Schneider J F, Nonneman D J, Wiedmann R T, Vallet J L, Rohrer G A
USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933.
USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
J Anim Sci. 2014 Sep;92(9):3792-803. doi: 10.2527/jas.2014-7788. Epub 2014 Jul 1.
Reproductive efficiency has a great impact on the economic success of pork production. Ovulation rate is an early component of reproduction efficiency and contributes to the number of pigs born in a litter. To better understand the underlying genetics of ovulation rate, a genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 1,180 females with ovulation measurements ranging from never farrowed to measurements taken after parity 2. A total of 41,848 SNP were tested using the Bayes C option of GenSel. After the Bayes C analysis, SNP were assigned to sliding windows of 5 consecutive SNP by chromosome-position order beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on SSCX. The 5-SNP windows were analyzed using the Predict option of GenSel. From the Predict analysis, putative QTL were selected having no overlap with other 5-SNP window groups, no overlap across chromosomes, and the highest genetic variation. These putative QTL were submitted to statistical testing using the bootstrap option of GenSel. Of the putative QTL tested, 80 were found to be statistically significant (P < 0.01). Ten QTL were found on SSC1, 12 on SSC2, 4 on SSC3, 8 on SSC4, 3 on SSC5, 3 on SSC6, 3 on SSC7, 4 on SSC8, 2 on SSC9, 4 on SSC10, 1 on SSC12, 4 on SSC13, 2 on SSC14, 4 on SSC15, 4 on SSC16, 6 on SSC17, 4 on SSC18, and 1 on SSCX. Sixteen QTL were found to be statistically significant at the P < 0.001 level. Six additional QTL were significant at the P = 0.001 level. These 22 QTL accounted for 71.10% of the total genetic variance. The most compelling candidate genes in these regions include Estrogen receptor 1, growth differentiation factor 9, and inhibin βA. These QTL, when combined with information on genes found in the same regions, should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.
繁殖效率对生猪生产的经济效益有重大影响。排卵率是繁殖效率的一个早期组成部分，对一窝仔猪的出生数量有影响。为了更好地了解排卵率的潜在遗传学，开展了一项全基因组关联研究。从1180头母猪中采集DNA样本，并使用Illumina猪SNP60芯片进行检测，这些母猪的排卵测量数据范围从不曾产仔到经产2胎之后的测量值。使用GenSel的贝叶斯C选项对总共41848个单核苷酸多态性（SNP）进行了检测。在贝叶斯C分析之后，按照染色体位置顺序将SNP分配到由5个连续SNP组成的滑动窗口中，从SSC1上的前5个SNP开始，到SSCX上的最后5个SNP结束。使用GenSel的预测选项对5-SNP窗口进行分析。从预测分析中，选择了推定的数量性状位点（QTL），这些位点不与其他5-SNP窗口组重叠，不跨染色体重叠，并且具有最高的遗传变异。使用GenSel软件的自助法选项对这些推定的QTL进行统计检验。在检测的推定QTL中，发现80个具有统计学显著性（P < 0.01）。在SSC1上发现10个QTL，SSC2上12个，SSC3上4个，SSC4上8个，SSC5上3个，SSC6上3个，SSC7上3个，SSC8上4个，SSC9上2个，SSC10上4个，SSC12上1个，SSC13上4个，SSC14上2个，SSC15上4个，SSC16上4个，SSC17上6个，SSC18上4个，SSCX上1个。在P < 0.001水平上发现16个QTL具有统计学显著性。另外6个QTL在P = 0.001水平上显著。这22个QTL占总遗传方差的71.10%。这些区域中最有说服力的候选基因包括雌激素受体1、生长分化因子9和抑制素βA。这些QTL与同一区域中发现的基因信息相结合，应该能提供有用的信息，可用于商业猪群的标记辅助选择、标记辅助管理或基因组选择应用。
