Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

Restriction site-associated DNA sequencing or genotyping-by-sequencing (GBS) approaches allow for rapid and cost-effective discovery and genotyping of thousands of single-nucleotide polymorphisms (SNPs) in multiple individuals. However, rigorous quality control practices are needed to avoid high levels of error and bias with these reduced representation methods. We developed a formal statistical framework for filtering spurious loci, using Mendelian inheritance patterns in nuclear families, that accommodates variable-quality genotype calls and missing data—both rampant issues with GBS data—and for identifying sex-linked SNPs. Simulations predict excellent performance of both the Mendelian filter and the sex-linkage assignment under a variety of conditions. We further evaluate our method by applying it to real GBS data and validating a subset of high-quality SNPs. These results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for GBS loci that is complementary to standard coverage and Hardy–Weinberg filters. The described method, implemented in the software MendelChecker, will improve quality control during SNP discovery in nonmodel as well as model organisms.     

Fertile transgenic plants obtained from tritordeum inflorescences by tissue electroporation

 Tissue electroporation was applied to a member of the Triticeae family, namely tritordeum (Hordeum chilense Roem.×Triticum turgidum L. Conv. durum), for the generation of fertile transgenic plants. Two transgenic plants were recovered following the treatment of 361 explants of immature inflorescences (although they were subsequently found to result from the same transformation event). The expression of both inserted marker genes (uidA and bar) was confirmed using standard assays, while transgene integration was confirmed using PCR and Southern hybridization analyses. Integration pattern, segregation ratio and the inheritance of transgene expression in T₁ progeny were consistent for the presence of a single transgene locus containing five to ten plasmid insertions. Although this procedure has been applied to other cereal species, stable transformation of the Triticeae using tissue electroporation has not previously been reported. Received: 28 October 1999 / Revision received: 25 August 2000 / Accepted: 29 August 2000     

Paternal inheritance of mitochondrial DNA in the sheep (Ovine aries)

Paternal inheritance of mitochondria DNA in sheep was discovered by examination of 152 sheep from 38 hybrid families for mtDNA D-loop polymorphisms using PCR-RFLP, amplification of repeated sequence somain, and PCR-SSCP of the D-loop 5' end region of a 253 bp fragment. Our findings have provided the first evidence of paternal inheritance of mtDNA in sheep and possible mechanisms of paternal inheritance were discussed.     

大豆对斜纹夜蛾幼虫抗性遗传的发展表达过程

采用植物数量性状遗传体系分离分析方法,通过4个感抗杂交组合研究了在网室人工接入斜纹夜蛾幼虫的条件下大豆抗斜纹夜蛾植株反应发育过程的遗传。不论P1、P2、F1、F2、F2：3多世代联合分析或单个分离世代分析,结果均表明大豆对斜纹夜蛾幼虫的抗性为两对主基因 多基因遗传模式。但在大豆生长发育的不同时期,随害虫数量的变化,其抗虫性遗传呈动态变化过程。在两对主基因充分表达日期,主基因的遗传率较高,达70.40%-99.21%,环境影响较小;多基因遗遗传率较低,为0.00%-22.29%。     

褐飞虱对马拉硫磷的抗性遗传和交互抗性研究

毒力测定显示,抗马拉硫磷品对杀螟松、二嗪磷、异丙威和仲丁威都有明显的交互抗性产生,但对醚菊酯和吡虫啉没有表现出显的交互抗性。抗性遗传研究显示,正交和反交后代F1和F1'的显性值D分别为0.4014和0.3780,说明抗性主效基因是不完全显性的。通过自交后代F2和回交后代BC的LD-p线观察及与期望曲线比较,证明抗性遗传由两个或两个以上的基因控制。     

Isolation and characterization of streptomycin-resistant mutants in Nicotiana plumbaginifolia

Summary Streptomycin-resistant colonies were isolated from protoplast cultures of haploid Nicotiana plumbaginifolia based on their ability to green in medium containing 1 mg/ml streptomycin sulfate. The frequency of resistant colonies was 0.9×10^–5 in nonmutagenized culture, and increased ten-fold following treatment of culture with 10 g/ml N-methyl-N-nitro-N-nitrosoguanidine. Of a total of 52 resistant clones isolated, 2 gave rise to haploid, 15 to diploid, and 3 to tetraploid plants upon transfer of calli to differentiation medium. Leaf-segment and protoplast assays showed that all diploid regenerates were resistant to streptomycin but sensitive to chloramphenicol, kanamycin, lincomycin, neomycin, and spectinomycin. Plants in most diploid clones were fertile and able to set seeds when self-fertilized and crossed reciprocally to wild-type plants. Inheritance of streptomycin resistance was studied in the diploid clones and, without exception, the resistance was transmitted maternally. Comparative studies of the ultrastructure of organelles and protein synthesis in isolated chloroplasts between wild-type and resistant clones in the presence of streptomycin suggest that streptomycin resistance is controlled by chloroplasts.     

Statistical techniques for detection of major genes in animal breeding data

Summary Statistical techniques for detection of major loci and for making inferences about major locus parameters such as genotypic frequencies, effects and gene action from field-collected data are presented. In field data, major genotypic effects are likely to be masked by a large number of environmental differences in addition to additive and nonadditive polygenic effects. A graphical technique and a procedure for discriminating among genetic hypotheses based on a mixed model accounting for all these factors are proposed. The methods are illustrated by using simulated data.Journal Paper No. J-12733 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 1901     

Non-mendelian inheritance of mitochondrial DNA and ribosomal DNA in the myxomycete, Didymium iridis

Summary The inheritance of both the mitochondrial DNA (mtDNA) and the nuclear-encoded extrachromosomal ribosomal DNA (rDNA) has been studied in the myxomycete, Didymium iridis, by DNA-DNA hybridization of labeled probes to total DNA at various stage of the life cycle. Both the mtDNA and rDNA populations rapidly become homogeneous in individuals, but there is a qualitative difference in the patterns of inheritance of these two molecules. One parental rDNA type was preferentially inherited in all crosses; selective replication of this molecule is tentatively proposed as the mechanism of inheritance. In contrast, either parental mtDNA type could be inherited. Since the inherited population of parental mtDNA molecules are not partitioned into cells in this coenocytic organism, no known mechanism of inheritance can explain the rapid and apparently random loss of one parental mtDNA type in individuals.     

Phenolics of Pyrus interspecific hybrids

The leaf phenolics of a number of Pyrus interspecific hybrids (from controlled hand-crosses) and the parental individuals have been examined. In most instances it was found that the presence of certain phenolics in the hybrids is of diagnostic value in predicting the identities of one or both of the original parents. The flavone and flavonol glycosides appear to be inherited as simple dominant characters (whether inherited from male or female parents) but phenolics such as epicatechin, catechin, caffeoylcalleryanin and p-hydroxybenzoic acid did not always appear to show such simple dominance.