Comparative Analysis Of Genetic Structure Research Articles

Comparative Analysis of Genetic Structure and Diversity in Five Populations of Yellowtail Kingfish (Seriola aureovittata)

To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (Fst) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (Nm) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms.

Assessing the genetic diversity of twenty one Colombo limon L. genotypes through multivariate and covariance matrix analysis

Assessing the genetic diversity of twenty one Colombo limon L. genotypes through multivariate and covariance matrix analysis

Analysis of the genetic structure of a population of Lebedyn cattle by microsatellite markers

Microsatellites – a separate class of molecular genetic markers, are widely used for the study of genetic variability, in particular in populations of animals bred by artificial selection under the influence of microevolutionary processes. The object of study is the gene pool of a population of animals of the Lebedyn cattle breed, which is under threat of extinction. The sample comprised 30 individuals from the farm "Komyshans'ke" in Sumy region. The analysis of population genetic structure was performed using 10 microsatellite loci recommended by FAO-ISAG: ETH225, BM2113, ETH3, BM1818, BM1824, ILSTS006, INRA023, TAGLA053, TAGLA12, ETH10. Amplification products were separated in polyacrylamide gels of different concentrations (5–8%), both native and denaturing. All studied loci were polymorphic. The number of detected alleles per locus ranged from 4 to 8 (on average 5 alleles per locus), the size of which ranged from 115 bp (ETH3) to 307 bp (ILSTS006). The majority of the investigated loci (except ETH3) belonged to valuable informative markers (PIC > 0.5). The most polymorphic TGLA053 (8 alleles), BM2113 (6) and ETH3 (6) loci have been identified. In general, the minimum number of alleles (4) was fixed in 50% loci. The main population genetic parameters for the studied loci have been calculated. The highest values of heterozygosity (He), and effective number of alleles (ne) was characterized for loci BM2113, ILSTS006, TGLA053 and ETH225. With the exception of ETH3 and VM1818 loci, the experimental group of animals is in a state of genetic equilibrium. The average value of the Wright fixation index indicates a tendency to increase in the number of homozygous individuals (inbreeding). Comparative analysis of genetic structure of breeds that have a common origin (Lebedyn (PJSC "Mykhaylivka"), Ukrainian grey (DPDG "Polyvanivka"), Red steppe (DPPR "Stepne"), etc.) has been carried out. The obtained results give grounds to assert that in the experimental population of the Lebedyn breed there are processes that lead to a decrease in genetic diversity. In order to overcome the negative effects of artificial reproduction in the gene pool of small populations of cattle, which include Lebedyn cattle, it is appropriate to use microsatellite markers in the selection and breeding work.

Study of Genetic Diversity and Population Structure of the Yak (Bos grunniens) in the Sayan-Altai Region

The paper reports the first study of genetic diversity of the domestic yak in the Sayan-Altai region of Russia (Altai and Tuva) and Mongolia (Khuvsgul and Gobi) on the basis of the polymorphism analysis of the mtDNA D-loop hypervariable region. It has been demonstrated that, among all the studied populations, Tuva yaks are characterized by the highest haplotype diversity. Four new haplotypes, A4, A13, D9, and E3, have been described for the first time. The analysis of the contribution of maternal genetic component to the yak intrabreed and interbreed mtDNA diversity revealed two large clades. For the first time, comparative analysis of genetic structure of the Russian yak populations was carried out using 15 microsatellite loci. Low genetic difference between the populations was revealed, which may apparently be accounted for by the specific features of farm breeding, in particular, by animal exchange between the adjacent territories of the Sayan-Altai region.

Comparative Analysis of Genetic Structure of by SSR and AFLP

The genetic structure data of Nile tilapia from SSR assay were compared with that from AFLP. The ratio of polymorphic sites percentage from SSR to AFLP averaged 1.683 17, the average ratio of population specific Fst indices was 1.249 87, and the ratio of gene diversity in group averaged 1.676 60, respectively in 5 populations. The ratio of genetic distance among 5 populations of Nile tilapia from SSR to AFLP averaged 3.972 02, whereas the ratio of genetic identity averaged 0.937 92. The results about SSR and AFLP could provide reference for other similar studies in this field.

Порівняльний аналіз генетичної структури веслоноса (Polyodon spathula) українських популяцій

Порівняльний аналіз генетичної структури веслоноса (Polyodon spathula) українських популяцій

Comparative analysis of genetic structure in Magnaporthe oryzae isolates from indica and japonica hosts in China

To study the genetic diversity of Magnaporthe oryzae isolates from indica and japonica hosts in China, we fingerprinted 57 isolates from 10 Chinese provinces or areas using Pot2-rep-PCR, which generated different DNA fingerprint patterns between the indica and japonica isolates. The band patterns were more complex in indica isolates than those in japonica isolates. Cluster analysis of the DNA fingerprint patterns also distinguished the indica and japonica isolates. At the 78 % similarity level, the 57 isolates divided into 15 groups.

Порівняльний аналіз генетичної структури мікропопуляції сірої української породи великої рогатої худоби за ДНК-маркерами

Порівняльний аналіз генетичної структури мікропопуляції сірої української породи великої рогатої худоби за ДНК-маркерами

Comparative Analysis of Genetic Structure and Diversity of Sorghum (Sorghum bicolor L.) Local Farmer’s Varieties from Sudan

Comparative Analysis of Genetic Structure and Diversity of Sorghum (Sorghum bicolor L.) Local Farmer’s Varieties from Sudan

Comparative analysis of genetic structure and variability in wild and cultivated pomegranates as revealed by morphological variables and molecular markers

In this study, the genetic variability and relationships among wild and cultivated pomegranate genotypes from the north of Iran were investigated by morphological characters and RAPD molecular markers. Principal component analysis showed that the first three components explained 61.64 % of the total morphological variation for studied genotypes. Fruit neck diameter, anthocyanin index, TSS, aril juice, fruit flavor index, petiole length, fruit peel thickness and seed hardness were predominant in the first component and contributed most of the total variation. Fruit characteristics such as titratable acidity were negatively correlated (r = −0.56) with TSS (r = −0.56) and pH (r = −0.86) and also, seed hardness showed negative correlation with aril length and aril diameter. Clustering from morphological data allocated individuals into two main clusters with high variation. Two hundred and twenty-nine fragments were scored of which 174 of them were polymorphic with 76.9 % polymorphism. Genetic similarity ranged from 0.15 to 0.78 with an average of 0.42, indicating high genetic variation among studied genotypes. High molecular and morphological variability indicated that this germplasm includes rich and valuable plant materials for pomegranate breeding.

Complex genetic patterns and a phylogeographic disjunction among New Zealand mud snails Zeacumantus subcarinatus and Z. lutulentus

The comparative analysis of genetic structure and phylogeography of marine species can reveal the relative importance of common biogeographic barriers and species-specific evolutionary histories. In the present study, mitochondrial COI sequences from a total of 724 individuals collected from 38 localities throughout New Zealand during 2006 and 2007 were used to examine the genetic structure and demographic histories of the intertidal gastropods Zeacumantus subcarinatus and Zeacumantus lutulentus. For both species, results revealed isolation of populations located along the northern South Island and southern and western North Island, and extensive genetic structure throughout the remainder of their ranges. Despite this, long-distance dispersal and secondary admixture of divergent haplotypes was evident, especially for the widespread Z. subcarinatus. These findings reveal the importance of common barriers to gene flow and highlight how the interaction of inherent dispersal limitations of direct-developing marine organisms and periodic long-distance movements can produce complex genetic patterns.

Comparative analysis of genetic structure in natural populations of two Arabidopsis species with different degree of panmixia

Comparative analysis of genetic structure of northern natural populations of two Arabidopsis species with different degrees of panmixia was performed. The variability of 121 RAPD loci in seven populations of model plant A. thaliana possessing high degree of self fertility was studied together with 93 RAPD loci in population of cross-pollinating species A. lyrata ssp. petraea. The population of A. l. petraea demonstrated higher level of genetic variability (P 99% = 62.50%; H(exp) = 0.169) than the populations of A. Thaliana, which is obviously connected with biological features of reproduction of the species. A significant level of genetic variability (P 99% = 42.27%; H(exp) = 0.126) was revealed in populations of A. thaliana, which is not typical for self-pollinating plant species. The high population polymorphism of A. thaliana in the northern part of its range may be connected with adverse environmental conditions. The genetic distances between populations of the species studied (average DN = 0.494) confirm close relatedness between A. thaliana and A. l. petraea.