Journal of Genetics and Genomics

Recent Progress in Elucidating the Structure, Function and Evolution of Disease Resistance Genes in Plants

Jinling Liu, Xionglun Liu, Liangying Dai, Guoliang Wang

2007, 34(9): 765-776. doi: 10.1016/S1673-8527(07)60087-3

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Abstract:
Plants employ multifaceted mechanisms to fight with numerous pathogens in nature. Resistance (R) genes are the most effective weapons against pathogen invasion since they can specifically recognize the corresponding pathogen effectors or associated protein(s) to activate plant immune responses at the site of infection. Up to date, over 70 R genes have been isolated from various plant species. Most R proteins contain conserved motifs such as nucleotide-binding site (NBS), leucine-rich repeat (LRR), Toll-interleukin-1 receptor domain (TIR, homologous to cytoplasmic domains of the Drosophila Toll protein and the mammalian interleukin-1 receptor), coiled-coil (CC) or leucine zipper (LZ) structure and protein kinase domain (PK). Recent results indicate that these domains play significant roles in R protein interactions with effector proteins from pathogens and in activating signal transduction pathways involved in innate immunity. This review highlights an overview of the recent progress in elucidating the structure, function and evolution of the isolatedR genes in different plant-pathogen interaction systems.

Variations of Melanocortin Receptor 1 (MC1R) Gene in Three Pig Breeds

Guiling Dun, Xianglong Li, Hongzhan Cao, Rongyan Zhou, Lanhui Li

2007, 34(9): 777-782. doi: 10.1016/S1673-8527(07)60088-5

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Abstract:
Variations of Melanocortin Receptor 1 (MC1R) were investigated using sequencing, PCR-RFLP and PCR-SSCP, in three pig breeds, Landrace, Yorkshire, and Duroc. Five polymorphic sites were found, in which 668G→C occurred within 5′ UTR, nt894insCC in coding region resulting in a premature stop at codon 56, and 1318C→T, 1554G→A, 1197G→A in coding region resulting in Ala164Val, Ala243Thr, and Asp124Asn respectively. All individuals in Landrace and Yorkshire present homozygous 668GG, 1197AA, 1318CC, and 1554GG, and have CC insertions at the 894 site, whereas the individuals in Duroc present a contrast homozygous 668CC, 1197GG, 1318TT, and 1554AA, and have no CC insertions at the corresponding site. No heterozygote has been found at these mutation sites. Presumably, 668G→C, 1318C→T, and 1554G→A may be associated with the recessive red color in the Duroc breed, and nt894insCC making 1197G→A nonsense may be associated with the white color in Landrace and Yorkshire breeds.

Disruption of nifA Gene Influences Multiple Cellular Processes in Sinorhizobium meliloti

Ziying Gong, Jiabi Zhu, Guanqiao Yu, Huasong Zou

2007, 34(9): 783-789. doi: 10.1016/S1673-8527(07)60089-7

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Abstract:
Sinorhizobium meliloti nifA is important in fixing nitrogen during symbiosis. A nifA null mutant induces small white invalid nodules in the roots of host plant. The additional phenotypic alterations associated with the disruption of the nifA gene are reported in this study. Under a free-living state, S. meliloti nifA mutant reduces its ability to swarm on a half-solid plate. Interestingly, the AHL (Acylhomoserine lactones) contents in the nifA mutant are lower than that of the wild type during the lag phase, whereas it is reversed in the logarithmic and stationary phases. Quantitative spectrophotometric assays reveal that the total amount of extracellular proteins of the nifA mutant are lower than that of the wild type. In addition, the mutant abolishes its nodulation competitive ability during symbiosis. These findings indicate that NifA plays a regulatory role in multiple cellular processes in S. meliloti.

Study of Transcription Activity of X-Box Binding Protein 1 Gene in Human Different Cell Lines

Fengjin Guo, Fangzhou Song, Jing Zhang, Jing Li, Yong Tang

2007, 34(9): 790-799. doi: 10.1016/S1673-8527(07)60090-3

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Abstract:
Human X-box binding protein 1 (XBP1), an important transcription factor, participates in many signal transduction processes. To further investigate the biological function of XBP1, sequences of XBP1 promoter and its two deletion mutants were first determined using bioinformatic analysis. The report vectors containing XBP1 promoter and its deletion mutants were then constructed, namely, p1-XBP1p, p2-XBP1p, and p3-XBP1p. Each reporter vector was separately transfected into HepG₂, L0₂, K562, SMMC-7721, HSF, and Lipocyte Ito Cell line using FuGENE 6 transfection reagents. The activity of chloramphenicol acetyltransferase (CAT) in each group of transfected cells was detected by ELISA assay, which in turn reflects the transcription activity of theXBP1 gene promoter. The activity involving p3-XBP1p was the highest in HepG₂, which was 12.4-fold of that of pCAT3-Basic. The activities of p3-XBP1p in K562 and SMMC-7721 were the second and the third highest, which were 10.9-fold and 10.0-fold of that of the pCAT3-Basic, respectively. The CAT activity in L0₂ was lower than that in the above-mentioned abnormal cell, and no reporter activity was detected in HSF and Ito Cell. The XBP1 transcription and expression in K562, HepG₂ and SMMC-7721 were found to be higher than that in L0₂, HSF and Ito cells, based on the results of real-time RT-PCR and Western blot. The XBP1 transcription and expression in L0₂, HSF was lower, whereas that in Ito cells was totally lacking. The result was similar to that of CAT-ELISA. Therefore, the XBP1 gene promoter can drive its downstream gene expression and its activity is cell line-dependent. The core sequence of XBP1 promoter was found between -227bp and 66bp sequence. This sequence was closely associated with the transcriptional activity of XBP1 promoter.

Genetic Polymorphism of Mitochondrial DNA in Dong, Gelao, Tujia, and Yi Ethnic Populations from Guizhou, China

Binbin Li, Fuguang Zhong, Hongsheng Yi, Xianran Wang, Liangfang Li, Lilan Wang, Xiaolan Qi, Lifu Wu

2007, 34(9): 800-811. doi: 10.1016/S1673-8527(07)60091-5

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Abstract:
To reveal the genetic structures and relationships of the four ethnic populations from the maternal inheritance and explore the origins and migrations of nationalities, the genetic polymorphism of mtDNA in Dong, Gelao, Tujia, and Yi populations from Guizhou was studied by direct sequencing of hypervariable segment I(HVS I) and PCR-RFLP of coding region. Thirty-seven (sub-) haplogroups were identified in the classification tree of mtDNA haplogroups. Haplogroup distributions and principal component (PC) analysis showed that the Dong has high frequencies of south-prevalent haplogroups, which indicates that it is a typically southern population. The Yi harbors high frequencies of the south-prevalent and northern-prevalent haplogroups, which demonstrates that it inherits the maternal characteristics from both southern and northern populations. The Yi and Gelao cluster together, the reason for which might be that their ancestries frequently underwent gene exchanges and mixtures.

Phylogeny of Apaturinae Butterflies (Lepidoptera: Nymphalidae) Based on Mitochondrial Cytochrome Oxidase? Gene

Min Zhang, Tianwen Cao, Rui Zhang, Yaping Guo, Yihao Duan, Enbo Ma

2007, 34(9): 812-823. doi: 10.1016/S1673-8527(07)60092-7

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Abstract:
The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit?(COI). The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of theCOI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.

Hereditary Behavior of bar Gene Cassette is Complex in Rice Mediated by Particle Bombardment

Yan Zhao, Qian Qian, Huizhong Wang, Danian Huang

2007, 34(9): 824-835. doi: 10.1016/S1673-8527(07)60093-9

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Abstract:
Particle bombardment transformation using minimal gene cassette (containing the promoter, open reading frame and terminator) is the novel trend in plant genetic transformation, and its use helps to alleviate the undesirable effects of plasmid vector backbone sequences on transgenic plants. In the present article, studies related to the hereditary behavior of bar gene cassette in T₁ to T₃ generations of the transgenic rice (Oryza sativa L.) lines transformed by particle bombardment have been discussed. The selectable marker bar gene cassette that integrated with the rice genome had multiple copies and showed complex segregation behaviors including the presence of ‘false homozygotes’, with abnormal segregation ratios ranging from 35:1 to 144:1 (Basta-resistant: sensitive plants) in their progenies. In five out of ten original transgenic lines, bar gene can be stably transmitted as a dominant gene to self-pollinated T₂ progeny. The homozygotes were obtained in three transgenic lines in T₁ generation regardless of the multiple-copy integration patterns ofbar gene. Southern blotting analysis showed that multiple copies of bar gene cassette were linked, which formed transgene arrays in the host rice genome. The authors also observed stable transmission of integration patterns of bar gene cassette, as obtained from Southern blotting analysis, in the regularly segregated transgenic rice lines and loss of gene in an irregularly segregated transgenic line. The segregation behavior varied among the transgenic progenies that exhibited similar Southern hybridization patterns of bar gene. On the basis of these results, the multiple-copy integration, gene lost, and gene expression interaction were the major reasons for the complex segregation behaviors of bar gene cassette in transgenic rice plants.

Improvement for Agronomic Traits of Partial Waxy Wheat by Combination of Backcrossing with a PCR-based DNA Marker

Yuxiu Dong, Xiangyu Zhao, Jiawei Wang, Guoliang Yuan, Xiansheng Zhang

2007, 34(9): 836-841. doi: 10.1016/S1673-8527(07)60094-0

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To improve agronomic traits of partial waxy wheat, crossing between Chinese Baihuomai and wheat cultivars PH85-16, Jinan 17, and Yannong 15 was performed. The progeny plants were further backcrossed to these cultivars as recurrent parents for five generations. To get homozygous plants with the null allele at the Wx-D1 locus, self-pollination was carried out in the BC₅F₁ generation. Through another three generations, 6 partial waxy wheat lines were obtained, which had similar agronomic performance as their recurrent parents and carried the null allele at the Wx-D1 locus. In each generation, the Wx-D1 locus was identified by a PCR-based DNA marker and the agronomic traits were examined in progeny plants. The results from this study indicate that the use of backcrossing with a PCR-based DNA marker was useful in waxy wheat breeding. These partial waxy wheat lines can be used in field production.

Cloning of Salt Stress Responsive cDNA from Wheat and Resistant Analysis of Differential Fragment SR07 in Transgenic Tobacco

YongJun Liu, Aining Zhang, Jingfen JIA, Angzhen Li

2007, 34(9): 842-850. doi: 10.1016/S1673-8527(07)60095-2

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Abstract:
Analysis of the gene expression differentiation in leaves of wheat (Triticum aestivum L.) cultivar Baofeng 7228, under salt stress, was carried out by Differential-Display Reverse Transcription-polymerase Chain Reaction (DDRT-PCR.) Twenty-seven differential cDNA fragments were obtained. The expression of the SR07 fragment was induced noticeably by salt treatment, and the nucleotide sequence homology of 87% between the SR07 fragment and PIPs (water channel proteins) was observed. Further research showed that a 561 bp open read frame was present in the SR07 fragment. Plant expression vector of pCAMBIA-SR07 was constructed and three transformants of tobacco (Nicotiana tobacum) mediated by Agrobacterium tumefaciens plasmid were obtained. Resistance to salt, PEG, and mannitol stresses of the three transformants were examined. No significant difference (P > 0.05) was observed between the control and the transformants in resistance to salt stress, but there was significant difference ( P < 0.05) between the control and the transformants in resistance to PEG and mannitol stresses. Therefore, the expression of the SR07 fragment may play an important role in the water regulation of the plant.

Genetic Diversity of Maize (Zea mays L.) Landraces from Southwest China Based on SSR Data

Qilun Yao, Kecheng Yang, Guangtang Pan, Tingzhao Rong

2007, 34(9): 851-860. doi: 10.1016/S1673-8527(07)60096-4

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Genetic diversity of 54 maize landraces from southwest China was tested using bulk DNA samples and 42 microsatellite (SSR) loci distributed on 10 chromosomes of maize. A total of 256 alleles were detected among the landraces. At each locus, the number of alleles varied from 2 to 9, with an average of 6.1. On the basis of the genetic similarity coefficients, clustering analysis separated the landraces into four groups. The landraces collected from the same region were mostly grouped together. To reveal the genetic structure and genetic diversity within landraces, 165 individuals from 11 landraces were analyzed. Individual DNA samples proved to be superior to bulk DNA samples in identifying genetic diversity of landraces. A total of 330 alleles were detected in the 11 landraces. According to the results of the individual DNA sampling analysis, estimates of the mean number of alleles ‘A’, the effective allelic number ‘’, the observed heterozygosity ‘’, and expected heterozygosity ‘’ were 7.86, 3.90, 0.69, and 0.37, respectively. An obvious genetic deviation from Hardy-Weinberg expectation was observed both among and within landraces and a considerable genetic variation was revealed within rather than among landraces. In addition, genetic diversity of landraces was greater in Sichuan than in the other three regions. It can be concluded that maize landraces in southwest China were initially introduced to Sichuan and from there to adjacent areas.

2007 Vol. 34, No. 9