杜洛克与二花脸杂交猪群体SNP偏分离分析

偏分离（TRD）是生物中普遍存在的现象，本研究拟在高密度基因芯片判断基因型的大规模群体中挖掘猪基因组标记位点的偏分离位点并探究其潜在的遗传机制。本研究用60K Illumina Porcine SNP芯片对1 020头F2资源家系（杜洛克与二花脸杂交F0-F2群体）进行基因型分型，用偏分离分析软件TRDscan （BF>100）和TDT （P<0.01）方法在单个位点上检测偏分离信号，并对二者共有的显著信号位点附近100 kb窗口的基因进行功能分析。此外，本研究还利用单倍型分型的软件包PHASEBOOK采用多位点连锁分析的策略分析了父源和母源配子中的偏分离区域，并在该区域内搜寻潜在的QTLs。结果表明：1）在单位点的偏分离分析中共鉴定到44个显著的偏分离位点，筛选到23个相关基因；对父本和母本特异性偏分离效应进行分析时，分别鉴定到27和35个显著偏分离位点，其中，分别有11和25个位点的100 kb附近有已注释的功能基因。2）基于单倍型多位点连锁的偏分离结果显示，父本显著偏分离位点位于5和13号染色体上，在该偏分离区域内搜寻功能相关的QTL，共搜寻到3个与繁殖性状（木乃伊数、产活仔数、黄体数）有关的QTLs；分析母本偏分离位点时，在4、6和12号染色体上定位到显著偏分离区域，结合已知的猪QTL数据库，共找到了5个与繁殖性状相关的QTLs。本研究利用大规模猪家系数据系统地鉴别了猪基因组的偏分离位点，为解析猪中的偏分离现象和进一步探究其生物学机制提供了一定的参考作用。

Transmission Ratio Distortion Analysis of SNP in a Duroc×Erhualian Intercross Pigs Population

The phenomenon of transmission ratio distortion (TRD) is commonly observed in many organisms, and the purpose of this study is to excavate isolated porcine genomic marker sites and explore their potential genetic mechanisms in a large population with high density microarray to determine genotype. In this study, 60K Illumina Porcine SNP chip was used to genotype 1 020 F2 resource families (Duroc×Erhualian intercross F0-F2 populations). The transmission ratio distortion signal was detected at a single site by TRDscan (BF>100) and TDT (P<0.01), and the function of genes within 100 kb window near the significant signal site shared by the two were analyzed. In addition, a software package for haplotype typing PHASEBOOK was used to analyze the TRD region on paternal and maternal gametes, and multi-loci linkage analysis was utilized to search for potential QTLs within the region. The results showed that:1) In TRD analysis of single site, 44 significant TRD sites were identified and 23 related genes were screened; 27 and 35 significant TRD loci were identified by analyzing paternal and maternal specific TRD effects, among them, there were annotated functional genes near 100 kb of 11 and 25 loci, respectively. 2) Based on the TRD results of haplotype multi-site linkage, the significant paternal TRD sites were located on chromosome 5 and 13, and functionally related QTLs were searched in this TRD region, then 3 QTLs were found to be related to reproductive traits (number of mummies, number of live litters, and number of corpus luteum); The significant maternal TRD regions were located on chromosome 4, 6 and 12, combined with the known QTL database of pigs, 5 QTLs related to reproductive traits were found. The study used large-scale pig family data to systematically identify the TRD sites of pig genomes, which will provide a certain reference for analyzing the TRD phenomenon in pigs and further exploring its biological mechanism.