Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Abstract

Loci affecting swine intramuscular fat content, backfat thickness, carcass weight, and daily weight gain were assigned to regions of swine chromosome (SSC) 4, which were shown to correspond to human chromosome (HSA) 1p22→ q25 by ZOO-FISH, bidirectional chromosome painting, as well as by the linkage map of genes. In order to select candidate genes responsible for the above traits from the human genome database, precise correspondence between SSC4 and HSA1 is a prerequisite. In the present study, 27 genes, PTGFR, GBP1, GBP2, GFI1, GCLM, ABCD3, EXTL2, KCNA3, ADORA3, KCND3, WNT2B, NRAS, SYCP1, PTGFRN, IGSF2, NOTCH2, S100A10, SHC1, SSR2, LMNA, CCT3, CD5L, PEA15, FCER1G, EAT2, DDR2, and LAMB3, located in the HSA1 region corresponding to SSC4 or possibly SSC4, were assigned to the IMpRH map. The alignment of genes from centromere to telomere in the SSC4 q arm is basically conserved in HSA1p22→q25 with the direction from the q arm to the p arm, which is in good agreement with results from linkage mapping. In addition, the present study first demonstrated that WNT2B residing in the middle of the HSA1 region was assigned to SSC18 with a high lod score (> 5), and that at least three intrachromosomal rearrangements occurred in the region in the process of swine and human evolution. PTGFR, and LAMB3 localized at both ends of the HSA1 region were assigned to SSC6 and SSC9, respectively, which is consistent with regional correspondence reported earlier. In the course of the above analysis, microsatellite markers were developed in the proximity of eleven genes localized on SSC4, and three genes on other swine chromosomes.

A robust linkage map of the porcine autosomes based on gene-associated SNPs

“…This was done to validate the marker order that was calculated on our map. The previously mapped genes (listed according to the map order) are: PARK2 [37], ENPP1 [38], NTRK3 [39], VLDLR [40], COL15A1 [41], ALDOB [42], C9orf78 [43], CAPN1 [25], CAT [44], RPS13 [45], GNB2L1 [46], TPM4 [25], CKMT2 [47], MEF2C [48], SLC22A5 [16], SAR1B [49], HBEGF [50], HARS [51], NCF1 [52], UQCRC2 [53], ACTG2 [54], KCNS3 [42], ZHX1 [55], EXT1 [56], OXR1 [55], NDUFS2 [55], LMNA [57], CCT3 [58], PMF1 [59], GBA [60], PRKAB2 [61], S100A6 [40], ATP5F1 [53], EDG1 [62], SLC35A3 [63], ATP5B [44], EMP1 [64], NELL2 [64], NFYB [65], NFAT5 [66], TERF2 [53], SIRT2 [67], LGALS4 [67], GMFG [67], FCGRT [68], XRCC1 [27], FUT1 [26], PARK7 [69], MAD2L2 [69], EIF4G3 [69], RPA2 [69], TTR [70], FUBP1 [71], FLOT1 [72], BAT1 [19], HSPA1L [19], ATP6V1G2 [73], COL21A1 [74], RPS18 [75], STK38 [74], MTCH1 [74], GLO1 [74], MUT [76], GSTA3 [74], GZMH [19], CPE [77], FGA [1], UCP3 [44], CRYAB [44], SERPINC1 [78], F13B [24], CTSL2 [79], DCTN3 [80], PTCHD3 [81], GAD2 [82], ITIH2 [83], AKR1C3 [84], HMGB1 [19], MRPS31 [17], INTS6 [85], TOP2B […”

Physiology, Affecting Factors and Strategies for Control of Pig Meat Intramuscular Fat

“…Moreover, another seven additional markers to chromosome 4 removed the 'half-sib' QTL whereas the suggestive QTL affecting IMF content under line cross assumptions was regained [81]. However, other eleven microsatellite markers or candidate genes localized on porcine chromosome 4, affecting IMF content, backfat thickness and other traits [82].…”

SNP identification, linkage and radiation hybrid mapping of the porcine lamin A/C (LMNA) gene to chromosome 4q

“…According to Hiraiwa et al. (2003) an intrachromosomal rearrangement occurred on chromosome 4q in the process of pig and human evolution, in the region harbouring the genes SHC1 , SSR2 , LMNA and the markers SW270 , S0214 and SW1996 .…”