Silió L, Rodríguez M C, Fernández A, Barragán C, Benítez R, Óvilo C, Fernández A I
Departamento de Mejora Genética Animal, INIA, Madrid, Spain.
J Anim Breed Genet. 2013 Oct;130(5):349-60. doi: 10.1111/jbg.12031. Epub 2013 Jan 31.
Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi-generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP-derived metrics of homozygosity (r = 0.814-0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality-checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.
以纯合基因型或纯合子片段在常染色体基因组中所占比例来衡量的多位点纯合性，与使用猪60K SNP芯片进行基因分型的64头伊比利亚猪各自的系谱近亲繁殖系数进行了比较。这些猪来自一组实验动物，它们出生于一个封闭品系，具有较大的近亲繁殖变异，并且有多代完整记录的系谱。根据系谱计算的个体近亲繁殖系数与不同的基于SNP的纯合性指标高度相关（r = 0.814 - 0.919）。然而，在染色体水平上观察到分子近亲繁殖与系谱近亲繁殖之间的相关性并不相等，这主要取决于SNP的数量以及不同位点间杂合性的相关性。选择了一组192个中等频率的SNP对322头仔猪进行基因分型，以测试断奶后生长性能（日增重和90日龄体重）上的近亲繁殖衰退情况。根据168个经过质量检查的SNP基因型计算得出的纯合性对这些性状的负面影响与近亲繁殖系数的影响相似。结果表明，当种群结构或交配系统导致近亲繁殖存在较大差异时，几百个SNP可能有助于衡量近亲繁殖和近亲繁殖衰退。
