scholarly journals A geometrical framework for f –statistics

2020 ◽  
Author(s):  
Gonzalo Oteo–García ◽  
José–Angel Oteo
Keyword(s):  
Numerical Simulation ◽  
Phylogenetic Tree ◽  
Distance Matrix ◽  
Fixation Index ◽  
Population Admixture ◽  
Admixture Proportion ◽  
Genetic Distance Matrix ◽  
Detailed Derivation ◽  
Coalescence Times ◽  
F Statistics

AbstractA detailed derivation of the f–statistics formalism is made from a geometrical framework. It is shown that the f–statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree–like–ness criterion. The case of lack of treeness is interpreted in the formalism as presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so–called f4–ratio estimate and we show that a second one is related to a known result developed in terms of the fixation index FST. An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided.

GENETIC VARIABILITY IN Sechium spp. (Cucurbitaceae) EVALUATED WITH AFLP MARKERS

Agrociencia ◽  
2021 ◽  
Vol 55 (7) ◽  
pp. 611-626
Author(s):  
María Isabel Iñiguez Luna ◽  
Jorge Cadena Iñiguez ◽  
Moisés Cortés Cruz† ◽  
Francisco Javier Morales Flores ◽  
Kazuo N. Watanabe ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Fixation Index ◽  
Separate Species ◽  
Sechium Edule ◽  
Genetic Distance Matrix ◽  
Genetic Complexity ◽  
Genetic Cross ◽  
Very High

There are few studies in Mexico aimed at evaluating the genetic variability of Sechium spp. Despite certain biological variants are reported with very high potential to develop antineoplastic supplements to treat public health conditions. Using the Amplified Fragment Length Polymorphism (AFLP) technique, the genetic variability of a sample of 95 accessions of three species of Sechium (S. edule, S. chinantlense, S. compositum) was evaluated, with leaf DNA from the Banco Nacional de Germoplasma de Sechium edule en Mexico. Four combinations of AFPL were applied (EcoRI + ACC/MseI + CAC, EcoRI + ACC/MseI + CAT, EcoRI + ACC/MseI + CGC, and EcoRI + ACC/MseI + CGG). DNA samples were classified into three groups based on the flavour of the fruit (sweet, neutral, bitter). An average of 47.91% polymorphism, 0.16 heterozygosity, 32.83 number of polymorphic bands, and a zero Wright fixation index (Fst) was obtained. The evidence showed that the domesticated accessions (sweet, neutral) were separated from the bitter-taste genotypes. A monophyletic tree was generated with the genetic distance matrix and the neighbour-joining methodology. Analyses showed S. edule as the root taxon, deriving S. compositum and S. chinantlense as subgroups, and suggesting that there is not enough differentiation to treat them as separate species. The evaluated sample showed that there is no apparent reproductive barrier for genetic cross breeding. Genotypes behaved as a complex with evolutive dynamism; that genetic complexity would allow the design of new variants.

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Whole-genome modeling accurately predicts quantitative traits, as revealed in plants

2015 ◽  
Author(s):  
Laurent Gentzbittel ◽  
Cécile Ben ◽  
Mélanie Mazurier ◽  
Min-Gyoung Shin ◽  
Martin Triska ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Symbiotic Nitrogen Fixation ◽  
Natural Populations ◽  
Whole Genome ◽  
Population Admixture ◽  
Admixture Proportion ◽  
Genome Wide ◽  
Polygenic Adaptation ◽  
In The Wild ◽  
Wild Legume

AbstractMany adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture.We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral populations originally separated. We experimentally confirmed this hypothesis by predicting the differences in quantitative disease resistance levels among accessions in the wild legume Medicago truncatula. We discovered also that variation in genome admixture proportion explains most of phenotypic variation for several quantitative functional traits, but not for symbiotic nitrogen fixation. We shown that positive selection at the species level might not explain current, rapid adaptation.These findings prove the infinitesimal model as a mechanism for adaptation of quantitative phenotypes. Our study produced the first evidence that the whole-genome modeling of DNA variants is the best approach to describe an inherited quantitative trait in a higher eukaryote organism and proved the high potential of admixture-based analyses. This insight contribute to the understanding of polygenic adaptation, and can accelerate plant and animal breeding, and biomedicine research programs.

scholarly journals Population Structure of 93 Varieties of Rice ( Oryza Sativa L. subsp. Hsien Ting) in Qinba, China

2020 ◽  
Author(s):  
Yu Zhang ◽  
Ye wen Wang ◽  
Yue xing Wang ◽  
Shi mao Zheng ◽  
Wan ying Zhou ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Agronomic Traits ◽  
Distance Matrix ◽  
Mantel Test ◽  
Rice Varieties ◽  
Genetic Distance Matrix ◽  
History Of ◽  
Variation Explained ◽  
Population Genetic Variation

Abstract BackgroundThe Qinba region is the transition region between indica and japonica varieties with a long history of indica varieties planting. 72,824 SNPs data based on GBS method, 48 pairs core primers of SSRs, and 15 agronomic traits were employed to explore the population structure of 93 rice varieties. The Mantel test was used to analyze the distance matrix generated using NlaIII-GBS only, MseI-GBS only, by combining NlaIII-GBS and MseI-GBS data and SSR.ResultIn this study, a total of 379 alleles were obtained using 48 pairs core primer of SSR, encompassing an average of 8.0 alleles per primer. The PPB and PIC was 88.65% and 0.77, respectively. Among these, RM278 possess the highest TNB and NPB, and the PPB in 29 pairs of SSR markers was 100%. RM176 showed the highest PIC. MAF was set to 0.05, and 39,872, 35,547 and 67,621 SNPs were obtained via NlaIII-GBS only, MseI-GBS only, and merged NlaIII-GBS and MseI-GBS data, respectively. The IBS genetic similarity coefficient average was 0.74. The results showed that the correlation between the genetic distance matrix based on NlaIII-GBS and MseI-GBS was the largest (R2=0.88), followed by NlaIII-GBS and SSR (R2=0.35), then by merged NlaIII-GBS and MseI-GBS data and SSR (R2=0.33), and the smallest by MseI-GBS and SSR (R2=0.27). The results showed that the 93 rice varieties could be clustered into two subgroups. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations. Tajima’s D value was 1.66, and the FST between the two populations was 0.61, and the Nm was 0.16.ConclusionThe population genetic variation explained by SNP was larger than that explained by SSR. Through cluster analysis, the 93 samples were divided into 2 subgroups, with more than 97% of the samples clustered into one subgroup. The gene flow of 93 samples used in this study is larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of indica varieties in the Qinba region. However, the genetic structure of the rice population is simple and lacked rare alleles.

Oil Containment by Floating Boom under Wave-Current Coupling Conditions III: Prediction on Failure Velocity

2014 ◽  
Vol 955-959 ◽  
pp. 1491-1495
Author(s):  
Xing Feng ◽  
Wan Qing Wu ◽  
Gui Feng Yu
Keyword(s):  
Numerical Simulation ◽  
Companion Paper ◽  
Experimental Platform ◽  
Oil Boom ◽  
Coupling Conditions ◽  
Wave Parameters ◽  
Oil Spill Response ◽  
Current Coupling ◽  
Oil Density ◽  
Detailed Derivation

The numerical simulation of oil containment by floating boom under wave-current coupling conditions is presented in a companion paper. The present paper focuses on the use of the numerical experimental platform developed by FENG and WU for the prediction of oil containment failure velocity of floating boom under wave-current coupling conditions. Detailed derivation processes about the containment failure velocity formula are provided. The effects of oil parameters, wave parameters and oil boom parameters on oil containment failure velocity receive particular attention, and the influences of some of these parameters such as oil density, boom draft are quantified. The prediction model can provide an economic, convenient method for oil spill response.

scholarly journals Molecular characterization of papaya genotypes using AFLP markers

2011 ◽  
Vol 33 (3) ◽  
pp. 849-858 ◽  
Author(s):  
Eder Jorge de Oliveira ◽  
Juliana Leles Costa ◽  
Lucas Ferraz dos Santos ◽  
Fabiana Moraes de Carvalho ◽  
Aline dos Santos Silva ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Carica Papaya ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Inbred Lines ◽  
Genetic Distance Matrix ◽  
Pair Method ◽  
Polymorphic Bands

Due to the low genetic variability reported in the commercial plantations of papaya (Carica papaya L.), the objective of this study was analyze the genetic diversity of 32 genotypes including cultivars, landraces, inbred lines, and improved germplasm using the AFLP technique (Amplified Fragment Length Polymorphism). The genetic distance matrix was obtained using the Nei and Li genetic distance and clustering was performed using the unweighted pair-method with arithmetic mean (UPGMA). Using 11 combinations of EcoRI/MseI primers, 383 polymorphic bands were obtained. On average, 34.8 polymorphic bands were obtained per primer combination. Five clusters were formed. The traditional cultivar 'Sunrise' and the inbred line CMF-L30-08 were the closest genotypes, and the improved germplasm (CMF041) and landrace (CMF233) the most distant. The main papaya cultivars commercially grown in Brazil, as well as four inbred lines and three improved germplasm, were clustered together, however, were not grouped in the same branch. The genetic distance between the Sunrise and Golden cultivars was 0.329, and even arising from mutation and selection within the Sunrise variety, the Golden stores considerable genetic variability. Additional variability was observed in the inbred lines derived from papaya breeding program at Embrapa Cassava and Fruits.

Genetic and morphological evidence for a new cryptic species of Ectinogonia (Coleoptera: Buprestidae) from central Chile

Zootaxa ◽  
2017 ◽  
Vol 4303 (2) ◽  
pp. 284 ◽  
Author(s):  
SIMÓN ANGUITA-SALINAS ◽  
RODRIGO M. BARAHONA-SEGOVIA ◽  
ELIE POULIN ◽  
ALVARO ZÚÑIGA-REINOSO
Keyword(s):  
New Species ◽  
Genetic Distance ◽  
Cryptic Species ◽  
Distance Matrix ◽  
Morphological Evidence ◽  
Mountain Range ◽  
Central Chile ◽  
The Andes ◽  
Genetic Distance Matrix ◽  
Coi Sequences

The genus Ectinogonia Spinola, 1837 is a genus mainly found in Chile; it currently contains 17 species. Recent exploration in the Andes Mountain Range of the Bio Bio Region in Chile have resulted in the collection of specimens slightly different morphologically from all previously described species. The aim of this paper is to describe this new species of Ectinogonia using morphological and genetic evidence. To establish differences between species we described the external morphology and compared it to species that are morphologically similar (i.e. E. buqueti Spinola 1837 and E. intermedia Kerremans 1903). We also measured the genetic differences in COI sequences, constructing a distance matrix in which we compared it to species that are morphologically similar (E. buqueti and E. intermedia) and other species found in the same region (E. speciosa oscuripennis Moore 1994). We found that E. cryptica sp. n. differs from E. buqueti (which previously contained E. cryptica sp. n.) in pronotum and elytral patterns. The genetic distance matrix shows that E. cryptica sp. n. differs by 4.6% from all other Ectinogonia species compared, supporting the morphological evidence. 

scholarly journals Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 137-146 ◽  
Author(s):  
Martin Vivodík ◽  
Zelmíra Balázová ◽  
Zdenka Gálová ◽  
Lenka Petrovicová
Keyword(s):  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Start Codon ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Genetic Distance Matrix ◽  
Functional Genetic Variation ◽  
Amplicon Size

In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

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