Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.     

马尾松表达序列标签多态性初步分析

遗传图谱是现代分子数量遗传学研究的一个基本平台 ,在过去的十几年中 ,林木遗传学家在几十个树种中构建了分子标记连锁图谱 ,并进行了一些重要数量性状的QTL分析。 (Bradshawetal.,1994 ;Ceveraetal.,2 0 0 1;Deveyetal .,1994 ;Echtetal .,1997;Grattapagliaetal.,1994 ;Muka     

“Ch型”谷子显性核不育的遗传及其应用研究（Setaria italica）

通过对“Ch型”谷子显性核不育的遗传研究,证实“Ch型”的不育性与“澳大利亚谷”的细胞质无关,其育性是受两对显性连锁基因Ms-和Rf-上位互作控制的。其中Ms是显性不育基因,Rf是显性上位基因,当二者共同存在时,显性上位基因能抑制显性不育基因的表达,从而使不育表现可育。这种由杂交而来,并能找到“恢复系”的显性核不     

转基因抗虫棉Bt基因的遗传连锁分析

对中美两国所获得的转基因抗虫棉品种GK— 1 2、新棉 33B分别进行了 Bt基因的连锁测验。分析表明两个品种的试验结果相似 ,Bt基因未整合在棉花第 I、II、III、IV、V、VI、VII、IX、X、XI、XII、XIII、XVII连锁群及 cu、pg、gl1等基因所涉及的染色体上。阐明了 Bt基因染色体图谱定位的复杂性 ,并提出以原位杂交技术实现 Bt基因在棉花染色体组上的物理标图     

Fusarium wilt of chickpea: physiological specialization, genetics of resistance and resistance gene tagging

Chickpea wilt caused by Fusarium oxysporum f. sp. ciceris is one of the major yield limiting factors in chickpea. The disease causes 10–90% yield losses annually in chickpea. Eight physiological races of the pathogen (0, 1A, 1B/C, 2, 3, 4, 5 and 6) are reported so far whereas additional races are suspected from India. The distribution pattern of these races in different parts of the world indicates regional specificity for their occurrence leading to the perception that F. oxysporum f. sp. ciceris evolved independently in different regions. Pathogen isolates also exhibit differences in disease symptoms. Races 0 and 1B/C cause yellowing syndrome whereas 1A, 2, 3, 4, 5 and 6 lead to wilting syndrome. Genetics of resistance to two races (1B/C and 6) is yet to be determined, however, for other races resistance is governed either by monogenes or oligogenes. The individual genes of oligogenic resistance mechanism delay onset of disease symptoms, a phenomenon called as late wilting. Slow wilting, i.e., slow development of disease after onset of disease symptoms also occurs in reaction to pathogen; however, its genetics are not known. Mapping of wilt resistance genes in chickpea is difficult because of minimal polymorphism; however, it has been facilitated to great extent by the development of sequence tagged microsatellite site (STMS) markers that have revealed significant interspecific and intraspecific polymorphism. Markers linked to six genes governing resistance to six races (0, 1A, 2, 3, 4 and 5) of the pathogen have been identified and their position on chickpea linkage maps elucidated. These genes lie in two separate clusters on two different chickpea linkage groups. While the gene for resistance to race 0 is situated on LG 5 of Winter et al. (Theoretical and Applied Genetics 101:1155–1163, 2000) those governing resistance to races 1A, 2, 3, 4 and 5 spanned a region of 8.2 cM on LG 2. The cluster of five resistance genes was further subdivided into two sub clusters of 2.8 cM and 2.0 cM, respectively. Map-based cloning can be used to isolate the six genes mapped so far; however, the region containing these genes needs additional markers to facilitate their isolation. Cloning of wilt resistance genes is desirable to study their evolution, mechanisms of resistance and their exploitation in wilt resistance breeding and wilt management.     

黄瓜的分子标记和连锁图谱研究进展

黄瓜分子标记和遗传连锁图谱的研究工作相对番茄、小麦等作物比较落后,至今开展的分子标记研究多围绕黄瓜遗传关系分析进行,现有的几张遗传连锁图谱基本是由美国Staub研究小组完成,已被定位在图谱上的同工酶、RAPD、RFLP、SSR、AFLP等标记总数达到300多个,各标记间平均距离达到2.1cM,被整合在一起的遗传基因不足10个(F、B、de、ll、dm)。     

“东乡野生稻”及“02428”、“8504”、“CPSL017”广亲和性遗传的研究

以水稻“东乡野生稻”、“02428”、“8504”、“CPSL017”为材料,分别与籼型测验种南京11、IR36、测49;粳型标准测验种巴利拉、秋光、丰锦测交,杂种一代的小穗育性在77.1％～97.9％之间,其平均值“东野”为86.0％,“02428”为90.9％,“8504”为82.5％,“CPSL017”为91.7％。以CPSL017”为对照,研究了这四个品种的广亲和性遗传,结果表明;它们的广亲和性都是由一简单基因,即广亲和基因控制的,它仿的广亲和基因与色素原基因C~+连锁,位于第Ⅰ连锁群上,遗传规律符合单位点孢子体——配子体互作模式,也受微效基用的修饰作用。这四份广亲和性种质资源均为偏粳品种。     

利用RAPD 标记和种间杂交组合构建葡萄的分子标记连锁图谱

 利用随机扩增多态性DNA (RAPD) 在一个葡萄的种间杂交组合〔毛葡萄8324296 (Vitis quinquangularis) ×欧洲葡萄粉红玫瑰(V. vinifera) 〕的F1 群体中发展分子标记,共产生了89 个稳定的RAPD 标记,连同4 个形态标记(花型、霜霉病抗性、果皮颜色、果汁颜色) 构建了一个葡萄RAPD分子连锁图。该图覆盖基因组总长度为1 033 cM,标记间平均距离为17.8 cM, 为毛葡萄连锁图谱的构建提供了一个连锁框架。     

遗传连锁方法的历史,现状与发展

本文简要介绍了遗传学当中的连锁分析方法的历史，现状及其近几十年的发展，并对这些方法的优缺点进行了评价。     

Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study(GWAS) and linkage mapping

Wheat powdery mildew(Blumeria graminis f.sp.tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies.Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development.A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism(SNP)markers.The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15.Linkage disequilibrum(LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel.Association analysis using a mixed linear model(MLM) identified three loci for powdery mildew resistance on chromosome 2 B, designated QPm.stars-2BL1,QPm.stars-2BL2, and QPm.stars-2BL3.To evaluate the efficacy of GWAS in gene discovery,QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI420646 × OK1059060-126135-3.Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results.QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.