Pigmentation traits expressed in animals are visual characteristics that allow us to distinguish between breeds and between strains within breed. The objective of this study was to map quantitative trait loci （QTLs）...Pigmentation traits expressed in animals are visual characteristics that allow us to distinguish between breeds and between strains within breed. The objective of this study was to map quantitative trait loci （QTLs） affecting the pigmentation traits in approximately 800 F2 grand daughter dairy cattle from a Holstein-Friesian and Jersey cross breed cattle. Traits analyzed included pigmentation phenotypes on the body, teat and hoop. The phenoypes were collected from digital photos or visual inspection of live animals. QTL mapping was implemented using half-sib and line-of-descent inheritance models. Our analysis initially detected a number of significant QTLs on chromosomes： 2, 6, 13, 15, 18 and 22. The significant QTLs were divided into two groups： one group influencing the pigmentation color and the other group affecting the absence or level of pigmentation. The most significant QTL peaks were observed on Bovine taurus autosome 18 （BTA18） close to melanocortin 1 receptor （MC1R） for the color traits, on BTA6 close to the receptor tyrosine kinase （K/T） and BTA22 close to microphthalmia-associated transcription factor （M/TF） gene for the spotting traits. Association studies were conducted for candidate regions or genes known to affect pigmentation in dairy cattle.展开更多
目的综合分析强直性脊柱炎(ankylosing spondylitis,AS)家系的全基因组扫描基因定位的结果,探讨进一步研究和确定AS的遗传易感位点的思路和方法。方法采用基因组寻证荟萃分析(genome search meta analysis,GSMA)法,对符合该方法分析的4...目的综合分析强直性脊柱炎(ankylosing spondylitis,AS)家系的全基因组扫描基因定位的结果,探讨进一步研究和确定AS的遗传易感位点的思路和方法。方法采用基因组寻证荟萃分析(genome search meta analysis,GSMA)法,对符合该方法分析的4个AS家系的全基因组扫描结果包括参数连锁分析和非参数连锁分析的结果进行分析。根据连锁分析的最大值被赋值并按降序排列,从而计算出总的等级分值(Rsumrnk)。根据每个研究的受累个体数进行加权GSMA对结果进行修正。本研究共有479个家系,1151例AS患者。总的等级分析概率(Psumrnk)和有序的等级分析概率(Pord)<0.05被认为可能含有易感区域;GSMA Psumrnk<0.000417时,被认为在全基因组连锁中有显著意义。结果GSMA显示10组结果的Psumrnk和Pord均小于0.05,表明这些组内最可能含有AS的易感基因位点,这些组分别是6.2、16.3、6.1、3.3、6.3、16.4、10.5、17.1、2.5、2.9。GSMA生成的具有显著意义的全基因组连锁分析的证据位于6p22.3-p21.1(BIN6.2,Psumrnk<0.000417),包含HLA位点。结论本GSMA研究进一步证实了HLA位点是AS的主要易感区域,并初步提供非HLA区域包括16q,3p,10q,2p,17p和2q证据。展开更多
An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases w...An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear family. The importance of this generalization lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. The algorithm runs in O（m^3n^3） time, where m is the number of single nucleotide polymorphism （SNP） loci under consideration and n is the number of genotyped members in the pedigree. This zero-recombination haplotyping algorithm is extended to a maximum parsimoniously haplotyping algorithm in one whole genome scan to minimize the total number of breakpoint sites, or equivalently, the number of maximal zero-recombination chromosomal regions. We show that such a whole genome scan haplotyping algorithm can be implemented in O（m^3n^3） time in a novel incremental fashion, here m denotes the total number of SNP loci along the chromosome.展开更多
Background Hereditary spastic paraplegia （HSP） is a group of inherited neurodegenerative disorders with the shared characteristics of slowly progressive spasticity and weakness of the lower limbs. Thirteen loci for ...Background Hereditary spastic paraplegia （HSP） is a group of inherited neurodegenerative disorders with the shared characteristics of slowly progressive spasticity and weakness of the lower limbs. Thirteen loci for autosomal dominant HSP have been mapped. Methods A Chinese family with HSP was found in the Shandong province and Inner Mongolia Autonomous Region of China and genomic DNA of all 19 family members was isolated. After exclusion of known autosomal dominant loci, a genome wide scan and linkage analysis were performed. Results The known autosomal dominant loci of SPG3A, SPG4, SPG6, SPG8, SPG9, SPG10, SPG12, SPG13, SPG17, SPG19, SPG29, SPG31 and SPG33 were excluded by linkage analysis. The results of a genome wide scan demonstrated candidate linkage to a locus on chromosome 11 p14.1-p11.2, over an 18.88 cM interval between markers D11 S1324 and D11 S1933. A maximal, two point LOD score of 2.36 for marker D11S935 at a recombination fraction （e） of 0 and a multipoint LOD score of 2.36 for markers D11S1776, D11S1751, D11S1392, D11S4203, D11S935, D11S4083, and D11S4148 at θ=0, suggest linkage to this locus. Conclusion The HSP neuropathy in this family may represent a novel genetic entity, which will facilitate discovery of this causative gene.展开更多
基金supported by grants from Livestock Improvement Corporation (LIC) as part of the Boviquest project
文摘Pigmentation traits expressed in animals are visual characteristics that allow us to distinguish between breeds and between strains within breed. The objective of this study was to map quantitative trait loci （QTLs） affecting the pigmentation traits in approximately 800 F2 grand daughter dairy cattle from a Holstein-Friesian and Jersey cross breed cattle. Traits analyzed included pigmentation phenotypes on the body, teat and hoop. The phenoypes were collected from digital photos or visual inspection of live animals. QTL mapping was implemented using half-sib and line-of-descent inheritance models. Our analysis initially detected a number of significant QTLs on chromosomes： 2, 6, 13, 15, 18 and 22. The significant QTLs were divided into two groups： one group influencing the pigmentation color and the other group affecting the absence or level of pigmentation. The most significant QTL peaks were observed on Bovine taurus autosome 18 （BTA18） close to melanocortin 1 receptor （MC1R） for the color traits, on BTA6 close to the receptor tyrosine kinase （K/T） and BTA22 close to microphthalmia-associated transcription factor （M/TF） gene for the spotting traits. Association studies were conducted for candidate regions or genes known to affect pigmentation in dairy cattle.
基金supported in part by AARI,AICML,ALIDF,iCORE,and NSERC
文摘An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear family. The importance of this generalization lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. The algorithm runs in O（m^3n^3） time, where m is the number of single nucleotide polymorphism （SNP） loci under consideration and n is the number of genotyped members in the pedigree. This zero-recombination haplotyping algorithm is extended to a maximum parsimoniously haplotyping algorithm in one whole genome scan to minimize the total number of breakpoint sites, or equivalently, the number of maximal zero-recombination chromosomal regions. We show that such a whole genome scan haplotyping algorithm can be implemented in O（m^3n^3） time in a novel incremental fashion, here m denotes the total number of SNP loci along the chromosome.
基金This work was supported by grants from the National High Technology Research and Development Program of China （＂863＂ Program） （No. 2004AA227040）, the National Key Health Research Project Foundation of China during the 10th Five-Year Plan Period （No. 2004BA720A03） and the National Natural Science Foundation of China （No. 30300199 and No. 30671151）.
文摘Background Hereditary spastic paraplegia （HSP） is a group of inherited neurodegenerative disorders with the shared characteristics of slowly progressive spasticity and weakness of the lower limbs. Thirteen loci for autosomal dominant HSP have been mapped. Methods A Chinese family with HSP was found in the Shandong province and Inner Mongolia Autonomous Region of China and genomic DNA of all 19 family members was isolated. After exclusion of known autosomal dominant loci, a genome wide scan and linkage analysis were performed. Results The known autosomal dominant loci of SPG3A, SPG4, SPG6, SPG8, SPG9, SPG10, SPG12, SPG13, SPG17, SPG19, SPG29, SPG31 and SPG33 were excluded by linkage analysis. The results of a genome wide scan demonstrated candidate linkage to a locus on chromosome 11 p14.1-p11.2, over an 18.88 cM interval between markers D11 S1324 and D11 S1933. A maximal, two point LOD score of 2.36 for marker D11S935 at a recombination fraction （e） of 0 and a multipoint LOD score of 2.36 for markers D11S1776, D11S1751, D11S1392, D11S4203, D11S935, D11S4083, and D11S4148 at θ=0, suggest linkage to this locus. Conclusion The HSP neuropathy in this family may represent a novel genetic entity, which will facilitate discovery of this causative gene.
