Brym P, Sazanov A A, Kaminski S
Genetika. 2011 May;47(5):651-9.
A total of 312 boars (201 Landrace and 111 Large White) were genotyped with a custom-made low throughput genotyping microarray (called SNiPORK) based on array primer extension (APEX) technology. The results were used to association studies between genotyped SNP markers and daily gains, meat content and selection index. Among the 60 SNP markers analyzed, 14 of them showed statistically significant associations between the genotype and the level of at least one trait. In order to find extremely beneficial or unfavorable intergenic diplotype combinations, 5 SNP markers were selected: CASTA499C, MYF6 T255C, PKLR C384T, SFRSI C1146T and TNNT3T 153C, which showed statistically significant associations at P<or=0.01 within one of the traits and the frequency of homozygotes with a minor allele of at least 0.1. Among 10 possible permutations, statistically significant associations were found only for a combination of SNP markers in TNNT3 x SFRSI genes and, interestingly, for all combinations with SNP located within the calpastatin (CAST) gene commonly known as a gene influencing pork quality traits. This study also found that CAST allele A (which is beneficial for pork tenderness) is also favorable for growth rate. This effect is clearly increased with additive alleles C of myogenic factor MYF6 and troponin T3 (TNNT3) and is decreased with each allele Tfrom serine rich splicing factor 1 (SFRS1) gene. For meat content, the most favorable genotype of calpastatin gene was AC, the effect of which was generally increased with each C allele of MYF6 and TNNT3 and decreased with each allele T from SFRSl and PKLR (puruvate kinase) genes, respectively. The calpastatin AC genotype seemed to be beneficial for selection index, although in combination with the CC genotype of troponin T3, calpastatin genotypes AA and CC reached higher values. In the case of the combination of genotypes TNNT3 x SFRS1, the most preferable for all analyzed traits is the CC genotype of TNNT3, especially in combination with CTor CC genotypes in the SFRS1 gene. We conclude that searching for interaction effects between candidate SNPs (even of moderate influence) may lead to interesting and valuable findings enabled better understanding and applications of SNPs in pork yield and quality improvement programmes.
共有312头公猪（201头长白猪和111头大白猪）使用基于引物延伸技术（APEX）定制的低通量基因分型微阵列（称为SNiPORK）进行基因分型。结果用于基因分型的单核苷酸多态性（SNP）标记与日增重、肉含量和选择指数之间的关联研究。在分析的60个SNP标记中，其中14个在基因型与至少一个性状水平之间显示出统计学上的显著关联。为了找到极其有益或不利的基因间双倍型组合，选择了5个SNP标记：CASTA499C、MYF6 T255C、PKLR C384T、SFRSI C1146T和TNNT3T 153C，它们在P≤0.01时与其中一个性状以及次要等位基因纯合子频率至少为0.1的情况下显示出统计学上的显著关联。在10种可能的排列中，仅在TNNT3×SFRSI基因中的SNP标记组合中发现了统计学上的显著关联，有趣的是，对于与通常被称为影响猪肉品质性状的钙蛋白酶抑制蛋白（CAST）基因内的SNP的所有组合也发现了显著关联。本研究还发现，CAST等位基因A（有利于猪肉嫩度）对生长速度也有利。这种效应随着肌生成因子MYF6和肌钙蛋白T3（TNNT3）的加性等位基因C明显增强，而随着富含丝氨酸剪接因子1（SFRS1）基因的每个等位基因T而降低。对于肉含量，钙蛋白酶抑制蛋白基因最有利的基因型是AC，其效应通常随着MYF6和TNNT3的每个C等位基因而增强，分别随着SFRSl和PKLR（丙酮酸激酶）基因的每个等位基因T而降低。钙蛋白酶抑制蛋白AC基因型似乎对选择指数有益，尽管与肌钙蛋白T3的CC基因型组合时，钙蛋白酶抑制蛋白基因型AA和CC达到更高值。在TNNT3×SFRS1基因型组合的情况下，对于所有分析性状最优选的是TNNT3的CC基因型，特别是与SFRS1基因中的CT或CC基因型组合时。我们得出结论，寻找候选SNP之间的相互作用效应（即使影响程度适中）可能会带来有趣且有价值的发现，有助于更好地理解SNP在猪肉产量和品质改良计划中的应用。
