Journal of Genetics and Genomics

Termination of TGF-β Superfamily Signaling Through SMAD Dephosphorylation—A Functional Genomic View

Xia Lin, Yeguang Chen, Anming Meng, Xinhua Feng

2007, 34(1): 1-9. doi: 10.1016/S1673-8527(07)60001-0

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Abstract:
The transforming growth factor-β (TGF-β) and related growth factors activate a broad range of cellular responses in metazoan organisms via autocrine, paracrine, and endocrine modes. They play key roles in the pathogenesis of many diseases especially cancer, fibrotic diseases, autoimmune diseases and cardiovascular diseases. TGF-β receptor-mediated phosphorylation of R-SMADs represents the most critical step in the TGF-β signaling pathways that triggers a cascade of intracellular events from SMAD complex assembly in the cytoplasm to transcriptional control in the nucleus. Conversely, dephosphorylation of R-SMADs is a key mechanism for terminating TGF-β signaling. Our labs have recently taken an integrated approach combining functional genomics, biochemistry and development biology to describe the isolation and functional characterization of protein phosphatase PPM1A in controlling TGF-β signaling. This article briefly reviews how dynamic phosphorylation and dephosphorylation of SMADs control or fine-tune the signaling strength and duration and ultimately the physiological consequences in TGF-β signaling.

Genetic Analysis and Linkage Mapping in a Resource Pig Population Using Microsatellite Markers

Jinghu Zhang, Yuanzhu Xiong, Bo Zuo, Minggang Lei, Siwen Jiang, Feng'e Li, Rong Zheng, Jialian Li

2007, 34(1): 10-16. doi: 10.1016/S1673-8527(07)60002-2

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Abstract:
The use of markers and linkage map construction are important for QTL mapping in pigs. In this article, the genetic characteristics were studied and the linkage map was constructed in a pig resource population including 214 individuals by typing 39 microsatellite marker loci onSus scrofa chromosomes, SSC4, SSC6, SSC7, SSC8, and SSC13. Results indicated that the average allele number, the average observed heterozygosity (H_o), and the average polymorphism information content (PIC) in F₁ and F₂ population were 3.2, 0.528, 0.463 and 3.2, 0.496, 0.447, respectively. In the pig resource population, the average informative meiosis (IM) was 217.4 (44-316), and the average linkage map length between the two sexes on the five chromosomes were 172.3 cM (SSC4), 168.7 cM (SSC6), 191.7 cM (SSC7), 197.3 cM (SSC8), and 178.3 cM (SSC13). The orders of microsatellite marker loci in the linkage maps were identical to, but the length was greater than, those of USDA-MARC reference map. The results of this research showed the genetic relationship and genetic characteristics of the microsatellite markers in the pig resource family population, and the linkage map could be used to for QTL mapping in the subsequent study.

Study on Population Genetic Characteristics of Qinchuan Cows Using Microsatellite Markers

Weibin Sun, Hong Chen, Chuzhao Lei, Xueqin Lei, Yinghan Zhang

2007, 34(1): 17-25. doi: 10.1016/S1673-8527(07)60003-4

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Abstract:
To evaluate the genetic polymorphisms and to search for available molecular markers for Qinchuan cattle, 90 Qinchuan cows were genotyped with 12 microsatellite markers. A total of 247 alleles were detected, with the number of alleles ranging from 13 (INRA005) to 33 (HEL13), giving a mean number of 21 alleles per locus. The total and mean effective allele number were 142.6229 and 11.8852, respectively. Mean sampling variance of the allele frequency was 2.6036 × 10⁴. Allele size ranges of the 12 microsatellite loci were different. The observed heterozygosity and expected heterozygosity were from 0.7842 (INRA005) to 0.9775 (BM315) and 0.7952 (BM315) to 0.9446 (HEL13), respectively. Mean observed heterozygosity and mean expected heterozygosity were 0.9117 and 0.9047, respectively. Polymorphism information content values were from 0.7653 (INRA005) to 0.9420 (HEL13), and mean polymorphism information content of the 12 microsatellite loci was 0.8965. All the 12 microsatellite loci were highly polymorphic, which showed that there were rich genetic polymorphisms at these detected microsatellite loci in Qinchuan cows. At the 12 microsatellite loci, the mean fixation index was −0.0076, reflecting that the degree of heterozygote defect at these loci was not high and deviations from Hardy-Weinberg equilibrium were not significant.

Sequence Variation and Molecular Evolution of Hormone-Sensitive Lipase Genes in Species of Bovidae

Zhijie Ma, Jincheng Zhong, Zhihua Cheng, Li Liu, Huaipu Chang, Xiaolin Luo

2007, 34(1): 26-34. doi: 10.1016/S1673-8527(07)60004-6

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Abstract:
The partial sequences of exon I of hormone-sensitive lipase (HSL) genes in yak (Bos grunniens), cattle (Bos taurus), zebu (Bos indicus), and buffalo (Bubalus bubalis) were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig (Sus scrofa), human (Homo sapiens), mouse (Mus musculus), and rat (Rattus sp.) retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of theHSL genes in all species. The results showed that the homologies of the partial exon I sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs: 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon I of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.

QTL Mapping of Yield and Yield Components for Elite Hybrid Derived-RILs in Upland Cotton

Baohua Wang, Wangzhen Guo, Xiefei Zhu, Yaoting Wu, Naitai Huang, Tianzhen Zhang

2007, 34(1): 35-45. doi: 10.1016/S1673-8527(07)60005-8

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Abstract:
A population of 180 recombinant inbred lines (RILs) was developed by single seed descended from the cross of high yield Upland cotton (Gossypium hirsutum L.) varieties Zhongmiansuo12 (ZMS12) and 8891, the two parents of Xiangzamian2 (XZM2). A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment (separate analysis) and a set of data from means of the three environments (joint analysis). A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTLqLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F₁. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.

The Inheritance of Early Heading in the Rice Variety USSR5

Ling Jiang, Junfeng Xu, Xiangjin Wei, Songfeng Wang, Jiuyou Tang, Huqu Zhai, Jianmin Wan

2007, 34(1): 46-55. doi: 10.1016/S1673-8527(07)60006-X

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Abstract:
USSR5, a japonica rice variety from the former Soviet Union, is an extremely early maturing rice variety. To elucidate the genetic basis for its early heading, genetic analysis was carried out by crossing it with a set of major gene nearly isogenic lines (NIL) and QTL-isogenic lines. The early heading of USSR5 was attributed to the presence of photoperiod-insensitive alleles at E₁ and Se-1 gene, the photoperiod-sensitive inhibitor gene i-Se-1, and the dominant earliness gene Ef-1. Analysis of a backcrossed population (BC₁F₁) derived from the cross USSR5 × N22 indicated that two quantitative trait loci (QTL) for early heading were located on chromosomes 7 and 8, accounting for 27.4% and 11.2% of the phenotypic variance, respectively, with both early alleles originating from USSR5. From an F₂ population of the same cross, early heading QTLs were detected on chromosomes 1, 2, 7, 9, and 10, with individual QTL accounting for between 4.1% and 15.4% of the phenotypic variance. Early heading alleles at four of these five QTLs originated from USSR5. A comparison of chromosomal locations suggests that one of these QTLs may be identical with the known gene Hd4 (E₁). The relationship between the other QTLs and known genes for heading date are not clear. USSR5 is a promising source for propagating earliness for the development of improved early heading rice varieties.

Allozyme Diversity and Population Genetic Structure of Three Medicinal Epimedium Species from Hubei

Yanqin Xu, Zuozhou Li, Ying Wang, Hongwen Huang

2007, 34(1): 56-71. doi: 10.1016/S1673-8527(07)60007-1

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Abstract:
Three Epimedium species, E. pubescens Maxim., E. sagittatum (Sieb. & Zucc.) Maxim., and E. wushanense T. S. Ying, which are sympatrically distributed in the western Hubei Province, have been used in traditional Chinese medicine (TCM) for about 2,000 years. Genetic variability and population genetic structure of 11 natural populations of these Epimedium species were investigated using isoelectric focusing in thin-layer polyacrylamide slab gels. Of the 22 enzyme systems prescreened, six coding for 13 loci and 45 alleles were resolved, which were used for analyzing genetic diversity and population structure at both intraspecific and interspecific levels. The results showed that: 1) high levels of genetic diversity were observed in all three species (A = 2.6-3.2, P = 69.2%-84.6%, H_O = 0.274-0.377, H_E = 0.282-0.369), which were higher than that of other herbaceous and animal-pollinated species with similar life-history characteristics; 2) there was significant deviation from Hardy-Weinberg Equilibrium, with one half of the loci showing heterozygote excess and the other homozygote excess, in all populations, suggesting the complicated breeding system ofEpimedium species; 3) the low level of intraspecific and interspecific genetic differentiation (G_ST = 0.0246-0.0409 and 0.0495-0.1213, respectively) indicated a high level of gene flow among populations and close genetic relationship among the three species; and 4) UPGMA cluster analysis further showed that E. pubescens was more closely related to E. sagittatum than to E. wushanense, which was in good agreement with the morphological characters and the recent phylogenetic analysis of these species. On the basis of these results, it was concluded that the mixed breeding system, long-lived perennial life form, ancient evolutionary history, and seed dispersal by ants in Epimedium are responsible for the genetic variation and population structure of these species.

Transcriptional Regulation of 10 Mitochondrial Genes in Different Tissues of NCa CMS System in Brassica napus L. and Their Relationship with Sterility

Wenliang Wei, Hanzhong Wang, Guihua Liu

2007, 34(1): 72-80. doi: 10.1016/S1673-8527(07)60008-3

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Abstract:
Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F₁ using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCa CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atp1, cox1, cox2, cob, rrn5S, and rrn26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F₁, but no transcript was detected in floral buds of the maintainer line. The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F₁. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.

Construction of a High-efficient Expression Vector of Δ12 Fatty Acid Desaturase in Peanut and Its Prokaryotical Expression

Dongmei Yin, Dangqun Cui, Bin Jia

2007, 34(1): 81-88. doi: 10.1016/S1673-8527(07)60009-5

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Abstract:
A full-length sequence coding for Δ¹² fatty acid desaturase gene from peanut (Arachis hypogaea L.) was cloned into the expression vector, pRSETB, to generate recombinant plasmid pRSET/HO-A, which was subsequently transformed into expression Escherichia. coli BL21(DE3)pLysS. The Δ¹² fatty acid desaturase was highly expressed in E. coli BL21(DE3)pLysS in the presence of isopropyl-D-thiogalactopyranoside (IPTG). The fusion protein was purified and used to form a reaction system in vitro by adding oleic acid as substrate and incubating it at 20°C for 6 h. Total fatty acids was extracted and methlesterified and then analyzed with gas chromatography. A novel peak corresponding to linoleic acid methyl ester standards was detected with the same retention time. GC-MS (gas chromatogram and gas chromatogram-mass spectrometry) analysis showed that the novel peak was linoleic acid methyl ester. These results exhibited Δ¹² fatty acid desaturase activity, which could convert oleic acid to linoleic acid specifically.

2007 Vol. 34, No. 1