Journal of Genetics and Genomics

Genetic Screening of the Lipoprotein Lipase Gene for Mutations in Chinese Subjects with or without Hypertriglyceridemia

Yuhong Yang, Yunxiang Mu, Yu Zhao, Xinyu Liu, Lili Zhao, Junmei Wang, Yonghong Xie

2007, 34(5): 381-391. doi: 10.1016/S1673-8527(07)60041-1

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Abstract:
Objective: To investigate the association between the mutations in lipoprotein lipase gene and hypertriglyceridemia (HTG). Methods: The lipoprotein lipase (LPL) gene was screened for mutations in 386 Chinese subjects with (108 cases in the HTG group) or without HTG (278 cases in the control group), by single-strand conformation polymorphism (SSCP) analysis and DNA sequencing. Results: One novel silent mutation L103L, one missense mutation P207L, three splicing mutations Int3/3′-ass/C(-6) → T, and the common S447X polymorphism has been identified in the whole coding region and exon-intron junctions of the LPL gene were examined. Heterozygous P207L found in the HTG group was the first case reported in Asia and subsequently another P207L heterozygote was found in the proband's family, all of which suggested that P207L was one of the causes of familial combined hyperlipidemia, but was not so prevalent as that in French Canadian. Int3/3′-ass/C(-6) → T was found in both groups in the present study although it was regarded as a pathogenic variant to HTG earlier on. Moreover about the beneficial polymorphism S447X, there was also some supportive evidence that the levels of triglycerides (TG) in S447X carriers were significantly lower than noncarriers in the subjects without HTG. Conclusions: The association between theLPL variants and HTG is quite complicated and versatile, genotyping of LPL in a larger-scale screening should be necessary and justifiable.

Identification of Prosaposin as a Novel Interaction Partner for Rhox5

Fen Guo, Xiaofeng Huang, Shiqian Li, Limin Sun, Yueqin Li, Hongjian Li, Yi Zhou, Yanhui Chu, Tianhong Zhou

2007, 34(5): 392-399. doi: 10.1016/S1673-8527(07)60042-3

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Abstract:
Prosaposin (Psap) has multiple cellular functions. It is involved in the development of the reproductive system, nervous system, and prostate cancer as well as in the regulation of sphingolipid catabolism by activating several lysosomal hydrolases involved in the metabolism of various sphingolipids. In this research, it was found to be a novel interaction partner for Rhox5 using yeast two-hybrid screening. The interaction between Rhox5 and the full-length prosapsoin (the transcript without exon 8) as well as the C-terminal domain of prosaposin, was further confirmed in both yeast two hybrid analysis and in vitro assay. It suggested that the C-terminal domain of prosaposin may be critical for the Rhox5-prosaposin interaction. Given the important roles played by both Rhox5 and prosaposin in maintaining the differentiation of male reproductive organs, spermatogenesis, and fertilization, the interaction between Rhox5 and prosaposin might regulate the development of male reproductive organs dynamically.

Association of Polymorphisms of Leptin Gene with Body Weight and Body Sizes Indexes in Chinese Indigenous Cattle

Dongying Yang, Hong Chen, Xinzhuang Wang, Zhihuan Tian, Ligang Tang, Zhengfeng Zhang, Chuzhao Lei, Liangzhi Zhang, Yimin Wang

2007, 34(5): 400-405. doi: 10.1016/S1673-8527(07)60043-5

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Abstract:
PCR-SSCP was used to analyze the polymorphism of leptin gene in 539 samples of six cattle breeds, namely Nanyang (NY), Qinchuan (QC), Jiaxianred (JXR), Xizhen (XZ), Luxi (LX), and Holstein cow (HOL) breeds. PCR products with a 330 bp were amplified and sequenced. The results showed that the frequencies of alleles A/B of NY, QC, JXR, XZ, LX, and HOL breeds were 0.558/0.442, 0.492/0.508, 0.571/0.429, 0.658/0.342, 0.591/0.409, and 0.615/0.385, respectively. The association of variations of leptin gene with growth traits in NY, QC, JXR breeds was analyzed. Some indexes of the individuals with genotype BB were higher than that with genotype AA and AB in NY breed, such as the indexes of body length, heart length, body weight, hucklebone width, body height, and average day gain. The height at hip cross of the individuals with genotype BB was higher than that of those with genotype AA and AB in QC breed (P < 0.05). So leptin gene may be one of the candidate genes for growth traits with height at hip cross, but not for body weight, heart length, and body length trait. However, the height at hip cross and hucklebone width of the individuals with genotype AB and BB were higher than that of those with genotypeAA in JXR breed (P < 0.05), but the difference was not statistically significant in body weight and body sizes (body height, body length, and heart length). And the polymorphisms in leptin gene were caused by G → T transversion at the 66th bp position, A → C transversion at the 67th bp position and G → T transversion at the 299th bp position. These results may be applied to marker-assisted selection of Chinese cattle breeds.

Genetic Polymorphism of TLR4 Gene and Correlation with Mastitis in Cattle

Xingping Wang, Shangzhong Xu, Xue Gao, Hongyan Ren, Jinbao Chen

2007, 34(5): 406-412. doi: 10.1016/S1673-8527(07)60044-7

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Toll-like receptor 4 (TLR4) recognizes pathogen ligands and mediates signaling to initiate innate and adaptive immune responses. In this experiment, a 316 bp and 382 bp fragments of TLR4 gene named T4CRBR1 and T4CRBR2, of Chinese Holstein, Sanhe cattle, and Chinese Simmental was amplified by polymerase chain reaction (PCR), respectively. The genetic polymorphisms in the three populations were detected by Single-Strand Conformational Polymorphism (SSCP) in the first locus and by digesting the fragments with restriction endonuclease Alu? in the second one. Results showed that both alleles (A and B) of two loci were found in all the three populations and the value of polymorphism information content (PIC) indicated that these were a moderate polymorphism. Statistical results of χ² test indicated that two polymorphism sites in the three populations fitted with Hardy–Weinberg equilibrium (P > 0.05). After sequencing, A-G single nucleotide polymorphism (SNP) was identified at nucleotide 4,525 in intron 1 of TLR4 gene and C-T SNP was identified at nucleotide 1,397 in exon 3 of TLR4 gene. Meanwhile, the effect of polymorphism of TLR4 gene on somatic cell score (SCS) was analyzed, the results indicated that the cattle with allele A in T4CRBR1 showed lower somatic cell score than that of allele B (P < 0.05). In short, the allele A might play an important role in mastitis resistance in bovine.

Phylogenetic Relationships and Status Quo of Colonies for Gayal Based on Analysis of Cytochrome b Gene Partial Sequences

Guolong Ma, Hong Chang, Shiping Li, Hongyu Chen, Dejun Ji, Rongqing Geng, Chunfang Chang, Yonghong Li

2007, 34(5): 413-419. doi: 10.1016/S1673-8527(07)60045-9

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Thirty-three mutations and four different haplotypes were found when cytochrome b(Cytb) gene partial sequences of 12 gayals were analyzed. Together with sequences of Bos indicus, Bos taurus, Bos grunniens and Bos gaurus with Bubalus bubalis as the out group, the partial sequences of Cytb gene of gayals were aligned and base composition and nucleotide variation ofCytb gene were analyzed. The phylogenetic trees were constructed by the NJ method and the MP method respectively, both supporting almost the same topology. Gayal is an independent species of Bos from Bos indicus, Bos taurus and Bos gaurus. The results also indicate that a great proportion of gayal bloodline was invaded by other species, and the protection of gayal is facing a formidable situation.

QTL Mapping and Q×E Interactions of Grain Cooking and Nutrient Qualities in Rice Under Upland and Lowland Environments

Yongmei Guo, Ping Mu, Jiafu Liu, Yixuan Lu, Zichao Li

2007, 34(5): 420-428. doi: 10.1016/S1673-8527(07)60046-0

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Grain cooking and nutrient qualities are the most important components of rice (Oryza sativa L.) quality. A doubled haploid (DH) population from a cross between two japonica cultivars was used to examine the phenotypic values and potential QTLs for the quality traits. The cooking and nutrient quality traits, including the amylose content (AC), the gel consistency (GC), the gelatinization temperature (GT), and the protein content (PC), in rice grown under upland and lowland environments were evaluated. Significant differences for AC, GC, GT, and PC between upland and lowland environments were detected. The phenotypic values of all four traits were higher under upland environment than lowland environment. The value of PC under upland environment was significantly higher (by 37.9%) than that under lowland environment. This suggests that upland cultivation had large effect on both cooking and nutrient qualities. A total of seven QTLs and twelve pairs of QTLs were detected to have significant additive and epistatic effects for the four traits. Significant Q × E interaction effects of two QTLs and two pairs of QTLs were also discovered. The general contribution of additive QTLs ranged from 1.91% to 19.77%. The Q × E interactions of QTLsQGt3 and QAc6 accounted for 8.99% and 47.86% of the phenotypic variation, respectively, whereas those of the 2 pairs of epistatic QTLs, QAc6-QAc11b and QAc8-QAc9, accounted for 32.54% and 11.82%, respectively. Five QTLs QGt6b, QGt8, QGt11, QGc1, and QPc2, which had relatively high general contribution and no Q × E interactions, were selected to facilitate the upland rice grain quality breeding.

Interval Mapping of Quantitative Trait Loci Underlying Triploid Endosperm Traits Using F3 Seeds

Yongxian Wen, Weiren Wu

2007, 34(5): 429-436. doi: 10.1016/S1673-8527(07)60047-2

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A statistical method for mapping quantitative trait loci (QTLs) underlying endosperm traits is proposed. The method is based on a genetic model containing both the direct effects and maternal effects of an endosperm QTL and on an experimental design termed two-stage hierarchical design, in which the trait information is obtained from F₃ endosperms and molecular marker information is obtained from F₂ plants and F₃ embryos (plants). Results of computer simulations indicate that the method can efficiently map endosperm QTLs and precisely estimate both the direct and maternal effects of endosperm QTLs when the sample size is sufficiently large.

The Distribution of Repetitive DNAs Along Chromosomes in Plants Revealed by Self-genomic in situ Hybridization

Chaowen She, Jingyu Liu, Ying Diao, Zhongli Hu, Yunchun Song

2007, 34(5): 437-448. doi: 10.1016/S1673-8527(07)60048-4

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The distribution of repetitive DNAs along chromosomes is one of the crucial elements for understanding the organization and the evolution of plant genomes. Using a modified genomic in situ hybridization (GISH) procedure, fluorescence in situ hybridization (FISH) with genomic DNA to their own chromosomes (called self-genomic in situ hybridization, self-GISH) was carried out in six selected plant species with different genome size and amount of repetitive DNA. Nonuniform distribution of the fluorescent labeled probe DNA was observed on the chromosomes of all the species that were tested. The signal patterns varied among species and were related to the genome size. The chromosomes of the small Arabidopsis genome were labeled almost only in the pericentromeric regions and the nucleolus organizer regions (NORs). The signals in the relatively small genomes, rice, sorghum, and Brassica oleracea var. capitata L., were dispersed along the chromosome lengths, with a predominant distribution in the pericentromeric or proximal regions and some heterochromatic arms. All chromosomes of the large genomes, maize and barley, were densely labeled with strongly labeled regions and weakly labeled or unlabeled regions being arranged alternatively throughout the lengths. In addition, enhanced signal bands were shown in all pericentromeres and the NORs in B. oleracea var. capitata and in all pericentromeric regions and certain intercalary sites in barley. The enhanced signal band pattern in barley was found consistent with the N-banding pattern of this species. The GISH with self-genomic DNA was compared with FISH with C_ot-1 DNA in rice, and their signal patterns are found to be basically consistent. Our results showed that the self-GISH signals actually reflected the hybridization of genomic repetitive DNAs to the chromosomes, thus the self-GISH technique would be useful for revealing the distribution of the regions where repetitive DNAs concentrate along chromosomes and some chromatin differentiation associated with repetitive DNAs in plants.

Genetic Diversity in Cultivated Groundnut Based on SSR Markers

Ronghua Tang, Guoqing Gao, Liangqiong He, Zhuqiang Han, Shihua Shan, Ruichun Zhong, Cuiqiu Zhou, Jing Jiang, Yangrui Li, Weijian Zhuang

2007, 34(5): 449-459. doi: 10.1016/S1673-8527(07)60049-6

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Peanut (Arachis hypogaea L.) is an important source crop for edible oil and protein. It is important to identify the genetic diversity of peanut genetic resources for cultivar development and evaluation of peanut accessions. Thirty-four SSR markers were used to assess the genetic variation of four sets of twenty-four accessions each from the four botanical varieties of the cultivated peanut. Among the tested accessions, ten to sixteen pairs of SSR primers showed polymorphisms. The maximum differentiation index, which was defined as the degree of genetic differentiation, was as high as 0.992 in the tested accessions. Each accession could be discriminated by a specific set of polymorphic SSR primers, and the intra-variety genetic distance was determined among accessions, with an average of 0.59 in var. fastigiata 0.46 in var. hypogaea 0.38 in var. vulgaris and 0.17 in var. hirsuta. Dendrogrames based on genetic distances were constructed for the four botanical varieties, which revealed the existence of different clusters. It was concluded that there was abundant intra-variety SSR polymorphism, and with more and more SSR markers being developed, the intrinsic genetic diversity would be detected and the development of genetic map and marker-assisted selection for cultivated peanut would be feasible.

Production of Partial New-typed Brassica Napus by Introgression of Genomic Components from B. rapa and B. carinata

Maoteng Li, Jianmin Liu, Yanting Wang, Longjiang Yu, Jinling Meng

2007, 34(5): 460-468. doi: 10.1016/S1673-8527(07)60050-2

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A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A^r subgenome of B. rapa (A^rA^r) and C^c of B. carinata (B^cB^cC^cC^c) into natural B. napus (AⁿAⁿCⁿCⁿ). The progenies with 38 chromosomes that were derived from the self-pollinated seeds of pentaploid hybrids (A^rAⁿB^cC^cCⁿ) were used for further research. Some of the partial new-typed B. napus showed normal meiotic behavior, high portion of germinated pollen and normal embryological development. This indicates that the selected new-typedB. napus had a balanced genetic base. Molecular analysis showed that about 50% of the genome in the new-typed B. napus was replaced by A^r and C^c subgenome from B. rapa and B. carinata. Considering the genetic diversity among different lines of new-typed B. napus it was deduced that the introgression of the genomic components from B. rapa and B. carinata could widen the genetic diversity of rapeseed.

Genetic Study on JS399-19 Resistance in Hyphal Fusion of Fusarium graminearum by Using Nitrate Nonutilizing Mutants as Genetic Markers

Yu Chen, Changjun Chen, Jianxin Wang, Lihua Jin, Mingguo Zhou

2007, 34(5): 469-476. doi: 10.1016/S1673-8527(07)60051-4

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Twenty-two nitrate nonutilizing (nit) mutants were recovered from five wild-type isolates of Fusarium graminearum and fifty nit mutants were recovered from three JS399-19-resistant mutants of F. graminearum cultured on MMC medium. Some biological properties were compared between nit mutants and their parental isolates. The results showed that there were no significant differences in growth rate, cultural characters or pathogenicity between JS399-19-resistant nit mutants and their parental isolates. But the conidial production and the sexual reproduction ability changed to some extent. There was no cross resistance toward chlorate and JS399-19 in F. graminearum and the resistance could be stable through 20-time subcultures. Therefore, the nit could be used as a genetic marker for studying the genetics of JS399-19 resistance in F. graminearum which was used to study JS399-19 resistance transferability in hyphal fusion. Resistance in JS399-19 could not be transferred by hyphal fusion or could be transferred with low chance between two compatible isolates, which would delay the development of JS399-19 resistance in the field.

2007 Vol. 34, No. 5