scholarly journals Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Zhuanzhuan Yan ◽  
Fan Wu ◽  
Kai Luo ◽  
Yufeng Zhao ◽  
Qi Yan ◽  
...  
PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.


1992 ◽  
Vol 22 (1) ◽  
pp. 117-123 ◽  
Author(s):  
Anders Kvarnheden ◽  
Peter Engström

DNA fingerprinting techniques have significantly improved the resolution of the analysis of genetic polymorphisms in major eukaryotic taxa. The techniques are based on the use of specific DNA probes, which hybridize to families of related minisatellite loci that are dispersed in the genomes of a range of eukaryotes. These sequences are highly variable as a result of a variation in the numbers of a core repeat sequence at each locus. We wanted to establish whether one such probe, the DNA of the bacteriophage M13, could be used to detect hypervariable loci in the conifer Norway spruce, Piceaabies (L.) Karst., and to examine if the method could detect genetic differences at the level of populations and (or) individual trees. The results show that hypervariable minisatellite sequences that hybridize to the M13 probe are present in Norway spruce. The minisatellite sequences are stably inherited, and the variability within the species is sufficiently high to allow the distinction of different individuals. The differences between populations are of the same order of magnitude as those between trees within populations. The method is potentially useful in population genetics research on conifers, as well as in breeding programs.


2016 ◽  
Vol 92 (1) ◽  
pp. 38-64 ◽  
Author(s):  
Maria D. Esteve-Gassent ◽  
Ivan Castro-Arellano ◽  
Teresa P. Feria-Arroyo ◽  
Ramiro Patino ◽  
Andrew Y. Li ◽  
...  

Author(s):  
Frühling Rijsdijk ◽  
Pak Sham

Behavioural genetics is the study of the genetic basis of behavioural traits including both psychiatric disorders and ‘normal’ personality dimensions. Behavioural genetics derives its theoretical basis from population genetics. Soon after the laws of Mendelian inheritance were re-discovered in 1900, the implications of these laws on the genetic properties of populations were worked out. Such properties include segregation ratios, genotypic frequencies in random mating populations, the effect of population structure and systems of mating, the impact of selection, the partitioning of genetic variance, and the genetic correlation between relatives. Some appreciation of population genetics is necessary for a deep understanding of behavioural genetics. Because of the complexity of behavioural traits, genetic factors cannot be regarded in isolation, or as static. Instead, it is important to consider: (i) the relative contributions of genetic and environmental factors, (ii) the interplay between genetic and environmental factors, and (iii) the changing role of genetic factors in different stages of development from infancy to old age. The major study designs in behavioural genetics will be discussed in this chapter, namely family studies, twin studies, and adoption studies. Behavioural genetics, augmented by molecular genetics has the potential to identify specific genetic variants which influence behaviour. This will be considered in detail in Chapter 14. Mendelian inheritance Gregor Mendel first demonstrated the genetic basis of biological inheritance by studies of simple all-or-none traits in the garden pea. These traits were particularly revealing because they were completely determined by the genotype at a single chromosomal locus. Diseases caused by genetic mutation at a single locus are commonly called Mendelian or single-gene disorders. A dominant disorder is expressed when an individual has one or two copies of the mutant allele, whereas a recessive disorder is expressed only when both alleles at the locus are the mutant variant. Examples of Mendelian disorders of clinical significance in psychiatry are Huntington's disease and fragile X syndrome. Mendelian disorders tend to be relatively rare because they are usually subjected to severe negative selective pressure, due to their increased mortality. Most common disorders and continuous traits of interest in psychiatry have an aetiology involving multiple genetic and environmental factors. Categorical and dimensional traits Behavioural genetics is rooted in both psychiatry and psychology. Psychiatrists traditionally adopt a medical model where diseases are defined as categorical entities and diagnoses are either present or absent. Psychologists on the other hand prefer quantitative measures of cognitive ability, personality and other traits. The methodology of behavioural genetics research reflects this duality, although there is a trend to integrate the two approaches, especially for traits such as anxiety and depression where both diagnostic criteria and quantitative measures exist.


2021 ◽  
Author(s):  
Shengman Zhang ◽  
Yiran Xiong ◽  
Meng Tan ◽  
Siwei Chen ◽  
Zheng Han ◽  
...  

Abstract Daphnia magna belongs to the Cladocera order and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In our research, 26 novel microsatellite (SSR) markers were developed in an artificially domesticated of D. magna and 12 wild population of D. magna using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei’s genetic identity (H) ranged from 0.0926 to 0.3462, with a mean of 0.2233. Shannon’s Information index (I) ranged from 0.1333 to 0.4799, with an average of 0.3073; Shanxi province had the highest value and Hunan province had the lowest. Genetic distance and Nei’s genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan is relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the test D. magna samples into two major groups. These results indicate that the genetic diversity of D. magna is rich, and the genetic structure of D. magna differs considerably in different regions. These research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated population and conservation genetics research.


2021 ◽  
Author(s):  
Daniel J Balick ◽  
Daniel M Jordan ◽  
Shamil Sunyaev ◽  
Ron Do

The identification of genes that evolve under recessive natural selection is a longstanding goal of population genetics research with important applications to disease gene discovery. We found that commonly used methods to evaluate selective constraint at the gene level are highly sensitive to genes under heterozygous selection but ubiquitously fail to detect recessively evolving genes. Additionally, more sophisticated likelihood-based methods designed to detect recessivity similarly lack power for a human gene of realistic length from current population sample sizes. However, extensive simulations suggested that recessive genes may be detectable in aggregate. Here, we offer a method informed by population genetics simulations designed to detect recessive purifying selection in gene sets. Applying this to empirical gene sets produced significant enrichments for strong recessive selection in genes previously inferred to be under recessive selection in a consanguineous cohort and in genes involved in autosomal recessive monogenic disorders.


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