scholarly journals Distance-based exclusion method for parentage analysis using microsatellites (SSR) markers

2021 ◽  
Author(s):  
Gil-Muñoz Francisco ◽  
Abrahamsson Sara ◽  
García-Gil M Rosario
Keyword(s):  
Ssr Markers ◽  
Parentage Analysis ◽  
Resolving Power ◽  
Genotyping Errors ◽  
Distance Ratio ◽  
Real Dataset ◽  
Error Calculation ◽  
Biological Meaning ◽  
Exclusion Method

AbstractGenotyping mistakes represent a challenge in parental assignment where even small errors can lead to significant amounts of unassigned siblings. Different parental assignment algorithms have been designed to approach this problem. The Exclusion method is the most applied for its reliability and biological meaning. However, the resolving power of this method is the lowest for data containing genotyping errors. We introduce a new distance-based approach which we coin as Distance-Based Exclusion (DBE). The DBE method calculates the distance between the offspring haplotype and haplotype of each of the potential fathers. The father with the lowest distance is then assigned as candidate father according to a distance ratio (α). We have tested the Exclusion and DBE methods using a real dataset of 1230 offsprings subdivided into families of 25 individuals. Each family had six potential fathers and one known mother. Compared with the Exclusion method, the DBE method is able to solve 4.7% more individuals (64.4% Exclusion vs 69.1% DBE) using the most restrictive α tested without errors. DBE method can also be used together with the Exclusion method for error calculation and to further solve unassigned individuals. Using a two-step approach, we were able to assign 98.1% of the offsprings with a total predicted error of 4.7%. Considering the results obtained, we propose the use of the DBE method in combination with the Exclusion method for parental assignment.

Parentage analysis of natural citrus hybrid ‘Zhelong Zhoupigan’ based on nuclear and chloroplast SSR markers

2015 ◽  
Vol 186 ◽  
pp. 24-30 ◽  
Author(s):  
Hang Li ◽  
Xiaoming Yang ◽  
Lianshu Zhu ◽  
Hualin Yi ◽  
Lijun Chai ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Parentage Analysis ◽  
Chloroplast Ssr

Assessment of the genetic diversity and population structure of apricot (Prunus armeniaca L.) germplasm of the Northwestern Himalaya using SSR markers

2021 ◽  
pp. 1-10
Author(s):  
Aijaz A. Wani ◽  
Khalid Hussain ◽  
Showkat A. Zargar ◽  
Faizan Ahmad ◽  
Reetika Mahajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Geographical Location ◽  
Prunus Armeniaca ◽  
Resolving Power ◽  
Diversity Assessment ◽  
Prunus Armeniaca L ◽  
Genetic Pool ◽  
High Level

Abstract Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

scholarly journals Parentage Analysis in Pear Cultivars Characterized by SSR Markers

2003 ◽  
Vol 72 (3) ◽  
pp. 182-189 ◽  
Author(s):  
Tetsuya Kimura ◽  
Yutaka Sawamura ◽  
Kazuo Kotobuki ◽  
Nagao Matsuta ◽  
Tateki Hayashi ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Parentage Analysis

scholarly journals Comparative assessment of SSR, ISSR and AFLP markers for characterization of selected genotypes of Himalayan Chir pine (Pinus roxburghii Sarg.) based on resin yield

2014 ◽  
Vol 63 (1-6) ◽  
pp. 94-108 ◽  
Author(s):  
A. Rawat ◽  
S. Barthwal ◽  
H. S. Ginwal
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Issr Markers ◽  
Comparative Assessment ◽  
Aflp Markers ◽  
Resolving Power ◽  
Pinus Roxburghii ◽  
Inter Simple Sequence Repeats ◽  
Chir Pine ◽  
Simple Sequence

AbstractA set of 19 SSR (Simple Sequence Repeats), 9 ISSR (Inter-Simple Sequence Repeats) and 5 AFLP (Amplified Fragment Length Polymorphism) primer combinations were used to evaluate the variability among 53 genotypes of Pinus roxburghii selected based on resin yield from the natural zone of occurrence of this species in Uttarakhand, India. The selected trees of pine varied in resin yield from 0.25 to 8 kg/year/tree. Based on the comparative assessment of SSR, ISSR and AFLP markers, SSR markers were found most polymorphic with an average PIC value of 0.327 and 2.42 alleles per marker, while ISSR markers showed the highest effective multiplex ratio (15.536) and marker index (4.958). AFLP markers showed the maximum resolving power (8.099) which was comparable to the resolving power (8.059) of ISSR markers. UPGMA-based dendrogram using SSR markers revealed more distinct grouping of genotypes on the basis of resin yield as compared to ISSR and AFLP markers. AMOVA by collection site revealed no significant variation among the populations. Whereas, AMOVA by resin yield using SSR, ISSR and AFLP markers revealed FSTvalues to be 0.1096, 0.0483 and 0.2422 indicating moderate, low and great genetic differentiation among the groups. This clearly indicated that the variation at the molecular level was attributed to the resin yield and not the site of collection.

scholarly journals Parentage Analysis in Japanese Peaches using SSR Markers

2003 ◽  
Vol 53 (1) ◽  
pp. 35-40 ◽  
Author(s):  
Toshiya Yamamoto ◽  
Kouhei Mochida ◽  
Tsuyoshi Imai ◽  
Takashi Haji ◽  
Hideaki Yaegaki ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Parentage Analysis

scholarly journals Candidate gene based characterization of common bean genotypes

2018 ◽  
Vol 78 (3) ◽  
Author(s):  
Sajad Majeed Zargar ◽  
Nancy Gupta ◽  
Reetika Mahajan ◽  
Susheel Sharma ◽  
F. A. Nehvi ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Common Bean ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Power Estimation ◽  
Resolving Power ◽  
Yield Traits ◽  
Marker Index ◽  
High Level

A set of 96 common bean genotypes were characterized using 25 candidate gene based SSR markers associated with yield traits. Twenty three SSR markers were found polymorphic and their discriminatory power estimation was performed on the basis of PIC, resolving power and marker index that mainly explain ability of molecular markers to distinguish genotypes. An average of 0.33 PIC was observed where highest value was exhibited by the primer BM184. The primers BM170 and Bmd8 generated four alleles whereas BM170 showed maximum marker index of 1.28 and highest resolving power of 1.89 was found in case of primer BM180. Further, the genotypes were grouped in three major clusters based on DARwin5 software. High level of genetic diversity observed within the genotypes could be used to accelerate genetic improvement of germplasm in common bean targeting yield attributing traits.

scholarly journals Assessment of Genetic Variation within Commercial Iranian Pomegranate (Punica granatum L.) Cultivars, Using ISSR and SSR Markers

2017 ◽  
Vol 5 (6) ◽  
pp. 622
Author(s):  
Meysam Madadi ◽  
Zabihollah Zamani ◽  
Reza Fatahi
Keyword(s):  
Genetic Variation ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Punica Granatum ◽  
Issr Markers ◽  
Resolving Power ◽  
Horticultural Crops ◽  
Commercial Cultivars ◽  
Ssr Loci ◽  
Punica Granatum L

Pomegranate is one of the most important horticultural crops in Iran, and has been cultivated for thousands of years in this country. At this period due to selection of superior cultivars from nature or mutation emerged in these cultivars, and their vegetative propagation, substantial genetic variation has occurred within and among the cultivars. Thus, each cultivar may consist of different clones. According to this issue, diversity within four commercial cultivars of pomegranate was analyzed. Two molecular marker systems including ISSR and SSR were used to evaluate variability between 36 samples of four commercial cultivars. ISSR markers produced 114 amplification products, out of which 97 were polymorphic (83.23%). Mean resolving power was 2.96 for ISSR markers. 19 SSR molecular markers were used, 15 of which amplified polymorphic products, while the remaining ones monomorphic., The number of polymorphic alleles per locus ranged from two to four (average 3.6). The observed and expected heterozygosities ranged from 0.04 to 0.92 and 0.14 to 0.62, respectively. In addition, mean polymorphic information content was 0.45 for SSR loci. Our results showed that commercial Iranian pomegranate have different clones. Therefore, ISSR and SSR markers can be a useful tools for detecting clones of each cultivar.

scholarly journals Eficiența unor marcheri moleculari în discriminarea populațiilor de lupoaie originare din China

2021 ◽  
Author(s):  
Maria Duca ◽  
◽  
Ana Mutu ◽  
Ina Bivol ◽  
Steliana Clapco ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
Resolving Power ◽  
Information Index ◽  
Combined Use ◽  
Different Types ◽  
High Level ◽  
Different Levels

In this study, the effectiveness of different types of molecular markers in assessing genetic diversity of populations of O. cumana from China was determined. ISSR and SSR markers detected different levels of genetic variability among and within broomrape populations. SSR markers analysis showed high level of genetic variation within the populations as revealed by high average values of Nei's gene diversity (H=0,75) and Shannon's information index (I=1,44), while genotyping with ISSR markers showed greater ability to discriminate genotypes according to Resolving power (Rp=7,24). Thus, the combined use of ISSR and SSR markers allowed the detection of higher polymorphism than either set of marker alone.

scholarly journals Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

2016 ◽  
Vol 34 (4) ◽  
pp. 827-844 ◽  
Author(s):  
Ludivine Lassois ◽  
Caroline Denancé ◽  
Elisa Ravon ◽  
Arnaud Guyader ◽  
Rémi Guisnel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Parentage Analysis ◽  
Core Collections

Classification and diversity of sacred and American Nelumbo species: the genetic relationships of flowering lotus cultivars in Japan using SSR markers

2009 ◽  
Vol 7 (03) ◽  
pp. 260-270 ◽  
Author(s):  
Nakao Kubo ◽  
Masashi Hirai ◽  
Akio Kaneko ◽  
Daizo Tanaka ◽  
Kumaji Kasumi
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Genetic Relationships ◽  
Parentage Analysis ◽  
Site Specific ◽  
Genomic Libraries ◽  
Expressed Sequence ◽  
Simple Sequence

The water lotus, genusNelumbo, contains two species, the sacred (Nelumbo nucifera) and American lotuses (Nelumbo lutea). Hundreds of flowering lotus cultivars are currently known. However, their classification is unclear. For the classification ofNelumbocultivars, in addition to 35 simple sequence repeat (SSR) markers recently developed, we have developed 17 and 16 of newNelumboSSR markers from SSR-enriched genomic libraries and expressed sequence tag (EST) data, respectively. Out of these 68 SSRs, along with SSRs recently published by others, 52 showed clear polymorphisms in 98Nelumbosamples. A total of 300 alleles were observed, ranging from 2 to 11 alleles per locus, with an average of 5.77. Alleles specific for the American lotus-derived cultivars and a cluster of the American lotus-derived cultivars on a neighbour-joining tree confirmed genetic differences betweenN. luteaandN. nucifera. In addition, a possible differentiation between Chinese and Japanese cultivars was also suggested. Parentage analysis using the SSR markers confirmed four known parentages and predicted currently-unknown parentages of six cultivars. The present data have demonstrated that site-specific, co-dominant SSR markers enable more accurate classification, identification and comparison ofNelumbospecies.

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