scholarly journals Linkage Analysis and Map Construction in Genetic Populations of Clonal F1 and Double Cross

2015 ◽  
Vol 5 (3) ◽  
pp. 427-439 ◽  
Author(s):  
Luyan Zhang ◽  
Huihui Li ◽  
Jiankang Wang
Keyword(s):  
Analytic Solution ◽  
Frequency Estimation ◽  
Female Parent ◽  
Marker Locus ◽  
Maximum Likelihood Estimates ◽  
F1 Hybrids ◽  
Map Construction ◽  
Marker Loci ◽  
Raphson Method ◽  
Double Cross

Abstract In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.

Utility of Genetic Markers in the Study of Human Resemblance

1980 ◽  
Vol 29 (4) ◽  
pp. 255-262 ◽  
Author(s):  
W. J. Kimberling ◽  
D. E. Goldgar
Keyword(s):  
Likelihood Function ◽  
Genetic Correlations ◽  
Marker Locus ◽  
Maximum Likelihood Estimates ◽  
Dizygotic Twin ◽  
Gene Frequencies ◽  
Nonrandom Mating ◽  
Marker Loci ◽  
Twin Families ◽  
Sib Pairs

A method for the estimation of genetic correlations based upon analysis of genetic marker phenotypes is presented. At a given marker locus, the probability of observing a pair of individuals with a specific combination of phenotypes can be expressed as a function of the gene frequencies at that locus and the genetic correlation (R) between that pair. The likelihood of obtaining a sample of n such pairs with their phenotypes at m marker loci can be expressed as a product of nm such functions. From the likelihood function, maximum likelihood estimates of R can be obtained, and hypotheses about R may be tested. A sample of Swedish twin families (61 dizygotic twin pairs, 268 husband-wife pairs, and 164 sib pairs) were analyzed by this method using information from 21 markers. It was found that for the twin pairs, R = 0.458, which was significantly different from the R calculated for sib pairs (R = 0.5 58) but not significantly different from the expected 0.5. For the husband-wife pairs, it was found that R = 0.086, which did differ significantly from the expected value of 0, indicating the presence of nonrandom mating in this population.

Predicting in multivariate incomplete time series. Application of the expectation-maximisation algorithm supplemented by the Newton-Raphson method

2021 ◽  
Vol 68 (1) ◽  
pp. 17-46
Author(s):  
Adam Korczyński
Keyword(s):  
Time Series ◽  
Missing Data ◽  
Em Algorithm ◽  
Measurement Errors ◽  
Parameters Estimation ◽  
Maximum Likelihood Estimates ◽  
Original Algorithm ◽  
Expectation Maximisation ◽  
Newton Raphson ◽  
Raphson Method

Statistical practice requires various imperfections resulting from the nature of data to be addressed. Data containing different types of measurement errors and irregularities, such as missing observations, have to be modelled. The study presented in the paper concerns the application of the expectation-maximisation (EM) algorithm to calculate maximum likelihood estimates, using an autoregressive model as an example. The model allows describing a process observed only through measurements with certain level of precision and through more than one data series. The studied series are affected by a measurement error and interrupted in some time periods, which causes the information for parameters estimation and later for prediction to be less precise. The presented technique aims to compensate for missing data in time series. The missing data appear in the form of breaks in the source of the signal. The adjustment has been performed by the EM algorithm to a hybrid version, supplemented by the Newton-Raphson method. This technique allows the estimation of more complex models. The formulation of the substantive model of an autoregressive process affected by noise is outlined, as well as the adjustment introduced to overcome the issue of missing data. The extended version of the algorithm has been verified using sampled data from a model serving as an example for the examined process. The verification demonstrated that the joint EM and Newton-Raphson algorithms converged with a relatively small number of iterations and resulted in the restoration of the information lost due to missing data, providing more accurate predictions than the original algorithm. The study also features an example of the application of the supplemented algorithm to some empirical data (in the calculation of a forecasted demand for newspapers).

Power system frequency estimation utilizing the Newton-Raphson method

1994 ◽  
Vol 77 (3) ◽  
pp. 221-226 ◽  
Author(s):  
M. B. Durić ◽  
V. V. Terzija ◽  
I. A. Škokljev
Keyword(s):  
Power System ◽  
Frequency Estimation ◽  
Newton Raphson ◽  
System Frequency ◽  
Raphson Method

scholarly journals Genomic Profiling of F1 Hybrids of Durian (Durio zibethinus) Revealed by RAPD-PCR

2016 ◽  
Vol 24 (2) ◽  
pp. 69-76 ◽  
Author(s):  
Riry Prihatini ◽  
Farihul Ihsan ◽  
Ni Luh Putu Indriyani
Keyword(s):  
Molecular Analysis ◽  
Genetic Relationships ◽  
Female Parent ◽  
Similarity Coefficient ◽  
F1 Hybrids ◽  
Genomic Profiling ◽  
Pca Analysis ◽  
Genetic Characteristics ◽  
Durio Zibethinus ◽  
Rapd Pcr

Abstract The molecular analysis of 32 durian F1 hybrids, resulted from crossing of the Arp 8990 (female parent) and ‘Otong’ (male parent), was conducted in order to determine the genetic characteristics of hybrids and parents, as it would be followed/evidenced by the variability of traits produced from the cross breeding. The RAPD analyses of 14 primers resulted in 114 scoring bands, 112 (98.2%) of them were polymorphic, with 4 to 11 bands amplified per primer. The electrophoresis gel of the PCR results revealed that some hybrids produced different band patterns compared to the parents; this indicated the crossing between parents’ alleles and trait combinations from both the parents. The Dice-Sorensen similarity coefficient demonstrated that most of the hybrids had distant genetic similarities with both parents, which were ranged from 0.141 [71B(4) and 72B(15)] to 0.776 [71B(15) and 48B(1)]. The UPGMA method was used to construct the dendrogram, which grouped the hybrids in five clusters with distinct genetic relationships and was confirmed with the PCA analysis. This result implied that above crossing produced hybrids having characters different from the parents.

Resistance to the root-knot nematode Meloidogyne fallax in Solanum sparsipilum: analysis of the mechanisms

Nematology ◽  
2004 ◽  
Vol 6 (3) ◽  
pp. 389-400 ◽  
Author(s):  
Abou Bakari Kouassi ◽  
Marie-Claire Kerlan ◽  
Miroslaw Sobczak ◽  
Jean-Paul Dantec ◽  
Claudia Rouaux ◽  
...  
Keyword(s):  
Female Parent ◽  
Giant Cells ◽  
F1 Hybrids ◽  
Vascular Cylinder ◽  
Root Knot Nematode ◽  
Resistant Parent ◽  
Defence Reaction ◽  
Invasion And Migration ◽  
Solanum Sparsipilum ◽  
And Migration

AbstractThe genotype 88S.329.15 of Solanum sparsipilum was studied in order to analyse the genetic basis and the mechanisms of its resistance to Meloidogyne fallax. In infected plants grown at 20°C, juveniles invaded the root system with a clear delay and a lower infection rate in comparison to the susceptible S. tuberosum genotype BF15 H1. No defence reaction occurred during root invasion and migration toward the vascular cylinder. The juveniles induced development of feeding sites usually composed of several giant cells, which contained condensed cytoplasm, only small vacuoles, enlarged nuclei with pronounced nucleoli and almost no endoplasmic reticulum. Abundant necrosis of surrounding parenchymatous vascular cylinder cells lead to the degeneration of the giant cells. More than 90% of the invading juveniles failed to develop. The others developed as males. The resistance inheritance was analysed on 128 F1 hybrids obtained using the susceptible line BF15 H1 as the female parent and 88S.329.15 as the male parent. Among the progenies, 68 genotypes produced a necrotic reaction to nematode infection and 60 produced no necrosis. This 1 : 1 segregation pattern suggests a monogenic control of this defence reaction. Unlike the resistant parent 88S.329.15, some M. fallax females developed in the roots of necrotically responding hybrids. There was a normal distribution of mean numbers of adult females found in the roots of these genotypes. This result suggests that the ability of the resistant genotype 88S.329.15 to suppress development of females is quantitatively inherited and likely to be controlled by more than one locus. These data indicate that the mechanism of resistance is different from the resistance to Meloidogyne incognita conferred by the Mi gene of tomato.

scholarly journals Characterization for Drought Tolerance and Physiological Efficiency in Novel Cytoplasmic Male Sterile Sources of Sunflower (Helianthus annuus L.)

2018 ◽  
Author(s):  
Vikrant Tyagi ◽  
Gurpreet Kaur ◽  
Prashant Kaushik ◽  
Satwinder Kaur Dhillon
Keyword(s):  
Water Stress ◽  
Drought Tolerance ◽  
Seed Yield ◽  
Female Parent ◽  
F1 Hybrids ◽  
Male Sterile ◽  
Water Regimes ◽  
Cytoplasmic Male Sterile ◽  
Cytoplasmic Effects ◽  
Biological Yield

Abstract:Sunflower is sensitive to drought and its hybrids have a limited cytoplasmic diversity. The wild cytoplasmic sources of sunflower are not well exploited to their potential for drought tolerance and hybrid development. In this respect, we carried out a Line × Tester based genetic study using 19 sunflower genotypes representing, 13 cytoplasmic male sterile (CMS) lines from wild and conventional sources, 2 maintainer lines, and 4 restorer lines. The CMS and maintainer lines were crossed with restorer lines to develop sixty one-way F1 hybrids. The parents and their hybrids were evaluated under two water regimes viz., normal irrigated and water stress. A total of twelve important plant descriptors were studied over a period of two years. The significant differences were observed between parents and hybrids in both water regimes. Hybrids were higher in average values for all the descriptors than parents. The role of female parent was more prominent in the expression of traits in hybrids as compared to male parents. The CMS sources varied significantly regarding seed yield per plant and other physiological traits. Proline content was three times higher in parents and their hybrids under water stress, and it was not correlated with any other descriptor. Accession CMS-PKU-2A was identified as the best general combiner for leaf area and specific leaf weight. Whereas, CMS-234A was the best general combiner for biological yield and photosynthetic efficiency under both the conditions. The cross combinations CMS-ARG-2A × RCR-8297, CMS-234A × P124R, and CMS-38A × P124R were found significant for biological yield, seed yield and oil content under both environments. Overall, this study provides useful information about the cytoplasmic effects on important sunflower traits and drought stress tolerance when used in the different combinations.

Generation of interspecific hybrids for introgression of mungbean yellow mosaic virus resistance in Vigna radiata (L.) Wilczek

2018 ◽  
Author(s):  
Prince Lekhi ◽  
R. K. Gill ◽  
Satinder Kaur ◽  
T. S. Bains
Keyword(s):  
Microsatellite Markers ◽  
Mosaic Virus ◽  
Vigna Radiata ◽  
Female Parent ◽  
Germination Percentage ◽  
Yellow Mosaic Virus ◽  
F1 Hybrids ◽  
Polymorphic Markers ◽  
Vigna Species ◽  
Mungbean Yellow Mosaic Virus

Vigna radiata genotypes viz., SML 668 and SML 832 and V. mungo genotypes viz., Mash 114 and Mash 218 were crossed in all possible combinations during summer 2015 to generate F1 hybrids. Interspecific hybridization was attempted by using V. radiata genotypes as female parent. Pod set percentage varied from 5.5 percent (SML 832 x Mash 218) to 24.1 percent (SML 832 x Mash 114). The germination percentage ranged from 14.29 to 30.56. Maximum pollen fertility was observed in cross SML 668 x Mash 114 (28.36 percent) followed by SML 668 x Mash 218 (27.03 percent), SML 832 x Mash 218 (24.32 percent) and minimum in SML 832 x Mash 114 (22.59 percent).The purity of hybrids were tested through microsatellite markers. For parental polymorphism, microsatellite markers were selected from related Vigna species such as Vigna unguiculata, Vigna radiata and Vigna mungo. Out of 84 markers used, 46 were polymorphic i.e 54.76 per cent polymorphism between parents. These polymorphic markers were used for confirmation of hybrids produced from different crosses. All the F1 plants gave resistant reaction to Mungbean yellow mosaic virus (MYMV) indicating the introgression of resistance gene(s) from V. mungo to V. radiata.

Allozyme analysis of the hybrid Phoxinus eos × Phoxinus neogaeus (Pisces: Cyprinidae) in Nebraska

1982 ◽  
Vol 60 (5) ◽  
pp. 968-973 ◽  
Author(s):  
Gerard R. Joswiak ◽  
Richard H. Stasiak ◽  
William S. Moore
Keyword(s):  
F1 Hybrids ◽  
Allozyme Analysis ◽  
Parthenogenetic Species ◽  
Marker Loci

Twenty-three fish from two localities in Nebraska were electrophoresed for three marker loci that distinguish Phoxinus eos and P. neogaeus. Seven had patterns of pure P. eos and 16 were heterozygous at all three markers. Of these, two were morphologically similar to P. eos, while the rest more closely resembled neogaeus. All hybrids were female. Two hypotheses are suggested: (1) The F1 hybrids fall into two morphological groups, dependent on the species of the maternal progenitor and (2) the hybrids are a parthenogenetic species. No introgression was detected in this study and the question of hybrid reproduction remains unresolved.

Interspecific introgression of male sterility from tetraploid oilseed Brassica napus to diploid vegetable B. rapa through hybridisation and backcrossing

2013 ◽  
Vol 64 (7) ◽  
pp. 652 ◽  
Author(s):  
Zhengjie Wan ◽  
Yuanbao Tan ◽  
Minhui Shi ◽  
Yuejin Xu ◽  
Nader Aryamanesh ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Male Sterility ◽  
Morphological Characteristics ◽  
Female Parent ◽  
F1 Hybrids ◽  
Recurrent Parent ◽  
Male Sterile ◽  
Interspecific Introgression ◽  
C Genome ◽  
Inbreeding Line

Interspecific F1 hybrids were obtained from a cross between a male sterile Brassica napus (2n = 4x = 38, AA (20) and CC (18) genomes) and an inbreeding line B. rapa (Purple Cai-Tai inbred line 9418, 2n = 2x = 20, AA (20) genome) to introgress male sterility from a tetraploid into a diploid through backcrossing. The morphological characteristics of F1 plants were more like the female parent B. napus and segregated considerably in BC1 when backcrossed to the recurrent parent Purple Cai-Tai. The progeny became stable and more similar to Purple Cai-Tai by BC4. Most C genome chromosomes were found to be eliminated, based on cytogenetic analysis. The majority of chromosomes were eliminated at very early backcross stages, with only 20–26 chromosomes in BC1 plants, and some chromosomes were eliminated gradually with increased backcross generations. The BC4 plants were generally stable with exactly 20 chromosomes. Analysis by AFLP indicated that 49.5–68.7% of the total bands eliminated from F1 to BC4 were female parent specific, and ~12% of B. napus bands were retained with increased backcrossing. The genetic materials controlling sterility from the female parent B. napus were introgressed successfully into the BC4 plants even though most B. napus chromosomes/genetic materials were eliminated during the backcross process.

scholarly journals Obtaining interspecific hybrids, and molecular analysis by microsatellite markers in grapevine

2011 ◽  
Vol 46 (11) ◽  
pp. 1480-1488 ◽  
Author(s):  
Mariane Ruzza Schuck ◽  
Luiz Antonio Biasi ◽  
Ada Michele Mariano ◽  
Bernardo Lipski ◽  
Summaira Riaz ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Interspecific Hybridization ◽  
Molecular Analysis ◽  
Interspecific Hybrids ◽  
Female Parent ◽  
F1 Hybrids ◽  
Reciprocal Crosses ◽  
Self Pollination ◽  
Vitis Labruscana ◽  
Muscadinia Rotundifolia

The objective of this work was to assess the potential of interspecific hybridization of Vitis labruscana and Muscadinia rotundifolia by using artificial cross-pollinations. Microsatellite markers were used to confirm interspecific hybridizations and the identity of the parental genotypes. In crosses in which M. rotundifolia was used as the female parent, no true hybrids were obtained. In the reciprocal crosses, 114 seedlings were identified as true V. labruscana x M. rotundifolia hybrids. Self pollination occurred in direct and in reciprocal crosses. The crossings between 'Bordo' x 'Carlos', 'Magnolia', 'Regale' and' Roanoke', and between' Isabel' x 'Bountiful', 'Carlos', 'Magnolia', 'Regale' and 'Roanoke' were confirmed. The 15 markers evaluated showed that two M. rotundifolia parental genotypes had the same fingerprint profile, indicating a like lyplanting error. The success of hybridization depends mainly on the species and on the cultivar used as the female parent. Microsatellite markers are efficient to confirm the paternity of interspecific F1 hybrids and to determine the correct identity of M. rotundifolia cultivars.

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