Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.
BMC Genet. 2010 Nov 1;11:97. doi: 10.1186/1471-2156-11-97.
A variety of analysis approaches have been applied to detect quantitative trait loci (QTL) in experimental populations. The initial genome scan of our Duroc x Pietrain F2 resource population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model.
In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR) significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15.
Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.
多种分析方法已被应用于实验群体中检测数量性状基因座（QTL）。我们的杜洛克×皮特兰 F2 资源群体的最初基因组扫描包括 510 只 F2 动物，它们使用 124 个微卫星标记进行基因分型，并使用线交模型进行分析。第二次扫描时，对 954 只 F2 动物进行了 9 条染色体上的 20 个额外标记的基因分型，对 444 只额外的 F2 动物进行了第一次扫描中使用的 20 个标记的基因分型。第二次扫描应用了三种最小二乘孟德尔 QTL 分析模型：线交模型、半同胞模型和组合线交和半同胞模型。
总共使用线交模型检测到 26 个 QTL，使用半同胞模型检测到 12 个 QTL，使用组合线交和半同胞模型检测到 3 个额外的 QTL，这些 QTL 用于生长性状，具有 5%的错误发现率（FDR）显著水平。在线交分析中，在 SSC6 上检测到 10、13、16、19 和 22 周龄脂肪沉积的高度显著 QTL。在半同胞分析中，在 SSC7 上检测到 19 周龄腰肌肉面积的 QTL，在 SSC15 上检测到 19 和 22 周龄第 10 肋骨背膘的 QTL。
额外的标记和动物有助于缩小置信区间并增加 QTL 检测的检验统计量。不同的模型允许检测到新的 QTL，表明在亲本品种中替代等位基因的频率不同。
