Genetic variation in natural populations of Hordeum brevisubulatum native to the Songnen Prairie in northeastern China: Comparison of four nuclear DNA markers

2007 ◽  
Vol 87 (4) ◽  
pp. 773-780 ◽  
Author(s):  
Mu Li ◽  
Wanli Guo ◽  
Lanjuan Hu ◽  
Xiaoming Liu ◽  
Yufei Zhang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Nuclear Dna ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Northeastern China ◽  
Nuclear Dna Markers ◽  
The Individual ◽  
Genomic Regions ◽  
Hordeum Brevisubulatum ◽  
Issr Primers

Hordeum brevisubulatum (Trin) Link, a perennial wild grass, shows high tolerance to salinity- and/or alkaline-eroded soil, and is an important forage grass. Nonetheless, the genetic variation within and among natural populations of this species has not been investigated. In this study, four PCR-based dominant nuclear DNA markers, i.e., amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), retrotransposon-microsatellite-amplifiedpolymorphism (REMAP), and random amplified polymor phic DNA (RAPD) were used to investigate the genetic variation of a total of 80 plants with an average of 20 individual plants randomly collected from each of the four natural populations of H. brevisubulatum distributed in the Songnen Prairie in northeastern China. Results indicated that all four markers detected a surprisingly high level of genetic variation among the individual genotypes both within and among populations. Specifically, (i) of the 708 bands produced by 10 AFLP primer pairs, 223 (32%) were polymorphic, corresponding to a genetic similarity coefficient (Dice) range of 0.703 to 0.895 with a mean of 0.793; (ii) of the 174 bands produced by 12 ISSR primers, 149 (85%) were polymorphic, corresponding to a genetic similarity coefficient range of 0.524 to 0.826 with a mean of 0.676; (iii) of the 104 bands produced by REMAP (one retrotransopon-specific primer in combination with each of 8 ISSR primers), 89 (85%) were polymorphic, leading to an average similarity coefficient range of 0.494–0.840 with a mean of 0.688, and; (iv) of the 150 bands produced by 17 RAPD primers, 117 (77%) were polymorphic, giving a similarity coefficient range of 0.526–0.909 with a mean of 0.713. Thus, all four markers are highly informative in detecting genetic variations among the individual genotypes in natural populations of H. brevisubulatum. Nevertheless, no correlation was detected among the markers, suggesting that they likely targeted to different genomic regions of H. brevisubulatum. Whereas ISSR, REMAP and RAPD showed significantly higher levels of polymorphism than AFLP, only the latter was capable of grouping some of the plants largely in accordance with their geographic localities, suggesting population differentiation probably occurred preferentially at genomic regions targeted to by AFLP primers. Key words: Genetic diversity, Hordeum brevisubulatum, Molecular markers, Population differentiation

scholarly journals GENETIC DIVERSITY AMONG NATURAL POPULATIONS OF Keteleeria evelyniana Mast. IN CENTRAL HIGLANDS OF VIETNAM USING SSR MARKERS

2018 ◽  
Vol 56 (3) ◽  
pp. 275
Author(s):  
Tran Thi Lieu ◽  
Dinh Thi Phong ◽  
Vu Thi Thu Hien
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Similarity Matrix ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Private Alleles ◽  
Softwood Species

Keteleeria evelyniana Mast. is a big softwood species with high economic values. Therefore, the number of these trees are rapidly decreasing due to rampant exploitation as well as its habitat loss and recently, the species is considered vulnerablein Vietnam. In this study, we assessed the genetic variation among seventy K. evelyniana samples of three natural populations in Lam Dong, Dak Lak and Kon Tum using 16 microsatellite markers. The results showed that thirteen markers were polymorphic. A total 39 DNA fragments were amplified, among them, thirty – five were polymorphic (accounting for 89.74%). Among studied populations, the level of genetic diversity at Lam Dong (Na = 2.063; Ne = 1.730; Ap = 0.375; I = 0.558; Ho = 0.459 and He = 0.367) was the highest. Analysis of molecular variance (AMOVA) showed that the total level of molecular changes between populations was 34.65% and between individuals in the same population was 65.35%. Private alleles (Ap) and inbreeding values (Fis) of K. evelyniana species were founded of all three populations in Lam Dong, Dak Lak and Kon Tum (0.375 and -0.234; 0.188 and -0.065; 0.063 and -0.047, respectively). The gene flow (Nm) also occurred among the K. evelyniana populations with the average of Nm = 5.423. A dendrogram (UPGMA) constructed based on the similarity matrix of 70 K. evelyniana samples divided into two main groups with their genetic similarity coefficient ranged from 76.5% (Ke26 and Ke44) to 99% (Ke23 and Ke25). The obtained results indicated the importance of conserving the genetic resources of K. evelyniana species in Tay Nguyen.

scholarly journals Sexual and Apomictic Seed Reproduction in Aronia Species with Different Ploidy Levels

HortScience ◽  
2019 ◽  
Vol 54 (4) ◽  
pp. 642-646
Author(s):  
Jonathan D. Mahoney ◽  
Thao M. Hau ◽  
Bryan A. Connolly ◽  
Mark H. Brand
Keyword(s):  
Genetic Variation ◽  
Fragment Length Polymorphism ◽  
Similarity Coefficient ◽  
Ploidy Levels ◽  
Black Chokeberry ◽  
Deciduous Shrubs ◽  
Rosaceae Family ◽  
The Individual ◽  
Tetraploid Progeny ◽  
Jaccard’S Similarity Coefficient

The genus Aronia Medik., also known as chokeberry, is a group of deciduous shrubs in the Rosaceae family, subtribe Pyrinae. The four commonly accepted species include A. arbutifolia (L.) Pers., red chokeberry; A. melanocarpa (Michx.) Elliott, black chokeberry; A. prunifolia (Marshall) Reheder, purple chokeberry; and A. mitschurinii (A.K. Skvortsov & Maitul). Wild and domesticated Aronia species are found as diploids, triploids, and tetraploids. Genetic improvement of polyploid Aronia genotypes has been limited by suspected apomixis, which may be widespread or distinct to tetraploids. The objectives of this study were to elucidate the reproductive mechanisms of Aronia species and reveal the occurrence of apomixis within the genus and along ploidy lines. Twenty-nine Aronia accessions [five A. melanocarpa (2×), five A. melanocarpa (4×), eight A. prunifolia (3×), four A. prunifolia (4×), six A. arbutifolia (4×), and one A. mitschurinii (4×)] were used in this study. Intra-accession variability was evaluated by growing out progeny from each open-pollinated maternal accession and comparing plant phenotypes, ploidy levels, and amplified fragment length polymorphism (AFLP) marker profiles between the progeny and maternal accession. Progeny of diploid and tetraploid maternal plants had ploidy levels identical to maternal plants, except for UC009 (A. melanocarpa, 2×) which produced a mix of diploids and tetraploids. UC143 and UC149 (A. prunifolia, 3×) produced all triploid offspring, whereas all other triploid accessions produced offspring with variable ploidy levels including 2×, 3×, 4×, and 5×. Pentaploid Aronia has not been previously reported. Diploid accessions produced significant AFLP genetic variation (0.68–0.78 Jaccard’s similarity coefficient) in progeny, which is indicative of sexual reproduction. Seedlings from tetraploid accessions had very little AFLP genetic variation (0.93–0.98 Jaccard’s similarity coefficient) in comparison with their maternal accession. The very limited genetic variation suggests the occurrence of limited diplosporous apomixis with one round of meiotic division in tetraploid progeny. Triploid accessions appear to reproduce sexually or apomictically, or both, depending on the individual. These results support our understanding of Aronia reproductive mechanisms and will help guide future breeding efforts of polyploid Aronia species.

Genetic variation of Picea jezoensis populations in South Korea revealed by chloroplast, mitochondrial and nuclear DNA markers

2009 ◽  
Vol 122 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Yoshinari Moriguchi ◽  
Kyu-Suk Kang ◽  
Kab-Yeon Lee ◽  
Seok-Woo Lee ◽  
Yong-Yul Kim
Keyword(s):  
Genetic Variation ◽  
South Korea ◽  
Dna Markers ◽  
Nuclear Dna ◽  
Picea Jezoensis ◽  
Nuclear Dna Markers

scholarly journals Understanding and using quantitative genetic variation

2010 ◽  
Vol 365 (1537) ◽  
pp. 73-85 ◽  
Author(s):  
William G. Hill
Keyword(s):  
Genetic Variation ◽  
Complex Traits ◽  
Natural Populations ◽  
Multiple Traits ◽  
Individual Gene ◽  
Term Selection ◽  
Laboratory Selection ◽  
Gene Level ◽  
Breeding Programmes ◽  
The Individual

Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet.

scholarly journals POPULATION GENETICS OF ALLOZYME VARIATION IN NEUROSPORA INTERMEDIA

Genetics ◽  
1975 ◽  
Vol 80 (4) ◽  
pp. 785-805
Author(s):  
P T Spieth
Keyword(s):  
Genetic Variation ◽  
Vegetative Reproduction ◽  
Vascular Plant ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Regular Feature ◽  
Local Populations ◽  
Neurospora Intermedia ◽  
Pattern Of Variation ◽  
High Level

ABSTRACT Electrophoretically detectable variation in the fungus Neurospora intermedia has been surveyed among isolates from natural populations in Malaya, Papua, Australia and Florida. The principal result is a pattern of genetic variation within and between populations that is qualitatively no different than the well documented patterns for Drosophila and humans. In particular, there is a high level of genetic variation, the majority of which occurs at the level of local populations. Evidence is presented which argues that N. intermedia has a population structure analogous to that of an annual vascular plant with a high level of vegetative reproduction. Sexual reproduction appears to be a regular feature in the biology of the species. Substantial heterokaryon function seems unlikely in natural populations of N. intermedia. Theoretical considerations concerning the mechanisms underlying the observed pattern of variation most likely should be consistent with haploid selection theory. The implications of this constraint upon the theory are discussed in detail, leading to the presentation of a model based upon the concept of environmental heterogeneity. The essence of the model, which is equally applicable to haploid and diploid situations, is a shifting distribution of multiple adaptive niches among local populations such that a given population has a small net selective pressure in favor of one allele or another, depending upon its particular distribution of niches. Gene flow among neighboring populations with differing net selective pressures is postulated as the principal factor underlying intrapopulational allozyme variation.

scholarly journals Female Genotypes Affect Sperm Displacement in Drosophila

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1487-1493 ◽  
Author(s):  
Andrew G Clark ◽  
David J Begun
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Natural Populations ◽  
Isogenic Line ◽  
Female Fitness ◽  
Sperm Displacement ◽  
Extensive Variation ◽  
Polymorphic Genes ◽  
Displacement Parameter ◽  
Competitive Success

Abstract Differential success of sperm is likely to be an important component of fitness. Extensive variation among male genotypes in competitive success of sperm in multiply mated females has been documented for Drosophila melanogaster. However, virtually all previous studies considered the female to be a passive vessel. Nevertheless, under certain conditions female fitness could be determined by her role in mediating use of sperm from multiple males. Here we ask whether females differ among genotypes in their tendency to exhibit last-male precedence. Competition of sperm from two tester male genotypes (bwD and B3-09, a third-chromosome isogenic line from Beltsville, MD) was quantified by doubly mating female lines that had been rendered homozygous for X, second, or third chromosomes isolated from natural populations. The composite sperm displacement parameter, P2′, was highly heterogeneous among lines, whether or not viability effects were compensated, implying the presence of polymorphic genes affecting access of sperm to eggs. Genetic variation of this type is completely neutral in the absence of pleiotropy or interaction between variation in the two sexes.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

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