Distinct geographical structure across species units evidenced by chloroplast DNA haplotypes and nuclear ribosomal ITS genotypes of Corylopsis (Hamamelidaceae) in the Japanese islands

The geographical distribution of chloroplast DNA (cpDNA) haplotypes and nuclear ribosomal internal transcribed spacer (nrITS) genotypes of Japanese Corylopsis (Hamamelidaceae), which consists of four species, was investigated. Two hundred and five individuals belonging to four species from 30 populations, covering the entire geographical range, were studied. Based on approximately 1108 bp of the three non-coding regions of cpDNA, nine haplotypes were detected, and each was distinguished from adjacent haplotypes by one substitution. Based on approximately 507-bp nrITS sequences, 47 genotypes were detected, for which three clades were identified in the phylogenetic analysis. There was inconsistency between the cpDNA haplotypes, nrITS genotypes, and classification of Corylopsis taxa, possibly because of incomplete lineage sorting or introgressive hybridization. The distribution of the haplotypes was highly structured geographically, and N _ST (0.893) was significantly greater than G _ST (0.819), implying that the current distribution of Corylopsis species was structured phylogeographically during Quaternary climatic oscillations. The haplotype composition and results of analysis of molecular variance showed that the populations in Hokuriku were highly divergent, suggesting that they are long-term persistent populations arising from refugia during the Quaternary climatic oscillations. Refugial populations in Chugoku and Shikoku may have lost genetic diversity because of a bottleneck resulting from a small population size, followed by post-glacial range expansion. Pre-existing refugia may have been so small that the subsequent range expansion replaced the pre-existing genetic structure.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 501–518.     

Can genomics clarify the origins of Boreioglycaspis melaleucae in California,USA?

The Australian psyllid Boreioglycaspis melaleucae is a biological control agent of Melaleuca quinquenervia in Florida (USA) but was observed attacking M. quinquenervia trees in southern California (USA). Genotyping revealed the California population matched three of eight Australian haplotypes and all three Florida haplotypes. It remains unclear if the California psyllid population arrived directly from Australia or via Florida.     

Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.     

DISC1 gene polymorphisms and the risk of schizophrenia in an Iranian population: A preliminary study

Background: Schizophrenia, schizoaffective disorder, and bipolar illness are common psychological disorders with high heritability and variable phenotypes. The disrupted in schizophrenia 1 ( DISC1) gene, on chromosome 1q42, has an essential role in neurite outgrowth and cell signaling. The purpose of this study was to investigate the association of three single-nucleotide polymorphisms (SNPs; rs6675281, rs2255340, and rs2738864) with schizophrenia disorder. These three SNPs were chosen as they had been used in most of the previous studies. Methods: In a case-control study of Iranian population for the first time 778 blood samples were collected including, 402 schizophrenic patients and 376 healthy controls. Genomic DNA was extracted from peripheral blood using DNA extraction kit (BioFlux Co). The genotypes of rs6675281, rs2255340, and rs2738864 were detected by nested allele-specific multiplex polymersae chain reaction (PCR). Results: Our data revealed that the three SNPs are significantly associated with schizophrenia (rs2255349 C>T: confidence interval (CI), 2.115 to 3.268; P = 0.0000 OR: 2.629; rs2738864 C>T: CI, 1.538 to 2.339; P = 0.0000 OR: 1.897; rs6675281 C>T: CI, 2.788 to 4.662; P = 0.0009241 OR: 3.605). Through applying the expectation-maximization (EM) algorithm, we calculated the haplotype frequency, and finally performed haplotype analysis with Bonferroni correction and data preprocessing methods and the results showed rs66875281 to have the highest association. Discussion: Our findings primarily showed that DISC1 gene polymorphisms contribute to schizophrenia risk and have a significant association with this disorder among Iranian population. The strategy was found to be easy, rapid, specific, and consistent for the co-occurring detection of the DISC1 polymorphisms. We could finally confirm that the polymorphisms are related to schizophrenia studied in Iranian population.     

A new single nucleotide polymorphism in the rabbit (Oryctolagus cuniculus) myostatin (MSTN) gene is associated with carcass composition traits

This study aimed at the identification of genetic variations in the myostatin (MSTN) gene and testing their effects on carcass quality traits. We comparatively sequenced Giant Grey (GG) and New Zealand White (NZW) rabbits that were founders of a cross‐bred population. Alignment of our sequence data with the GenBank sequence of the rabbit MSTN gene (Ensembl Gene ID ENSOCUG00000012663) identified three single nucleotide polymorphisms (SNPs). The two novel SNPs (c.?125T>C, c.373+234G>A) and one known SNP (c.747+34C>T) were subsequently analysed for linkage with carcass composition traits in 363 F₂ animals of the cross GG × NZW. Significant linkage was found between c.373+234G>A and nine carcass composition traits (P < 0.05). No significant effects were found for c.?125T>C and c.747+34C>T. Because the linked SNP is located in intron 1 and no genetic variation was found in the coding region, further investigations are necessary to understand the functional effect of the c.373+234G>A variant on the variability of the traits.     

Genetic variations in the SPP1 promoter affect gene expression and the level of osteopontin secretion into bovine milk

Osteopontin (OPN) is now recognized as an important cytokine and extracellular integrin‐binding protein at the crossroads of inflammation and homeostasis. In a previous study, we found that OPN gene (SPP1) polymorphisms are associated with milk performance traits and somatic cell score (SCS), a parameter used to estimate the genetic value of udder health in dairy cattle. In this study, we assessed whether the genetic variations had an impact on SPP1 promoter activity, immune response and the level of OPN secreted into milk. The influence of DNA polymorphisms on the promoter activity of SPP1 was confirmed in vitro. To measure the impact of the genetic variations on OPN secretion into milk, we measured OPN levels in both plasma and milk throughout lactation. Cows were grouped by the OPN haplotypes associated with a high (H2 × H3) or low (H1 × H4) SCS. For both H2 × H3 and H1 × H4, the OPN level in plasma remained low throughout lactation, although the concentration in the milk of H1 × H4 cows increased more in late lactation. Moreover, the macrophages of H1 × H4 cows expressed a lower SPP1 and proinflammatory IL6 in response to infection. Regarding the immune cell response, cows with the genetic potential to secrete higher OPN levels during late lactation had macrophages expressing fewer proinflammatory cytokines, a situation that might explain the genetic association with low somatic cells. Although OPN's favorable roles during late lactation remain to be elucidated, the tissue remodeling properties associated with OPN may be beneficial for reducing the incidence of infection during the transition period in lactating cows.     

Genome‐wide scans to detect positive selection in Large White and Tongcheng pigs

Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long‐range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient F_ST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.     

Genetic variations at the human growth hormone receptor (GHR) gene locus are associated with idiopathic short stature

GH plays an essential role in the growing child by binding to the growth hormone receptor (GHR) on target cells and regulating multiple growth promoting and metabolic effects. Mutations in the GHR gene coding regions result in GH insensitivity (dwarfism) due to a dysfunctional receptor protein. However, children with idiopathic short stature (ISS) show growth impairment without GH or GHR defects. We hypothesized that decreased expression of the GHR gene may be involved. To test this, we investigated whether common genetic variants (microsatellites, SNPs) in regulatory regions of the GHR gene region were associated with the ISS phenotype. Genotyping of a GT‐repeat microsatellite in the GHR 5′UTR in a Montreal ISS cohort (n = 37 ISS, n = 105 controls) revealed that the incidence of the long/short (L/S) genotype was 3.3× higher in ISS children than controls (P = 0.04, OR = 3.85). In an Italian replication cohort (n = 143 ISS, n = 282 controls), the medium/short (M/S) genotype was 1.9× more frequent in the male ISS than controls (P = 0.017, OR = 2.26). In both ISS cohorts, logistic regression analysis of 27 SNPs showed an association of ISS with rs4292454, while haplotype analysis revealed specific risk haplotypes in the 3′ haploblocks. In contrast, there were no differences in GT genotype frequencies in a cohort of short stature (SS) adults versus controls (CARTaGENE: n = 168 SS, n = 207 controls) and the risk haplotype in the SS cohort was located in the most 5′ haploblock. These data suggest that the variants identified are potentially genetic markers specifically associated with the ISS phenotype.