QTL Mapping On Porcine Chromosome 3, 4 And 7 And Isolation, Identification Of Six Candidate Genes

With the applications of DN A marker technologies to the field of pig breeding, the molecular breeding techniques including the marker-assisted selection (MAS) and marker-assisted introgression (MAI) have emerged. The use of molecular markers combining with traditional breeding methods accelerated the progress of genetic improvement in pigs. The basis of MAS or MAI was to seek the major gene or marker which contributed genetically much to the target traits. Linkage mapping and candidate gene approach are two main methods of identifying major gene controlling quantitative traits. In this study, the pig reference family of three generations was established by mating three LargeWhite boars to seven Meishan sows. One hundred and forty F2 offspring were phenotyped for carcass traits and meat quality traits. All animals were genotyped for twenty-four microsatellites on Sus scrofa chromosome (SSC) 3, 4 and 7. Using CRIMAP software, the linkage map of these chromosomes was constructed. Least square regression interval mapping was used for QTL detection. Meanwhile, based on QTL mapping results, pig and human comparative map and physiological or biochemical functions of gene, six candidate genes were selected from human chromosome 1, 3, 17 and 19, of which five were novel genes in pigs. These genes were isolated and identified with comparative genomics and bioinformatic approaches, etc. Association studies of the gene polymorphisms with production traits were performed and expression patterns of these genes in different tissues were also investigated. The main results are as follows:(1) In this population, average allele number of twenty-four microsatellites was 3.6, average informative meiosis 235, average heterozygosity and polymorphic information content 0.531 and 0.463, respectively. The lengths of sex-average linkage map of SSC3,4 and 7 were 161cM, 178.5cM, 179.1cM, respectively, and the corresponding average marker intervals were 20.1cM, 29.9cM and 24.9cM, respectively. The linkage map of these chromosomes in female were longer than in male. In all cases but one, map order of the markers was the same as that in the USDA-MARC map. The exception was a switch in order for SSC4 between SW841 and SW270.(2) In the present study, the population was subjected to QTL analysis for thirty-five traits. In all, seventeen QTL were detected at 5% chromosome-wise level, of which five were significant at the 1% chromosome-wise level. (1) For birth weight and live carcass traits, significant QTL at 5% chromosome-wise level for BWT were detected on SSC3 and SSC7; QTL affecting LLEH and LBFT2 were found on SSC4, which reached 5% and 1% chromosome-wise level, respectively. (2) For carcass traits, significant QTL at the chromosome-wise level for SP, BFT and LFW were detected on SSC4, of which QTL for SP and BFT3 reached 1% chromosome-wise level. Evidence also revealed significant QTL affecting LEA, BP, LFW and RNS on SSC7, of which RNS QTL reached 1% chromosome-wise level. (3) For meat quality traits, the most convincing result in theanalysis was evidence for a QTL affecting WM on SSC3, for which the chromosome significant level of 1% was obtained. Significant QTL at 5% chromosome-wise level affecting pH(SC) were localized to SSC4 and SSC7, respectively. Furthermore, there was suggestive evidence for a QTL on SSC4 affecting IMF that nearly approached the 5% chromosome-wise significance threshold. (4) Under two QTL model analysis, there existed two QTL influencing LFW on SSC4, and their additve and dominance effects were opposite.(3) The cDNA fragments of FHL3 gene including complete open reading frame (ORF) of Large White, Landrace, Duroc and Meishan breeds were isolated by reverse transcription polymerase chain reactions (RT-PCR) and the nucleotide sequences of the fragments were obtained with cloning and sequencing. The nucleotide sequence of Landrace breed has been deposited GenBank under accession number AY277587. Four introns of porcine FHL3 were amplified from genomic DNA of Landrace and Meishan breed and the resulting over...