Sanjabi ² , J. Fayazi ³ , M. Zandi ⁴ , J. Van der Werf ⁵

1 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
2 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
3 - Department of Animal Science, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Khuzestan, Iran
4 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
5 - School of Environmental and Rural Science, University of New England, Armidale, Australia

Received: 2023-05-23 Accepted : 2023-08-11 Published : 2023-12-01

Keywords: genomic selection, Bayesian method, genomic variance, Suffolk sheep, joint analysis,

Abstract :

Accurate estimation of genetic and non-genetic variance components with pedigree and genomic information is essential for the correct prediction of breeding values. Single nucleotide polymorphisms (SNPs) from Australian Suffolk sheep were used in this research (50K illumine). The characteristics of birth weight, weaning weight, length, and diameter of the wool warp were investigated. To study the relationship between allelic frequency and the amount of additive genetic variance explained. The SNPs were classified into five different groups of rare allelic frequency (MAF). Two statistical models were fitted a separate and joint analysis of each SNPs group statistical analyses were performed with the Bayesian method using the Gibbs sampling technique and the RKHS model (semiparametric method). The amount of genomic heritability estimated by all SNPs in the Bayesian approach were estimated as 0.46, 0.19, 0.75, and 0.48 for the traits of birth weight, weaning weight, length, and wool diameter, respectively. The total heritability estimated for different groups of rare allele frequencies, in the combined analysis were almost similar to the value obtained from all SNPs for all traits. Although the numbers of SNPs in different groups were similar, the amounts of genetic variance explained by MAF groups were different. For the two traits of birth weight and weaning weight, the first group with an allelic frequency of 0.01-0.1 had the highest amount of genomic heritability. The amount of genomic heritability of fibre diameter was variable in five MAF groups. The highest estimated value in the fifth group with rare allele frequency was 0.4-0.5 (about 0.21), and the lowest value was in the third group (0.2-0.3), which was estimated at 0.098. The staple length trait, the genetic variance distribution pattern justified by SNPs, fluctuated between the five MAF groups, and the heritability value varied from zero in the second and fourth groups to about 0.16 in the third group.

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