运用PRINS和体细胞杂种克隆板对猪新微卫星的定位

本研究采用引物原位DNA合成PRINS)技术,结合体细胞杂种克隆板,将新克隆的猪微卫星HAU02和HAU06定位于1q23-27、6q11-21.并对这两种基因定位方法的优缺点和应用进行了比较和讨论.这对于我国进行猪基因定位工作开展提供了思路;同时,新微卫星的定位为建立猪染色体物理图谱积累了有益的资料.     

人类GABARAPL2基因的染色体定位

为了确定人类GABAA受体相关蛋白相似蛋白2基因在染色体上的位置,根据该基因cDNA的3′非翻译区序列设计一对RH定位引物,以人／鼠体细胞腹辐杂种板Genebridge4(GB4)panel和G3panel试剂盒中的杂种细胞株基因组DNA为模板,在一定的条件下进行PCR扩,琼脂糖凝胶电泳结果分别插入Sanger和Stanford网站的RH定位分析系统进行统计学分析。结果PCR法在一些杂种细胞株中扩增出特异的目的片段,并经测序验证了其准确性。凝胶电泳结果在Sanger网站统计分析表明该基因与16号染色体上的AFM340ye5,AFM292xh5,AFM320wf1,AFMa066xd5,AFM249xc5位标紧密连锁;在Stanford网站统计分析表明该基因片与16号染色体上的SHGC－1457,SHGC－53415,SHGC－6782,SHGC－2228,SHGC－14629位标紧密连锁,LOD值均大于3。整合分析该染色体区带的物理图、遗传图及细胞图谱后,最终将基因定位在染色体16q22.3区带的D16s3016和D16s515位标之间。结论放射杂交定位法是一种新颖便捷的基因定位的方法,通过此法成功地进行了人类GABAA受体相关蛋白相似蛋白2基因的定位。     

人体基因组随机单拷贝顺序的分离及其在染色体上的定位

本文从构建杂种细胞14-7-1的基因组文库出发,用种特异的探针分离出含有人体基因组顺序的重组子,并进一步分析了其中13个克隆,得到8个单拷贝顺序。通过与已建立的杂种细胞克隆分布板杂交以及染色体的原位杂交方法,将1个单拷贝顺序FD11-1定位在11p11-q11上。由于已经报道在11号染色体上具有3个连锁群,它们分别位于11p15、11p13和11q13上,因此,FD11-1有可能为11号染色体连锁基因图的建立提供1个有意义的座位。     

猪电压依赖性阴离子通道1基因的分离及物理定位

从猪胚胎骨骼肌cDNA文库中筛选出一克隆子,通过测序及电子延伸获得包含全长CDS的猪VDAC1基因cDNA序列。比对发现此基因在核苷酸和氨基酸水平与人及小鼠都具有较高的同源性。应用辐射杂种板(RH)对此基因进行染色体的精确定位,定位结果显示VDAC1基因定位在猪2号染色体长臂。     

用放射杂交板定位鸡的MC4R基因以及其在鸡和人染色体上同源区的比较分析

黑素皮质素受体(melanocortin-4 receptor,MC4R)基因的突变与猪、鼠和人等的食欲、肥胖和生长有关联性,然而对鸡的MC4R基因的功能却知之甚少。为了确定鸡的MC4R基因在染色体上的位置,使用鸡-仓鼠杂交板(ChickRH6)做了该基因的定位工作。通过扩增ChickRH6杂交板上的93个样品,然后经整合分析将mC4R基因定位在2号染色体上的标记MCW0062、BCL2和OVY附近,即2q12。这个连锁图上的5个标记基于两点分析与MC4R的LOD值都大于5。同时,以MC4R基因为标记做了鸡和人的染色体比较分析。结果显示鸡的2号染色体(GGA2)和人的18号染色体(HSA18)存在同源区,且基因BCL2和肥胖基因(obesity)位于MC4R基因附近。推测鸡的MC4R基因与人的MC4R基因可能具有相似的功能。该研究揭示了鸡和人MC4R基因的染色体分布,并用杂交放射板将鸡的MC4R基因定位在2号染色体的12区带。     

应用ＣＡＴＳ法分离和鉴定猪ＧＦＡＰ基因的研究

根据比较锚定序列宗踪（ＣＡＴＳ）法,选择人和小鼠胶质细胞原纤维酸性蛋白（ＧＦＡＰ）基因的同源区域设计引,用ＰＣＲ方法从二花脸猪基因组中分离到４１２bp的基因片段,经与基因资料库中已训功能基因的同源性比较,该片段可鉴定为猪的ＧＦＡＰ基因,利用猪－啮齿类体细胞杂克隆板将ＧＦＡＰ基因定位于猪１２号染色体１２p11-(2/3)P13区域。     

水稻EPSP合酶基因的克隆、结构分析和定位

5-烯醇丙酮莽草酸-3-磷酸(EPSP)合酶是芳香族氨基酸合成途径中的一个关键酶, 该基因在植物抗除草剂基因工程中具有重要的应用价值. 根据水稻EPSP合酶基因的EST序列设计探针, 在水稻TAC基因组文库中筛选到16个阳性克隆. 对阳性克隆E11进行亚克隆, 由此获得了由3661核苷酸组成的水稻EPSP合酶基因全序列. 序列分析和同源性比较揭示, 该基因由8个外显子和7个内含子组成. 以窄叶青8号/京系17组合构建的DH群体和分子图谱将水稻EPSP合酶基因定位于水稻第6条染色体的上端.     

猪CDC16基因的电脑克隆

利用与人CDC16基因高度同源的猪的EST BP430622、AJ656153、CJ022837和BP161802成功电脑克隆了猪CDC16基因cD．NA全长,结果表明,该基因cDNA全长为2057b,5’-UTR长119bp,3’-UTR长75bp,猪CDC16蛋白由617个氨基酸组成,与人、鼠和酵母的同源性分别为97．6％,95．3％,38．5％,大鼠和小鼠的同源性最高,其次是猪,然后是人。     

利用传递不平衡分析在多群体中鉴别猪脐疝易感基因

在本实验室前期利用白色杜洛克×二花脸F₂资源家系开展脐疝易感位点全基因组扫描定位的基础上,文章在7号染色体上的SWR1928和10号染色体上的SW830易感标记区域,结合脐疝发病机制在多群体中进行脐疝位置功能候选基因的筛选和易感位点的精细定位。在两个显著关联的微卫星位点区域搜寻到12个位置功能候选基因,采用比较测序法,选取12个候选基因内共计40个SNP位点在白色杜洛克×二花脸资源家系F₂/F₃脐疝群体中进行基因分型,利用Plink v1.07软件对基因型数据进行质量控制和传递不平衡(Transmission disequilibrium test,TDT)分析。结果表明,IL16(Interleukin 16)基因中的g.708C>T位点和CDC73(Cell division cycle 73)基因中的g.10664G>A位点与脐疝的关联性达到显著水平(P<0.05)。对这两个位点在西方商业猪种脐疝患病家系中进行基因分型和TDT验证分析,发现CDC73基因中的g.10664G>A位点仍与猪脐疝呈显著关联(P<0.05)。同时对CDC73基因中与资源家系脐疝呈弱相关的两个SNP位点g.10546A>G和g.10811A>G在西方商业猪种中进行TDT验证分析,发现这两个SNP位点与商业猪种脐疝发生的关联性达到极显著水平(P<0.01)。根据文章的分析结果,结合脐疝发生的生理机制及CDC73基因的生物学功能,推测CDC73基因可能为猪脐疝发生的易感基因。     

一个新的小鼠被毛突变位点（Uncv）的高分辨遗传图谱和物理图谱的构建

迄今为止 ,人们已经发现了 10 0多个影响小鼠和人的毛发发育的基因 ,在以前的研究中 ,Uncv被证实是一个新的影响小鼠被毛的位点 ,具体表现为纯合突变体为无毛 ,杂合突变体表现为稀毛。除此之外 ,纯合的突变体还表现为生长和发育的迟缓。克隆这一突变基因将有助于更好地了解人类毛发发育异常相关的疾病。尽管这一位点已经被定位在小鼠 11号染色体上 ,但是没有该区域的精细遗传图谱和物理图谱直接克隆该基因有一定的难度。利用了两组杂交方式 ,[BALB/c(Uncv/Uncv)×C3H ( / ) ]×BALB/c (Uncv/Uncv)和 [BALB/c (Uncv/Uncv)×C5 7BL/6 ( / ) ]×BALB/c(Uncv/Uncv) ,共 2 0 74个F2代个体 ,通过对 11号染色体上的 16个微卫星标记的基因分型连锁分析 ,最终把该基因定位于11号染色体上位于D11Mit337和D11Mit338之间的约 1.4cM之间的区域。随后 ,利用BAC文库杂交和BAC末端序列PCR锚定的方法 ,构建了由 35个BAC构成的高分辨的BAC重叠群 ,这一高分辨的遗传图谱和物理图谱的构建 ,为进一步克隆这一突变基因打下了基础。     

Rearranged gene order between pig and human in a quantitative trait loci region on SSC3

A quantitative trait locus (QTL) for ovulation rate on chromosome 3 that peaks at 36 cM has been identified in a Meishan-White composite resource population with an additive effect of 2.2 corpora lutea. As part of an effort to identify the responsible gene(s), typing of additional genes on the INRA-University of Minnesota porcine radiation hybrid (IMpRH) map of SSC3 and comparative analysis of gene order was conducted. We placed 52 known genes and expressed sequence tags, two BAC-end sequences and one microsatellite (SB42) on a framework map that fills gaps on previous RH maps. Data were analysed for two-point and multipoint linkage with the IMpRH mapping tool and were submitted to the IMpRH database (http://imprh.toulouse.inra.fr/). Gene order was confirmed for 42 loci residing in the QTL region (spanning c. 17 Mb of human sequence) by using the high-resolution IMpRH2 panel. Carthagène (http://www.inra.fr/internet/departments/MIA/T/CarthaGene) was used to estimate multipoint marker distance and order using all public markers on SSC3 in the IMpRH database and those typed in this study. For the high-resolution map, only data for markers typed in both panels were used. Comparative analysis of human and porcine maps identified conservation of gene order for SSC3q and multiple blocks of conserved segments for SSC3p, which included six distinct segments of HSA7 and two segments of HSA16. The results of this study allow significant refinement of the SSC3p region that contains an ovulation rate QTL.     

Improving the comparative map of porcine chromosome 9 with respect to human chromosomes 1, 7 and 11

Conserved segments have been identified by ZOO-FISH between pig chromosome 9 (SSC9) and human chromosomes 1, 7 and 11. To assist in the identification of positional candidate genes for QTL on SSC9, the comparative map was further developed. Primers were designed from porcine EST sequence homologous to genes in regions of human chromosomes 1, 7 and 11. Porcine ESTs were then physically assigned using the INRA somatic cell hybrid panel (INRASCHP) and the high-resolution radiation hybrid panel (IMpRH). Seventeen genes (PEPP3, RAB7L1, FNBP2, MAPKAPK2, GNAI1, ABCB1, STEAP, AKAP9, CYP51A1, SGCE, ROBO4, SIAT4C, GLUL, CACNA1E, PTGS2, C1orf16 and ETS1) were mapped to SSC9, while GUSB, CPSF4 and THG-1 were assigned to SSC3.     

Assignment of 204 genes localized on HSA17 to a porcine RH (IMpRH) map to generate a dense comparative map between pig and human/mouse

Bi- and uni-directional chromosome painting (ZOO-FISH) and gene mapping have revealed correspondences between human chromosome (HSA) 17 and porcine chromosome (SSC) 12 harboring economically important quantitative trait loci. In the present study, we have assigned 204 genes localized on HSA17 to SSC12 to generate a comprehensive comparative map between HSA17 and SSC12. Two hundred fifty-five primer pairs were designed using porcine sequences orthologous with human genes. Of the 255 primer pairs, 208 (81.6%) were used to assign the corresponding genes to porcine chromosomes using the INRA-Minnesota 7000-rad porcine x Chinese hamster whole genome radiation hybrid (IMpRH) panel. Two hundred three genes were integrated into the SSC12 IMpRH linkage maps; and one gene, PPARBP, was found to link to THRA1 located in SSC12 but not incorporated into the linkage maps. Three genes (GIT1, SLC25A11, and HT008) were suggested to link to SSC12 markers, and the remaining gene (RPL26) did not link to any genes/expressed sequence tags/markers registered, including those in the present study. A comparison of the gene orders among SSC12, HSA17, and mouse chromosome 11 indicates that intra-chromosomal rearrangements occurred frequently in this ancestral mammalian chromosome during speciation.     

Assignment of 117 genes from HSA5 to the porcine IMpRH map and generation of a dense human-pig comparative map

Twenty-two and eight significant quantitative trait loci for economically important traits have been located on porcine chromosomes (SSC) 2q and SSC16 respectively, both of which have been shown to correspond to human chromosome 5 (HSA5) by chromosome painting. To provide a comprehensive comparative map for efficient selection of candidate genes, we assigned 117 genes from HSA5 using a porcine radiation hybrid (IMpRH) panel. Sixty-six genes were assigned to SSC2 and 48 to SSC16. One gene was suggested to link to SSC2 markers and another to SSC6. One gene did not link to any gene, expressed sequence tag or marker in the map, including those in the present investigation. This study demonstrated the following: (1) SSC2q21-q28 corresponds to the region ranging from 74.0 to 148.2 Mb on HSA5q13-q32 and the region from 176.0 to 179.3 Mb on HSA5q35; (2) SSC16 corresponds to the region from 1.4 to 68.7 Mb on HSA5p-q13 and to the region from 150.4 to 169.1 Mb on HSA5q32-q35 and (3) the conserved synteny between HSA5 and SSC2q21-q28 is interrupted by at least two sites and the synteny between HSA5 and SSC16 is also interrupted by at least two sites.     

Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping

Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and G?ttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs. Received: 19 December 2000 / Accepted: 28 February 2001     

Assignment of 128 genes localized on human chromosome 14q to the IMpRH map

To provide a gene-based comparative map and to examine a porcine genome assembly using bacterial artificial chromosome-based sequence, we have attempted to assign 128 genes localized on human chromosome 14q (HSA14q) to a porcine 7000-rad radiation hybrid (IMpRH) map. This study, together with earlier studies, has demonstrated the following. (i) 126 genes were incorporated into two SSC7 RH linkage groups by C artha G ene analysis. (ii) In the remaining two genes, TOX4 linked to TCRA located in SSC7 by two-point analysis, whereas SIP1 showed no significant linkage with any gene/marker registered in the IMpRH Web Server. (iii) In the two groups, the gene clusters located from 19.9 to 36.5 Mb on HSA14q11.2-q13.3 and from 64.0 to 104.3 Mb on HSA14q23-q32.33 respectively were assigned to SSC7q21-q26. (iv) Comparison of the gene order between the present RH map and the latest porcine sequence assembly revealed some inconsistencies, and a redundant arrangement of 16 genes in the sequence assembly.     

A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17

Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering approximately 4836.9 cR12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is approximately 15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering approximately 2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.     

A first-generation EST RH comparative map of the porcine and human genome

We have constructed a first-generation EST radiation hybrid comparative map of the porcine genome by assigning 1058 markers to the IMpRH7000 panel. Chromosomal localization was determined with a 2pt LOD of 4.8 for 984 markers, using the IMpRH mapping tool. Annotated ESTs represent 46.2% or 489 of the markers. Marker distribution was not stochastic and ranged from 0.41 for SSC8 to 1.77 for SSC12, respectively. Two hundred fifty-one markers assigned to the physical map of the pig did not find a homologous sequence in V22 of the human genome assembly, indicative of gaps in the assembled human genome sequence. The comparative porcine/human map covers 3290 MB, or 98.3% of the presumed size of the human genome. However, 60 breakpoints were identified between chromosomes, as well as 90 micro-rearrangements within synteny groups. Six porcine chromosomes—SSC2, 5, 6, 7, 12, and 14—correspond to the three gene-richest human chromosomes, HSA17, 19, and 22, and show above average marker density. Porcine Chrs 1, 8, 11, and X display a low DNA/marker ratio and correspond to the 'genome deserts' on HSA 18, 4, 13, and X.     

Assignment of 64 genes expressed in 28-day-old pig embryo to radiation hybrid map

A swine resource family was constructed at the National Institute of Animal Industry, Japan, in order to determine the genetic regions responsible for economically important traits, including fetus development. To identify genes expressed in the early stage of embryo development, we cataloged and mapped genes expressed in a 28-day-old normal pig embryo. In this effort, we have mapped 64 genes, which have map information in human genome onto a swine radiation hybrid (RH) map, IMpRH. These mappings provided additional chromosomal homologies between swine and human to improve the comparative map between the two species. The distribution of the genes assigned to swine chromosomes are as follows: 9 genes were assigned on SSC6; 6 genes each assigned on SSC5 and SSC14; 5 genes each assigned on SSC3, SSC4, and SSC8; 4 genes each assigned on SSC1, SSC7, SSC9, and SSC15; 3 genes each assigned on SSC2, SSC13 and SSCX; and 1 gene each assigned on SSC10, SSC11, and SSC16. Moreover, the present findings revealed 18 new chromosomal homologies between pig and human. Briefly, SSC3 regions were indicated to correspond with HSA1 and HSA10; SSC4 with HSA6; SSC5 with HSA2, HSA15, and HSA16; SSC6 with HSA3, HSA6, and HSA20; SSC7 with HSA11; SSC8 with HSA3, HSA6, and HSA7; SSC9 with HSA8; SSC13 with HSA1; SSC14 with HSA13; SSC15 with HSA19; SSC16 with HSA9. Received: 19 December 2000 / Accepted: 13 March 2001     

High-resolution comprehensive radiation hybrid maps of the porcine chromosomes 2p and 9p compared with the human chromosome 11

We are constructing high-resolution, chromosomal 'test' maps for the entire pig genome using a 12,000-rad WG-RH panel (IMNpRH2(12,000-rad))to provide a scaffold for the rapid assembly of the porcine genome sequence. Here we present an initial, comparative map of human chromosome (HSA) 11 with pig chromosomes (SSC) 2p and 9p. Two sets of RH mapping vectors were used to construct the RH framework (FW) maps for SSC2p and SSC9p. One set of 590 markers, including 131 microsatellites (MSs), 364 genes/ESTs, and 95 BAC end sequences (BESs) was typed on the IMNpRH2(12,000-rad) panel. A second set of 271 markers (28 MSs, 138 genes/ESTs, and 105 BESs) was typed on the IMpRH(7,000-rad) panel. The two data sets were merged into a single data-set of 655 markers of which 206 markers were typed on both panels. Two large linkage groups of 72 and 194 markers were assigned to SSC2p, and two linkage groups of 84 and 168 markers to SSC9p at a two-point LOD score of 10. A total of 126 and 114 FW markers were ordered with a likelihood ratio of 1000:1 to the SSC2p and SSC9p RH(12,000-rad) FW maps, respectively, with an accumulated map distance of 4046.5 cR(12,000 )and 1355.2 cR(7,000 )for SSC2p, and 4244.1 cR(12,000) and 1802.5 cR(7,000) for SSC9p. The kb/cR ratio in the IMNpRH2(12,000-rad) FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH(7,000-rad) FW maps was 47.1 and 36.3, respectively, or an approximately 3.0-fold increase in map resolution in the IMNpRH(12,000-rad) panel over the IMpRH(7,000-rad) panel. The integrated IMNpRH(12,000-rad) andIMpRH(7,000-rad) maps as well as the genetic and BAC FPC maps provide an inclusive comparative map between SSC2p, SSC9p and HSA11 to close potential gaps between contigs prior to sequencing, and to identify regions where potential problems may arise in sequence assembly.