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Genetics Apr 2001Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to...
Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Topics: Animals; Bayes Theorem; Breeding; Computer Simulation; Genetic Markers; Haplotypes; Least-Squares Analysis; Linkage Disequilibrium; Models, Genetic; Quantitative Trait, Heritable
PubMed: 11290733
DOI: 10.1093/genetics/157.4.1819 -
Genes Dec 2020Global warming is negatively impacting on crop yield and Earth's climate changes can bring possible negative effects on the growth and reproductive success of crops...
Global warming is negatively impacting on crop yield and Earth's climate changes can bring possible negative effects on the growth and reproductive success of crops [...].
Topics: Agriculture; Climate Change; Crops, Agricultural; Genetic Markers; Genetic Variation; Plant Breeding; Temperature
PubMed: 33317175
DOI: 10.3390/genes11121481 -
Molecular Ecology Oct 2018The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human...
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next-generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker-based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
Topics: Genetic Markers; Genetics, Population; Humans; Models, Genetic; Pedigree
PubMed: 30107060
DOI: 10.1111/mec.14833 -
Fa Yi Xue Za Zhi Aug 2018Genetic markers in forensic DNA typing experienced the variable number of tandem repeats (VNTR) sequences and the short tandem repeats (STR) sequences. With the... (Review)
Review
Genetic markers in forensic DNA typing experienced the variable number of tandem repeats (VNTR) sequences and the short tandem repeats (STR) sequences. With the emerge of sequencing technology, the third generation of genetic markers were found out, which usually have two alleles including single nucleotide polymorphism (SNP) and insertion/deletion (InDel), also known as biallelic genetic markers. Because of the insertions or deletions of DNA fragments, InDel genetic marker reveals DNA fragment length polymorphism and widely distributes across the whole genome. InDel genetic marker is numerous and has the characteristics of STR and SNP genetic markers, which has been applied in the fields of genetics and anthropology. This review focuses on the research progress of InDel genetic marker in forensic science, aiming to review and summarize the main research findings in recent years and provide clues for future researches.
Topics: Alleles; DNA; DNA Fingerprinting; Forensic Genetics; Genetic Markers; INDEL Mutation; Microsatellite Repeats; Polymorphism, Single Nucleotide
PubMed: 30465411
DOI: 10.12116/j.issn.1004-5619.2018.04.016 -
TheScientificWorldJournal 2014Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding.... (Review)
Review
Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.
Topics: Breeding; Forecasting; Genetic Markers; Genetic Variation; Genomics; Gossypium; Polymorphism, Single Nucleotide
PubMed: 25401149
DOI: 10.1155/2014/607091 -
International Journal of Molecular... Dec 2016Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their... (Review)
Review
Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker ( c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase () gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.
Topics: Adiposity; Animals; Genetic Markers; Meat; Quantitative Trait, Heritable; Selection, Genetic; Sus scrofa
PubMed: 27983643
DOI: 10.3390/ijms17122100 -
Parasitology International Dec 2022Genetic mapping has been widely employed to search for genes linked to phenotypes/traits of interest. Because of the ease of maintaining rodent malaria parasites in... (Review)
Review
Genetic mapping has been widely employed to search for genes linked to phenotypes/traits of interest. Because of the ease of maintaining rodent malaria parasites in laboratory mice, many genetic crosses of rodent malaria parasites have been performed to map the parasite genes contributing to malaria parasite development, drug resistance, host immune response, and disease pathogenesis. Drs. Richard Carter, David Walliker, and colleagues at the University of Edinburgh, UK, were the pioneers in developing the systems for genetic mapping of malaria parasite traits, including characterization of genetic markers to follow the inheritance and recombination of parasite chromosomes and performing the first genetic cross using rodent malaria parasites. Additionally, many genetic crosses of inbred mice have been performed to link mouse chromosomal loci to the susceptibility to malaria parasite infections. In this chapter, we review and discuss past and recent advances in genetic marker development, performing genetic crosses, and genetic mapping of both parasite and host genes. Genetic mappings using models of rodent malaria parasites and inbred mice have contributed greatly to our understanding of malaria, including parasite development within their hosts, mechanism of drug resistance, and host-parasite interaction.
Topics: Animals; Disease Susceptibility; Drug Resistance; Genetic Markers; Malaria; Mice; Parasites; Rodentia; Virulence
PubMed: 35926693
DOI: 10.1016/j.parint.2022.102637 -
Zhejiang Da Xue Xue Bao. Yi Xue Ban =... Dec 2021As a novel genetic marker, microhaplotype can be applied in the field of forensic genetics. Microhaplotype has the advantages of high polymorphism, low mutation rate, no... (Review)
Review
As a novel genetic marker, microhaplotype can be applied in the field of forensic genetics. Microhaplotype has the advantages of high polymorphism, low mutation rate, no stutter products and short amplification fragments. Microhaplotype can effectively detect mixture, and quantitatively analyze the contributors of mixture. DNA with severe fragmentation can be successfully genotyped by microhaplotype. It can be used as ancestry informative marker to effectively divide the global continental population according to genetic structure. Microhaplotype system can provide more information than traditional short tandem repeat and help to identify complex relationships. It can provide new ideas for tumor source identification, cell line identification and prenatal paternity testing. Here we review the applications of microhaplotype, intending to provide references for forensic practice.
Topics: DNA; Female; Forensic Genetics; Genetic Markers; Genotype; Humans; Polymorphism, Single Nucleotide; Pregnancy
PubMed: 35347913
DOI: 10.3724/zdxbyxb-2021-0180 -
The Plant Journal : For Cell and... Mar 2023
Topics: Genetic Markers; Zea mays; Genetic Variation; Phenotype; Polymorphism, Single Nucleotide
PubMed: 36920972
DOI: 10.1111/tpj.16163 -
Frontiers in Bioscience (Landmark... Sep 2022As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research.... (Review)
Review
As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics.
Topics: Body Remains; DNA Fingerprinting; DNA, Ancient; Genetic Markers; High-Throughput Nucleotide Sequencing; Humans; Microsatellite Repeats
PubMed: 36224018
DOI: 10.31083/j.fbl2709271