Journal of Genetics and Genomics

Re-evaluation of the function of the male specific lethal complex in Drosophila

James Birchler, Lin Sun, Harvey Fernandez, Ryan Donohue, Weiwu Xie, Abhijit Sanyal

2011, 38(8): 327-332. doi: 10.1016/j.jgg.2011.07.001

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Abstract:
A set of proteins and noncoding RNAs, referred to as the male specific lethal (MSL) complex, is present on the male X chromosome in Drosophila and has been postulated to be responsible for dosage compensation of this chromosome – the up-regulation of its expression to be equal to that of two X chromosomes in females. This hypothesis is evaluated in view of lesser known aspects of dosage compensation such as the fact that metafemales with three X chromosomes also have equal expression to normal females, which would require a down-regulation of each gene copy. Moreover, when this complex is ectopically expressed in females or specifically targeted to a reporter in males, there is no increase in expression of the genes or targets with which it is associated. These observations are not consistent with the hypothesis that the MSL complex conditions dosage compensation. A synthesis is described that can account for these observations.

Characterization of a novel missense mutation on murine Pax3 through ENU mutagenesis

Yue Xiao, Lingling Zhang, Kuanjun He, Xiang Gao, Lun Yang, Lin He, Gang Ma, Xizhi Guo

2011, 38(8): 333-339. doi: 10.1016/j.jgg.2011.06.005

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Abstract:
N-ethyl-N-nitrosourea (ENU) mutagenesis has led to the elucidation of several regulator genes for melanocyte and skin development. Here we characterized a mutant from ENU mutagenesis with similar phenotype as that of Splotch mutant, including exencephaly, spina bifida and abnormal limbs in homozygotes as well as white belly spotting and occasionally loop-tail in heterozygotes. This novel mutant was named as . Through genome-wide linkage analysis in backcross progenies with microsatellite markers, the was confined to a region between D1MIT415 and D1MIT7 on chromosome 1, where notable Pax3 gene was located. Direct sequencing revealed that carried a nucleotide A894G missense transition in exon 6 of Pax3 gene that resulted in Asn to Asp substitution at amino acid 269 within the highly-conserved homeodomain (HD) DNA recognition module, which was the first point mutation found in this domain in mice. This N269D mutation impaired the transactivation capacity of Pax3 protein, but exerted no effect on Pax3 protein translation. The characterization of the new mutation expanded our understanding the transactivation and DNA-binding structure of Pax3 protein.

MDM2 SNP309 contributes to tumor susceptibility: A meta-analysis

Xiaoman Wo, Dong Han, Haiming Sun, Yang Liu, Xiangning Meng, Jing Bai, Feng Chen, Yang Yu, Yan Jin, Songbin Fu

2011, 38(8): 341-350. doi: 10.1016/j.jgg.2011.07.005

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Abstract:
The potentially functional polymorphism, SNP309, in the promoter region of MDM2 gene has been implicated in cancer risk, but individual published studies showed inconclusive results. To obtain a more precise estimate of the association between MDM2 SNP309 and risk of cancer, we performed a meta-analysis of 70 individual studies in 59 publications that included 26,160 cases with different types of tumors and 33,046 controls. Summary odds ratios (OR) and corresponding 95% confidence intervals (CIs) were estimated using fixed- and random-effects models when appropriate. Overall, the variant genotypes were associated with a significantly increased cancer risk for all cancer types in different genetic models (GG vs. TT: OR, 1.123; 95% CI, 1.056–1.193; GG/GT vs. TT: OR, 1.028; 95% CI, 1.006–1.050). In the stratified analyses, the increased risk remained for the studies of most types of cancers, Asian populations, and hospital- /population-based studies in different genetic models, whereas significantly decreased risk was found in prostate cancer (GG vs. TT: OR, 0.606; 95% CI, 0.407–0.903; GG/GT vs. TT: OR, 0.748; 95% CI, 0.579–0.968). In conclusion, the data of meta-analysis suggests that MDM2 SNP309 is a potential biomarker for cancer risk.

Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants sea cucumber (Apostichopus japonicus)

Jung-Ha Kang, Ki Hwan Yu, Jung-Youn Park, Chul-Min An, Je-Cheon Jun, Sang-Jun Lee

2011, 38(8): 351-355. doi: 10.1016/j.jgg.2011.06.002

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Abstract:
Color variation is a well-known feature of sea cucumbers (Apostichopus japonicus), which are classified into three groups based on their colors of red, green and black. It is also one of the most important traits related to how they taste, and it thereby affects their market price. Attempts were made to identify single-nucleotide polymorphisms (SNPs) and to analyze differences associated with SNP genotypes between green and red color variants using HSP70 as the target gene. The HSP70 gene, which is found universally in organisms from bacteria to humans, is one of the most evolutionarily conserved genes and the most widely studied biomarker of stress response. DNA fragments of 1074 bp covering a partial sequence of the sea cucumber HSP70 gene, were amplified from both red and green variants, and subsequently analyzed for the presence of SNPs. Twenty-seven polymorphic sites in total, including heterozygous sites, were observed. Of these, six sites were found to be significantly different SNP genotypes between green and red variants. Furthermore, PCR with an internal primer designed to include an allele-specific SNP at the 3′ end (site 443) showed differentiation between the two variants, 100% and 4.2% amplification in green and red variants, respectively. The validated SNPs may serve as informative genetic markers that can be used to distinguish variants at the early developmental stage, prior to color differentiation.

Gene expression profiling of Puccinia striiformis f. sp. tritici during development reveals a highly dynamic transcriptome

Xueling Huang, Xianming Chen, Tristan Coram, Meinan Wang, Zhensheng Kang

2011, 38(8): 357-371. doi: 10.1016/j.jgg.2011.07.004

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Abstract:
Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, one of the most important diseases of wheat worldwide. cDNA libraries had been constructed from urediniospores, germinated urediniospores and haustoria. However, little is known about the expression patterns of the genes related to the infection process and sporulation of the pathogen. In this study, a custom oligonucleotide microarray was constructed using sequences of 442 gene transcripts selected fromPst cDNA libraries. The expression patterns of the genes were determined by hybridizing the microarray with cDNA from Pst in vitro and Pst-infected wheat leaves. The time course study identified 55 transcripts that were differentially expressed during the infection process in a compatible interaction. They were identified to have functions related to the following biological processes, including carbohydrate and lipid metabolism, energy, cell signaling, protein synthesis, cell structure and division. In an incompatible interaction, 17 transcripts of the pathogen were differentially expressed in resistant wheat leaves inoculated with an avirulent Pst race, ten of which had similar expression patterns to those in the compatible interaction. Several candidates for pathogenicity and virulence/avirulence related genes were also identified. The results of quantitative real-time PCR validated the expression patterns of some selected genes. The study demonstrates that the custom oligonucleotide microarray technology is useful to determine the expression patterns of the pathogen genes involved in different types of the host–pathogen interactions and stages of development.

Discovery of quantitative trait loci for crossability from a synthetic wheat genotype

Li Zhang, Jin Wang, Ronghua Zhou, Jizeng Jia

2011, 38(8): 373-378. doi: 10.1016/j.jgg.2011.07.002

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Abstract:
Crossability between wheat and rye is an important trait for wheat improvement. No quantitative trait loci (QTLs) were detected from wheat ancestors previously. The objectives of this study were to dissect the QTLs for crossability using 111 introgression lines (ILs) derived from synthetic hexaploid wheat. A total of 1275 SSR markers were screened for polymorphism between the two parents, and 552 markers of them displayed polymorphism, of which 64 were selected for genotyping the 111 BC₅F₆ ILs. Field trials were performed in a Latinized α-lattice design in Luoyang and Jiaozuo of Henan Province of China in 2007–2008 and 2008–2009 cropping seasons. One-way ANOVA and interval mapping (IM) analysis were used to detect QTL for crossability between wheat and rye. A total of 13 putative QTLs were detected. Five of them, QCa.caas.1A, QCa.caas.2D, QCa.caas.4B, QCa.caas.5B and QCa.caas.6A, were detected in both trials and three of them, QCa.caas.2D, QCa.caas.4B and QCa.caas.6A, were novel. The positive effect allele of the four QTLs came from the donor parent Am3 except QCa.caas.6A that came from the recurrent parent Laizhou953. ILs with both higher positive effect alleles and favorable agronomic traits developed in present study are elite germplasm for wide crossing in wheat. Results from the current study suggest that wheat ancestors can be rich in new sources of crossability genes.

2011 Vol. 38, No. 8