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Biochemical Genetics (v.49, #9-10)

SSR Marker-Based DNA Fingerprinting and Cultivar Identification of Olives (Olea europaea) by Sezai Ercisli; Ahmet Ipek; Erdogan Barut (pp. 555-561).

Four well-known commercial olive cultivars (Domat, Edremit, Gemlik, and Memecik) and six local cultivars (Ziraat, Isrange, Tuz, Patos, Yag, and Marantelli) from northeastern Turkey were analyzed for genetic diversity and relationships using seven SSR primers (DCA-4, DCA-09, DCA-11, DCA-16, DCA-17, GAPU-89, UDO-14). The number of markers ranged from 3 (DCA-04 and DCA-17) to 6 (DCA-11, DCA-16, GAPU-89), with an average of 4.57 alleles per primer. UPGMA cluster analysis based on a simple matching similarity matrix grouped cultivars into two main clusters. Three pairs of cultivars (Ziraat and Gemlik, Isrange and Tuz, and Patos and Yag) were thought to be different cultivars although they produced identical SSR profiles. The results indicate the efficiency of SSR markers for evaluation of genetic diversity in olives and identification of misnamed individuals of the same genotype.

Keywords: Olive; Molecular markers; SSR; Genetic diversity

Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii by Taranjeet Kaur; Alan H. K. Ong (pp. 562-575).

This study describes the organization of the repetitive pattern in the mtDNA control region of Tomistoma schlegelii. Using newly designed primers, we detected length variations of approximately 50–100 bp among individuals, and only one individual showed a heteroplasmic band. Sequencing the region after CSB III revealed two main patterns: a repeat motif and a variable number tandem repeat (VNTR) pattern. The VNTR region, with a core unit of 104 bp, consisting of four motifs and a short AT chain, is implicated in the length variation seen among individuals of Tomistoma. A conserved motif seen in a family unit indicated that the repeat pattern was stably inherited from the maternal parent to all offspring. A combination of VNTR patterns specific to different crocodilians was seen in Tomistoma, and the overall secondary structure was shown to be similar to that in Crocodylus and Gavialis.

Keywords: Tomistoma ; mtDNA VNTR; Family unit; Interspecific comparison

Molecular Cloning and Expression Analysis of Porcine Ghrelin O-Acyltransferase by Tonghui Lin; Qingyong Meng; Dandan Sui; Dezhi Peng; Yang Li; Xiaofang Liu; Longfei Xie; Ning Li (pp. 576-586).

The peptide hormone ghrelin is secreted in the stomach, with unique N-octanoylation at serine 3, which is a requirement for its functionality. These functions include growth hormone release, appetite stimulation, gastrointestinal motility, glucose regulation, and cell proliferation. The enzyme responsible for ghrelin acylation was recently identified as ghrelin O-acyltransferase (GOAT). In this study, porcine GOAT was cloned and characterized. A full-length cDNA of GOAT of 2013 bp was obtained, which included a 70-bp 5′ UTR, a 635-bp 3′ UTR, and a 1308-bp open reading frame encoding a protein of 415 amino acids. The GOAT and ghrelin mRNAs are co-expressed in stomach, pancreas, and duodenum at high levels. GOAT was also detected in liver, lung, brain, testis, spleen, kidney, heart, muscle, lipid, and ovary. Our results provide an important basis for further research on GOAT function and the relationship between ghrelin and GOAT.

Keywords: Ghrelin O-acyltransferase; Ghrelin; Pig; Cloning; Expression

Lipoprotein Lipase (A1127G) Gene Polymorphism: A Case–Control Association Study by Rajneesh Tripathi; Sarita Agarwal; Venkataraman Ramesh (pp. 587-591).

Association of a Tandem Repeat Polymorphism in NFATc1 with Increased Risk of Perimembranous Ventricular Septal Defect in a Chinese Population by Haiyong Gu; Jie Gong; Wanshan Qiu; HaiLong Cao; Jing Xu; Suocheng Chen; Yijiang Chen (pp. 592-600).

The nuclear factor of activated T lymphocytes (NFATc1) plays a critical role during valvular and septal development. Genetic variants may influence the biological function of the protein and thus play a role in susceptibility to valvuloseptal defects. Tandem repeat polymorphisms and a common nonsynonymous polymorphism (Cys751Gly) of NFATc1 were genotyped in a hospital-based case–control study of 241 patients with valvuloseptal cardiac defects and 557 controls. The risk of valvuloseptal defect associated with the variant homozygote (LL) was significantly greater than that of the wild-type homozygote. Based on stratification analyses by congenital heart disease types, individuals with the LL genotype were postulated to have a higher risk of perimembranous ventricular septal defect (adjusted OR = 1.68, 95% CI = 1.02–2.78). These findings suggest the usefulness of the NFATc1 tandem repeat polymorphism as a biomarker of perimembranous ventricular septal defect susceptibility.

Keywords: NFATc1 ; Genetic polymorphisms; Ventricular septal defect; Molecular epidemiology

Molecular Characterization of Factor V Leiden G1691A and Prothrombin G20210A Mutations in Saudi Newborns with Stroke by Gihan E-H. Gawish (pp. 601-610).

This study examined a possible association between the mutations related to Factor V Leiden and Factor II (prothrombin) and stroke in Saudi neonates. A multiplex PCR was established to detect Factor V Leiden G1691A and prothrombin G20210A mutations in 72 neonatal stroke subjects and 70 healthy adult controls with no family history of thromboembolic diseases. The frequency of the homozygous normal genotype (GG) of both genes was found to be significantly lower in the stroke subjects than in the controls (P < 0.0001). The stroke cases also had higher frequencies of the combined Factor II heterozygous mutant form (GA) and the homozygous normal Factor V (GG) (P < 0.0001) and of the combined heterozygous Factor V and the homozygous normal Factor II genotypes (GG) (P = 0.0) than controls. The study concluded that prothrombin and Factor V Leiden may be important risk factors for neonatal stroke in Saudi children.

Keywords: Neonatal stroke; Factor V Leiden; Factor II; Prothrombin

Microsatellite Analysis of Homozygosity Progression of Heterozygous Genotypes Segregating in the Rice Subspecies Cross Pei’ai64s/Nipponbare by Yong-shu Liang; Qi-jun Zhang; Shi-quan Wang; Li-yong Cao; Zhi-qiang Gao; Ping Li; Shi-hua Cheng (pp. 611-624).

Progression to homozygosity of heterozygous genotypes was studied in a cross of the rice subspecies Pei’ai64s and Nipponbare, using a set of 157 polymorphic microsatellite (SSR) markers. The segregation of heterozygous genotypes ranged from 49.13% in the F₂ population to 4.52% in the F₆ population (progression value 11.15%). The heterozygous genotypes were widely distributed in 180 F₂ plants, 330 F₆ lines, and 157 SSR markers. Homozygosity progression showed a wide distribution in plants and SSR markers but not in chromosomes. The segregation of heterozygous genotypes was not significant between populations but varied greatly in F₂ plants, F₆ lines, and SSR markers. The correlation between the progression to homozygosity and the heterozygosity of SSR markers was significant at the chromosome level. The segregation of heterozygous genotypes in plants, SSR markers, and chromosomes was not completely in accordance with Mendel’s law. This information will help rice geneticists and breeders to understand heterozygous genotype segregation at the DNA level and to screen special markers for breeding.

Keywords: Rice (Oryza sativa L.); Subspecies cross; Microsatellite (SSR); Heterozygous genotype; Homozygosity progression

Isolation of 106 Microsatellite Markers for the Pacific Abalone from a Trinucleotide-Enriched Library by Zhen Zhang; Bu-jin Xu; Li-bo Zhang; Hui Sun; Qing-guo He; Shao-wen Wang; Xiao-wen Sun; Xiao Liu (pp. 625-637).

Molecular Cloning, Characterization, Polymorphism, and Association Study of the Interleukin-2 Gene in Indian Crossbred Cattle by Ved Prakash; Tarun K. Bhattacharya; Basanti Jyotsana; O. P. Pandey (pp. 638-644).

Identification of Differentially Expressed Genes During the Brachyurization of the Chinese Mitten Crab Eriocheir japonica sinensis by Peng Li; Jie Zha; Hongying Sun; Daxiang Song; Kaiya Zhou (pp. 645-655).

Expressed sequence tags (ESTs) obtained from two-directional suppression subtractive hybridization (SSH) of cDNA libraries derived from the pleon of the Chinese mitten crab were analyzed using mRNA subtractive hybridization. After cDNA cloning and sequencing, gene expression profiles were examined, focusing on brachyurization. We assembled 211 non-redundant ESTs from SSH library 1 (yielding 130 unique transcripts: 25 consensi, 105 singletons) and 669 from SSH library 2 (195: 51 consensi, 144 singletons). Functional analysis shows that these genes are putatively involved in various cellular processes (33%), ribosomal RNA/proteins (30%), molting (12%), signal transduction (6%), immune factor and stress proteins (6%), development (4%), energy metabolism (3%), and mitochondrial membrane protein, hormone metabolizing, and chaperone (1% each) of other organisms. Some 3% are of unknown function in SSH library 1. The results facilitate the functional study of candidate genes involved in early developmental processes, especially the regulation of brachyurization in this crab.

Keywords: Brachyurization; Eriocheir japonica sinensis ; Expressed sequence tags; Expression profile; Suppression subtractive hybridization

Cloning and Expression of One Chloroplastic Ascorbate Peroxidase Gene from Nelumbo nucifera by Chen Dong; Xingfei Zheng; Guolin Li; Cheng Pan; Mingquan Zhou; Zhongli Hu (pp. 656-664).

A novel ascorbate peroxidase (APX) cDNA was obtained from Nelumbo nucifera (Elian). The phylogenetic analysis indicated that N. nucifera APX grouped together with chloroplastic APX of high plants. The recombinant protein expressed by PET-30a vector showed APX activity (0.04 mM ascorbate min⁻¹ mg⁻¹ protein). The APX mRNA was expressed in young leaves, roots, terminal buds, and leafstalks. Synergistic expression of N. nucifera APX and MnSOD mRNA was indicated in the short-term response to mechanical wounding.

Keywords: APX; MnSOD; Synergistic expression

Polymorphism of M307 of the FUT1 Gene and Its Relationship with Some Immune Indexes in Sutai Pigs (Duroc × Meishan) by W. B. Bao; L. Ye; J. Zhu; Z. Y. Pan; G. Q. Zhu; X. G. Huang; S. L. Wu (pp. 665-673).

The alpha (1,2)fucosyltransferase (FUT1) gene has been identified as a candidate gene for controlling the expression of the enterotoxigenic Escherichia coli (ETEC) F18 receptor. Polymorphisms were detected at the M307 position in FUT1 of a breeding base population of Sutai pigs and their correlations to immune parameters analyzed. After digestion by Hin6I, three genotypes were identified at M307, AA (frequency 0.235), AG (0.609), and GG (0.156), with significant deviation from Hardy–Weinberg equilibrium (P < 0.01). The hemoglobin and white blood cell count of the AA genotype pigs were significantly higher than those of AG and GG pigs (P < 0.05). The results indicated that AA pigs not only are resistant to edema disease and post-weaning diarrhea in piglets but also have relatively strong resistance to disease in general.

Keywords: FUT1 gene; Swine; Immune indexes; Pig; Breeding for disease resistance

Genetic Structure of Indian Valerian (Valeriana jatamansi) Populations in Western Himalaya Revealed by AFLP by Subramani Rajkumar; Sunil Kumar Singh; Akshay Nag; Paramvir S. Ahuja (pp. 674-681).

Valeriana jatamansi Jones is a natural tetraploid species indigenous to the Indian Himalaya. To assess its genetic diversity and population structure, we analyzed six natural populations from the western Himalayan region using amplified fragment length polymorphism. An analysis of molecular variance found that 93% of the genetic variation of V. jatamansi was within populations and 7% among populations. The correlation between genetic and geographic distances (r = 0.14) was not significant. Though the populations are well separated, the lack of distinct genetic variation between populations may be due to either recent rapid fragmentation from a wide and continuous area resulting in genetically similar populations or wide dispersal of seed by wind, since the follicles are feathery. Polyploidy may be the reason for the lack of genetic impoverishment due to fragmentation.

Keywords: Valeriana jatamansi ; AFLP; Population genetic structure; Western Himalaya; Natural tetraploid; Medicinal plant

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Biochemical Genetics (v.49, #9-10)

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Biochemical Genetics (v.49, #9-10)