Selection In Genetic Variation Research Articles

Estimates of genetic variability, heritability and genetic advance for agronomic and yield traits in soybean (Glycine max L.)

A study with 20 soybean genotypes was conducted in 2015 and 2016 to determine the genetic variability, heritability and genetic advance for some agronomic and yield traits in some soybean genotypes for selection criteria in a breeding programme. The field experiments were laid out in a randomized complete block design (RCBD) and replicated three times. Analysis of variance (ANOVA) revealed significant variation among the genotypes indicating that the planting materials were genetically divergent from each other. The estimates of genetic variability showed that phenotypic coefficient of variation (PCV) were higher than the genotypic coefficient of variation (GCV) for all the traits. Portraying the importance of environmental factors in the variations shown. High value of PCV and GCV were observed for traits such as plant height, number of leaves, number of pods and seed yield indicating the presence of sufficient genetic variation for selection in these traits. High heritability coupled with high genetic advance observed for plant height and number of pods suggests that selection could be effective for these traits. Key words: Genetic advance, heritability, soybean, traits, variability.

The role of natural selection in shaping genetic variation in a promising Chagas disease drug target: Trypanosoma cruzi trans-sialidase

Rational drug design creates innovative therapeutics based on knowledge of the biological target to provide more effective and responsible therapeutics. Chagas disease, endemic throughout Latin America, is caused by Trypanosoma cruzi, a protozoan parasite. Current therapeutics are problematic with widespread calls for new approaches. Researchers are using rational drug design for Chagas disease and one target receiving considerable attention is the T. cruzi trans-sialidase protein (TcTS). In T. cruzi, trans-sialidase catalyzes the transfer of sialic acid from a mammalian host to coat the parasite surface membrane and avoid immuno-detection. However, the role of TcTS in pathology variance among and within genetic variants of the parasite is not well understood despite numerous studies. Previous studies reported the crystalline structure of TcTS and the TS protein structure in other trypanosomes where the enzyme is often inactive. However, no study has examined the role of natural selection in genetic variation in TcTS. To understand the role of natural selection in TcTS DNA sequence and protein variation, we examined a 471 bp portion of the TcTS gene from 48 T. cruzi samples isolated from insect vectors. Because there may be multiple parasite genotypes infecting one insect and there are multiple copies of TcTS per parasite genome, all 48 sequences had multiple polymorphic bases. To resolve these polymorphisms, we examined cloned sequences from two insect vectors. The data are analyzed to understand the role of natural selection in shaping genetic variation in TcTS and interpreted in light of the possible role of TcTS as a drug target. The analysis highlights negative or purifying selection on three amino acids previously shown to be important in TcTS transfer activity. One amino acid in particular, Tyr342, is a strong candidate for a drug target because it is under negative selection and amino acid substitutions inactivate TcTS transfer activity. Author summaryChagas disease is caused by the protozoan parasite Trypanosoma cruzi and transmitted to humans and other mammals primarily by Triatomine insects. Being endemic in many South and Central American countries and affecting millions of people the need for new more effective and safe therapies is evident. Here, we examine genetic variation and natural selection on DNA (471 bp) and amino acid (157 aa) sequence data of the T. cruzi trans-sialdiase (TcTS) protein, often suggested as a candidate for rational drug design. In our surveyed region of the protein there were five amino acid residues that have been shown to be integral to the function of TcTS. We found that three were under strong negative selection making them ideal candidates for drug design; however, one was under balancing selection and should be avoided as a drug target. Our study provides new information into identifying potential targets for a new Chagas drug.

Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress

Somatic variation in DNA can cause cells to deviate from the preordained genomic path in both disease and healthy conditions. Here, using exome sequencing of paired tissue samples, we show that the normal human brain harbors somatic single base variations measuring up to 0.48% of the total variations. Interestingly, about 64% of these somatic variations in the brain are expected to lead to non-synonymous changes, and as much as 87% of these represent G:C>T:A transversion events. Further, the transversion events in the brain were mostly found in the frontal cortex, whereas the corpus callosum from the same individuals harbors the reference genotype. We found a significantly higher amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the corpus callosum of the same subjects (p<0.01), correlating with the higher G:C>T:A transversions in the cortex. We found significant enrichment for axon guidance and related pathways for genes harbouring somatic variations. This could represent either a directed selection of genetic variations in these pathways or increased susceptibility of some loci towards oxidative stress. This study highlights that oxidative stress possibly influence single nucleotide somatic variations in normal human brain.

Metastatic Competence Can Emerge with Selection of Preexisting Oncogenic Alleles without a Need of New Mutations.

Several experimental models faithfully recapitulate many important facets of human metastatic disease. Here, we have performed whole-exome sequencing in five widely used experimental metastasis models that were independently derived through in vivo selection from heterogeneous human cancer cell lines. In addition to providing an important characterization of these model systems, our study examines the genetic evolution of metastatic phenotypes. We found that in vivo selected highly metastatic cell populations showed little genetic divergence from the corresponding parental population. However, selection of genetic variations that preexisted in parental populations, including the well-established oncogenic mutations KRAS(G13D) and BRAF(G464V), was associated with increased metastatic capability. Conversely, expression of the wild-type BRAF allele in metastatic cells inhibited metastatic outgrowth as well as tumor initiation in mice. Our findings establish that metastatic competence can arise from heterogeneous cancer cell populations without the need for acquisition of additional mutations and that such competence can benefit from further selection of tumor-initiating mutations that seed primary tumorigenesis.

An-2 Encodes a Cytokinin Synthesis Enzyme that Regulates Awn Length and Grain Production in Rice

A wide range of morphological and physiological traits have changed between cultivated rice Oryza sativa and wild rice Oryza rufipogon under domestication. Here, we report cloning of the An-2 gene, encoding the Lonely Guy Like protein 6 (OsLOGL6), which catalyzes the final step of cytokinin synthesis in O. rufipogon. The near-isogenic line harboring a wild allele of An-2 in the genetic background of the awnless indica Guangluai 4 shows that An-2 promotes awn elongation by enhancing cell division, but decreases grain production by reducing grains per panicle and tillers per plant. We reveal that a genetic variation in the An-2 locus has a large impact on reducing awn length and increasing tiller and grain numbers in domesticated rice. Analysis of gene expression patterns suggests that An-1 regulates the formation of awn primordial, and An-2 promotes awn elongation. Nucleotide diversity of the An-2 locus in cultivated rice was found to be significantly reduced compared with that of wild rice, suggesting that the An-2 locus was subjected to artificial selection. We therefore propose that the selection of genetic variation in An-2 was due to reduced awn length and increased grain yield in cultivated rice.

Plant-driven genome selection of arbuscular mycorrhizal fungi.

Plant-driven genome selection of arbuscular mycorrhizal fungi.

Transmission inter-espèces, adaptation à l’homme et pathogénicité des virus influenza d’origine animale

The emergence in 2009 of a novel A(H1N1)v influenza virus of swine origin and the regular occurrence since 2003 of human cases of infection with A(H5N1) avian influenza viruses underline the zoonotic and pandemic potential of type A influenza viruses. Influenza viruses from the wild aquatic birds reservoir usually do not replicate efficiently in humans. Domestic poultry and swine can act as intermediate hosts for the acquisition of determinants that increase the potential of transmission and adaptation to humans, through the accumulation of mutations or by genetic reassortment. The rapid evolution of influenza viruses following interspecies transmission probably results from the selection of genetic variations that favor optimal interactions between viral proteins and cellular factors, leading to an increased multiplication potential and a better escape to the host antiviral response. Whereas influenza viruses usually cause asymptomatic infections in wild aquatic birds, they may be highly pathogenic in other species. Molecular determinants of host-specificity and pathogenesis have been identified in most viral genes, notably in genes that encode viral surface glycoproteins, proteins involved in the viral genome replication, and proteins that counteract the host immune response. However, our knowledge of these numerous and interdependant determinants remains incomplete, and the molecular mechanisms involved are still to be understood.

Genetic diversity among populations and breeding lines from recurrent selection in Brassica napus as revealed by RAPD markers

AbstractRecurrent selection facilitated by dominant male sterility has been conducted to broaden the genetic basis for cultivar development in Brassica napus. This study aimed to evaluate the genetic variation in four base populations (C0‐C3) and breeding lines from two of the populations produced during recurrent selection by random amplified polymorphic DNA (Rapd) markers. Genetic variation in four populations declined gradually with the advance of selection cycles as measured by expected genetic heterozygosity (from 0.2058 in C0 to 0.1536 in C3) but the decline was not statistically significant. When compared with the average genetic distances for 21 germplasm collections with wide geographical and genetic origins (0.4712) and seven breeding lines from pedigree selection (0.2059), seven breeding lines selected from the C1 population and 11 from the C3 population had a larger average genetic distance (0.5339 and 0.5486, respectively). Clustering analysis indicated that the lines from recurrent selection had a much lower genetic similarity than lines from pedigree selection. Our results suggest that base populations derived from recurrent selection could provide a wider genetic variation for selection of breeding lines with more broad genetic bases.

Heavy Metal Resistance and Accumulation Characteristics in Willows

ABSTRACT The resistance of Salix to Cu, Cd, Ni, and Zn was investigated in hydroponic culture, with phytoextraction potential evaluated for Cu. Root elongation (indicative of resistance level) was significantly affected, with considerable variation between and within individual clones. Resistance appeared to be clone- or hybrid-specific, rather than species-specific. S. caprea clones (and hybrids) were among the most resistant, but a secondary S. caprea clone from a different provenance was much less tolerant. S. viminalis and S. triandra clones were the most sensitive. Highest resistance was found in response to Cd, while Cu and Ni were extremely toxic. A resistant S. caprea ecotype originating from a metalliferous mine spoil was identified using this technique. Copper concentration reached a maximum of 2000, 400, and 82 μg g-1 (d.wt) in roots, wood, and foliage, respectively, after 1 month in hydroponic culture. The level of variation in the response of Salix to metals may cause difficulties in phytoremediation screening programs, but may be essential in providing genetic variation for selection of metal resistance traits, where the contaminant profile is heterogeneous, mixed, or subject to change. Clone selection for metal phytoextraction is feasible, but a longer field-scale study on metal-contaminated soils is needed before their role in phytoremediation can be confirmed.