Effects of Different Mutation Rates and Randomness on the Distribution of Linkage Disequilibrium

Background Mutation has recently received much attention on its role in the evolution and genetics of complex trait. The linkage disequilibrium (LD) distribution can be affected by mutation as reported recently, in which the same mutation rates were adopted in the transition matrix. However, effects of different types, rates and randomness of mutation on LD distribution remain unexplored. Results Here, we considered in the transition matrix mutations at each locus to be of different types and rates (i.e. nucleotide transition or transversion treated differently), to examine how the LD distribution between two genetic loci was affected. After examining consecutively factors such as effective population size, recombination and selection, different mutation types and rates could further change the dynamics of LD distribution. However, at the current scale of mutation rate (weak at 10−9-10−8), mutation seemed to play only a minor role, compared to recombination and selection. A simple model further showed that mutation randomness increased the ruggedness of LD curves, which fluctuated around the steady state. Conclusions Taken together, different mutation rates and randomness could further disturb the dynamics of LD distribution. Our findings can help better understand the role of mutation in molecular evolution and complex trait genetics.

HIGH-TILLERING AND DWARF 12 regulates photosynthesis and plant architecture by affecting carotenoid biosynthesis in rice

Photosynthesis and plant architecture are important factors influencing grain yield in rice (Oryza sativa L.). Here, we identified a high-tillering and dwarf 12 (htd12) mutant and analyzed the effects of the HTD12 mutation on these important factors. HTD12 encodes a 15-cis-ζ-carotene isomerase (Z-ISO) belonging to the nitrite and nitric oxide reductase U (NnrU) protein family, as revealed by positional mapping and transformation experiments. Sequence analysis showed that a single nucleotide transition from guanine (G) to adenine (A) in the 3’ acceptor site between the first intron and second exon of HTD12 alters its mRNA splicing in htd12 plants, resulting in a 49-amino acid deletion that affects carotenoid biosynthesis and photosynthesis. In addition, compared with the wild type, htd12 had significantly lower concentrations of ent-2’-epi-5-deoxystrigol (epi-5DS), a native strigolactone, in both roots and root exudates, resulting in an obvious increase in tiller number and decrease in plant height. These findings indicate that HTD12, the rice homolog of Z-ISO, regulates chloroplast development and photosynthesis by functioning in carotenoid biosynthesis, and modulates plant architecture by affecting strigolactone concentrations.

Genetic Polymorphism Analysis of Mitochondrial DNA from Chinese Guangdong Liannan Yao ethnic group

Background Genetic polymorphism and haplotype distribution characteristics analysis of mitochondrial DNA in Chinese Guangdong Liannan Yao group was conducted in this study, to provide genetic basis for tracing the origin and historical migration of Liannan Yao people.Results 46 mutation sites were found, and among which single nucleotide transition was the most commonly observed variant (86.17%). Multiple (sub)haplogroups were detected in Liannan Yao ethnic group, among which haplogroup D was the most common haplogroup (29.80%), and the least were C and Y(0.48% respectively). Conclusions The Liannan Yao population had the commonalities of the ethnic groups in southern China, but it was significantly different from other Chinese ethnic populations. The present results revealed that Liannan Yao ethnic group was genetically closer related to Fujian She ethnic population, Yunnan Yao population, and Hunnan Miao population. The data enriched the Chinese mtDNA database and provided a reference for forensic identification and screening for potential pathogenic mutations.

Nucleotide Transition 390C-T in the Wilms' Tumor 1 Gene: A Risk Factor of Hypospadias?

Introduction: The gene Wilms' tumor 1 (WT1) encodes a unique transcription factor. Its defects are known to cause a wide range of complex genitourinary malformations and may contribute to non-syndromic forms of hypospadias. Materials and Methods: We performed WT1 mutation analysis and copy number analysis of WT1-interacting protein in 13 Hungarian patients diagnosed with isolated hypospadias. Results: Sequencing of WT1 revealed a high frequency of heterozygosity for transition 390C-T (5 heterozygotes out of 13 patients, including 2 brothers). WT1-interacting protein had a normal copy number in all patients. Conclusion: Nucleotide substitution 390C-T may play a role in the pathogenesis of non-syndromic hypospadias. The genotype-phenotype correlation should be confirmed by a larger-scale analysis.

SEQUENCE POLYMORPHISM OF MITOCHONDRIAL DNA HYPERVARIABLE REGIONS I AND II IN MALAY POPULATION OF MALAYSIA

The analysis of the control region of human mitochondrial genome (mtDNA) especially hypervariable regions I (HVI) and II (HVII) segments have been proven to be useful for human identification. For forensic application of mtDNA profiling in Malaysia, a comprehensive database on both HVI and HVII regions are essential. In order to identify polymorphic positions and to determine their frequency in the Malay population, mtDNA HVI and HVII regions of 103 maternally unrelated individuals were amplified ,sequenced and compared with Cambridge reference sequence (CRS). Sequence comparison led to the identification of a total of 446 and 604 location polymorphisms in mtDNA HVI and HVII regions respectively. This polymorphisms defined by 88 haplotypes (81 unique) in the HVI and 78 haplotypes (64 unique) in the HVII regions. In combined HVI and HVII defined 101 haplotypes (99 unique) was defined. In the HVII region All the individuals in HVII showed nucleotide transition event from A G at nucleotide position 073 and 263 and an insertion of cytosine (315.1C) at nucleotide position 315. The genetic diversity and probability of random match in combined HVI and HVII of 103 Malay individuals was found to be 0.9996 and 0.0101 respectively.Scientific World, Vol. 12, No. 12, September 2014, page 24-29

Analysis of primary structure loops from Hairpins 35 and 48 of the Nematoda SSU rRNA gene provides further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida

A comparison of small subunit (SSU) rDNA sequences has revealed that a rare nucleotide transition A→G and a trans-version G→Y occurred simultaneously in the evolutionarily conserved loops of Hairpins 35 and 48 of the SSU rRNA geneof Tripylina Brzeski 1963, Trischistoma Cobb 1913 and Rhabdolaimus de Man 1880. The same pair of substitutions oc-curred in all Enoplida analysed but not in other nematodes. This evidence from the primary structure of Hairpins 35 and48 indicates that Tripylina, Trischistoma and Rhabdolaimus are members of Enoplida, supporting previous phylogenetic analyses.

C242T Polymorphism in CYBA Gene (p22phox) and Risk of Coronary Artery Disease in a Population of Caucasian Italians

Background: specific polymorphisms of genes regulating intracellular redox balance and oxidative stress are related to atherogenesis. Some studies have identified a relationship between progression of atherosclerosis and C242T mutation in CYBA gene coding for p22phox, a subunit of the NADH/NADPH oxidase system.Design: we investigated whether the C242T nucleotide transition is associated with the presence of coronary artery disease (CAD) in a population of 494 Caucasian Italians undergoing coronary angiography to diagnose the cause of chest pain.Results: the frequency of the T mutant allele that we found in 276 patients with angiographically documented CAD was significantly higher compared to what we observed in 218 subjects with normal coronary arteries (Controls) (respectively: 0.400 and 0.332,p< 0.01). The prevalence of the T allele was even stronger when we compared: 1) early onset (age ≤55) vs late onset (age ≥65) single-vessel CAD patients (respectively: 0.75 and 0.48,p< 0.05), and 2) the subgroup of CAD patients with at least one ≥98% stenosis in a coronary vessel vs those with no ≥98% stenosis in a coronary vessel (respectively: 0.425 and 0.365,p< 0.05).Conclusions: these results support the increased risk of developing early CAD and of having rapid progression of coronary stenosis in subjects carrying the C242T nucleotide transition among the Italian population.