G46B is a promising holding line used for three-lines breeding strategy in hybrid rice, but it is susceptible to blast disease caused by Pyricularia grisea. To improve its blast resistance, three rice varieties, Digu, BL-1, and Pi-4, with blast resistance genes, Pi-d(t), Pi-b, and Pi-ta2, respectively, were used to be crossed with G46B, and 15 plants with these three blast resistance genes, Pi-d(t)1, Pi-b, and Pi-ta2, were selected from their F2 and B1C1 populations via a marker-aided crossing procedure. Among them, four plants were heterozygotes in the three resistance genes, with the genotype of Pi-d(t)1 pi-d(t)/Pi-b pi-b/ Pi-ta2 pi-ta2; ten plants were heterozygotes in two of the three resistance genes, of which six with the genotype of Pi-d(t)1 Pi-d(t)1/Pi-b pi-b/Pi-ta2 pi-ta2, three with the genotype of Pi-d(t)1 pi-d(t)1/Pi-b pi-b/Pi-ta2 Pi-ta2, and one with the genotype of Pi-d(t)1pi-d(t)1/Pi-b Pi-b/Pi-ta2 pi-ta2; and only one plant was homozygote in two of the three resistance genes with the genotype of Pi-d(t)1 Pi-d(t)/Pi-b pi-b/Pi-ta2 Pi-ta2. These results demonstrate the capacity of maker-assisted selection (MAS) in gene pyramiding for rice blast resistance and its enhancement for the efficiency in rice resistance breeding.
Crosses, Genetic ; Genes, Plant ; Genetic Markers ; Genotype ; Oryza ; genetics ; Plant Diseases ; genetics ; Selection, Genetic

OBJECTIVETo evaluate the effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS).

METHODSThree populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The starting frequencies of the QTL's favorable allele were 0.1, 0.3 and 0.5, respectively. The economic return was calculated by gene flow method.

RESULTSThe selection efficiency was higher than 100% when DR markers were used in GAS for 5 traits. The selection efficiency for NBA was the highest, and the lowest was for ADG whose QTL had the lowest variance. The mixed model applied DR markers and obtained higher extra genetic gain and extra economic returns. We also found that the lower the frequency of the favorable allele of the QTL, the higher the extra return obtained.

CONCLUSIONGAS is an effective selection scheme to increase the genetic gain and the economic returns in pig breeding.

Animals ; Breeding ; economics ; methods ; Genetic Markers ; Models, Genetic ; Quantitative Trait Loci ; Selection, Genetic ; Swine

One of the main topics in population genetics is identification of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome-scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species' demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoretical and practical aspects in near future.
Adaptation, Physiological ; genetics ; Demography ; Evolution, Molecular ; Genetics, Population ; Genome ; Models, Genetic ; Polymorphism, Genetic ; Selection, Genetic ; genetics

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's T² test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.
Genetic Association Studies ; Genetic Testing ; Ovarian Neoplasms ; Phenotype ; Principal Component Analysis ; Selection, Genetic ; Transcutaneous Electric Nerve Stimulation

Plasmodium vivax merozoite surface protein-1 (PvMSP1) gene codes for a major malaria vaccine candidate antigen. However, its polymorphic nature represents an obstacle to the design of a protective vaccine. In this study, we analyzed the genetic polymorphism and natural selection of the C-terminal 42 kDa fragment within PvMSP1 gene (Pv MSP142) from 77 P. vivax isolates, collected from imported cases of China-Myanmar border (CMB) areas in Yunnan province and the inland cases from Anhui, Yunnan, and Zhejiang province in China during 2009–2012. Totally, 41 haplotypes were identified and 30 of them were new haplotypes. The differences between the rates of non-synonymous and synonymous mutations suggest that PvMSP142 has evolved under natural selection, and a high selective pressure preferentially acted on regions identified of PvMSP133. Our results also demonstrated that PvMSP142 of P. vivax isolates collected on China-Myanmar border areas display higher genetic polymorphisms than those collected from inland of China. Such results have significant implications for understanding the dynamic of the P. vivax population and may be useful information towards China malaria elimination campaign strategies.
China ; Genetic Variation* ; Haplotypes ; Malaria ; Merozoite Surface Protein 1* ; Merozoites* ; Myanmar ; Plasmodium vivax* ; Plasmodium* ; Polymorphism, Genetic ; Selection, Genetic* ; Silent Mutation

The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous(NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S > or = 3), negatively selected genes (NS/S < or = 1/3) and neutral selection genes (0.9 < NS/S < 1.1). We characterized human genes targeted by natural selection. Negatively selected human genes were markedly associated with disease occurrence, but not positively selected genes. Interestingly, positively selected genes displayed an increase in potentially deleterious nonsynonymous SNPs with an increased frequency of tryptophan and tyrosine residues, suggesting a correlation with protective effects against human disease. Furthermore, our nonsynonymous/synonymous ratio data imply that specific human genes, such as ALMS1 and SPTBN5 genes, are differentially selected among distinct populations. We confirmed that inferences of natural selection using the NS/S ratio can be used extensively to identify functional genes selected during the evolutionary adaptation process.
Clinical Coding ; Genome, Human ; Humans ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Tryptophan ; Tyrosine

OBJECTIVEIn order to investigate the relationship between selection pressure and the prevalence of antigenic clusters, we sequenced and analyzed the H3N2 influenza virus from China between 1992 and 2012.

METHODSThe H3N2 influenza virus (n = 1206) in China from 1992 to 2012 was analyzed, include global selection pressure and sites positive selection pressure analysis.

RESULTSConsidering all the H3N2 influenza viruses during these 21 years, a total of four amino acid sites subject to positive selection. The global selection pressure varies with the variation of different antigenic clusters and three years with peak bottom selection pressure were identified.

CONCLUSIONThe global selection pressure rise from the peak bottom, a new antigenic clusters will appear andprevalent in the population, indicating the best time to replace the vaccine strain.

Antigens, Viral ; immunology ; China ; Influenza A Virus, H3N2 Subtype ; genetics ; immunology ; Influenza Vaccines ; Selection, Genetic ; Time Factors

No abstract available.
Receptors, Odorant ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Livestock ; Genomics* ; Genotype ; Olfactory Receptor Neurons

Like the body of Hominin, mind is the result of natural selection. Therefore, an evolutionary approach in the biological aspects is essential for an intrinsic understanding of mental disorders. However, the evolutionary medical approach to mental disordershas not been well researched because evolutionary psychiatry is not widely accepted, and the conceptual paradigm has not been unified. Nevertheless, some evolutionary hypotheses about some mental disorders have been proposed, including the following: 1) thesimple disease argument that mental disorder is a mere disease, 2) the genomic lag hypothesis that current genes are incompatible with evolutionary environmental changes, 3) the developmental mismatch hypothesis that brain development cannot reflect entire-information of surrounding environment, 4) the trade-off hypothesis that costs are offset by other adaptive benefits, 5) the by-product hypothesis that mental disorders are inevitable outcome of evolutionary design, 6) the cliff-edge model that the encephalizationin the Hominin caused mental disorders, 7) the inclusive fitness hypothesis that costs of individual are compensated by benefits of kinship, 8) the antagonistic polymorphism hypothesis that differential costs and benefits according to sex or age cause ofpolymorphic psychological traits 9) the heterozygote advantage hypothesis that the heterozygous genotypes have higher relative fitness, so they can persist even though homozygous genotypes cause mental disorders, and 10) a genomic imprinting hypothesis that conflicts between maternal genes and paternal genes cause mental disorders. I will summarize and compare the evolutionary hypotheses of mental disorders and present the lim itations of each hypothesis.
Brain ; Cost-Benefit Analysis ; Genomic Imprinting ; Genotype ; Heterozygote ; Hominidae ; Humans ; Mental Disorders ; Selection, Genetic

OBJECTIVETo assess the impact of natural selection and genetic background on the polymorphisms of HLA-G 3-untranslated regions (UTR) among five ethnic Chinese populations.

METHODSPCR and DNA sequencing were used to determine the polymorphisms among 432 individuals from the five ethnic populations. Their genetic background was determined by genotyping of 10 short tandem repeats (STRs).

RESULTSEight variations were identified among Gelao, Mongolian and Kirgiz populations, while only 7 were found in Shui and Dai people. For all 3 southern populations (Gelao, Shui, and Dai), the observed heterozygosites (Ho) was higher than expected heterozygosities (He). But this was reversed for the 2 northern populations (Mongolian and Kirgiz). The Ho and He of the 10 neutral STRs were in random distribution. Ewens-Watterson testing based on haplotypes of the HLA-G 3'UTR has suggested that a natural selection had occurred in the region where Dai and Shui had inhabited, but not in the northern region where Mongolian and Kirgiz population inhabited. Polygenetic trees based on the HLA and STRs were also different.

CONCLUSIONThe HLA-G 3'UTR of Dai and Shui people who lived in southern China may have subjected to a selection pressure. Based on current knowledge, this pressure may have been driven by a pathogenic selection.

3' Untranslated Regions ; genetics ; China ; ethnology ; Female ; HLA-G Antigens ; genetics ; Humans ; Male ; Microsatellite Repeats ; Polymorphism, Genetic ; Selection, Genetic