scholarly journals Genetic Diversity and Differentiation of Relict Plant Liriodendron Populations Based on 29 Novel EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 334 ◽  
Author(s):  
Xiaofei Long ◽  
Yuhao Weng ◽  
Siqin Liu ◽  
Zhaodong Hao ◽  
Yu Sheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Eastern China ◽  
Genetic Distances ◽  
Breeding Strategy ◽  
Western China ◽  
The Usa ◽  
Ssr Loci ◽  
Liriodendron Chinense

Surviving relict populations of species that were more widespread in ancient times can teach us a lot, such as evolution and genetic differentiation. One such relict plant is Liriodendron, of which populations remain in China (L. chinense (Hemsl.) Sarg.) and the USA (L. tulipifera L.). Studying the genetic structure of these populations would give insight into the genetic differentiation and the breeding strategy. In this work, we developed and characterized 29 novel simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) from hybrid Liriodendron (Liriodendron chinense × tulipifera) callus. In total, 29 SSRs with perfect primer-designed were used to assess genetic diversity and differentiation. The set of polymorphic EST-SSR loci was identified in 48 Liriodendron individuals, represented by 35 individuals sampled from 14 provenances of L. chinense and 13 individuals sampled from 5 provenances of L. tulipifera. Our results indicated that L. chinense populations possess slightly higher genetic diversity than L. tulipifera populations. Based on genetic distances, 48 Liriodendron individuals clustered into three groups (the eastern China L. chinense, the western China L. chinense and L. tulipifera), although the STRUCTURE analysis of the Liriodendron populations revealed just two clear genetic clusters (L. chinense and L. tulipifera). Among these 29 novel markers, ESSR119 showed an obvious species-specific characteristic which can be very useful in marker-assisted selection (MAS). In general, all these EST-SSR markers may have agronomic potential and constitute a basis for future studies on the identification, innovation, and even preservation of Liriodendron germplasms.

scholarly journals Combining Quantitative Data on Growth, Wood Density and Other Traits with SSR Markers to Evaluate Genetic Diversity and Structure in a Planted Population of Eucalyptus camaldulensis Dehn.

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1090
Author(s):  
Xiuhua Shang ◽  
Roger J. Arnold ◽  
Zhihua Wu ◽  
Peijian Zhang ◽  
Guo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Quantitative Trait ◽  
Eucalyptus Camaldulensis ◽  
Genetic Distances ◽  
Bark Thickness ◽  
Seed Sources ◽  
Pilodyn Penetration ◽  
Ssr Loci

Eucalyptus camaldulensis Dehn. is one of the most morphologically and genetically variable Eucalyptus species. Growth, Leptocybe invasa Fisher & La Salle susceptibility, pilodyn penetration and other traits up to age 36 months were assessed in a seed source/family trial in China comprising 112 seedlots representing five natural stand and six exotic seed sources. Genetic diversity and population structure of this trial population were also analyzed using 48 simple sequence repeat (SSR) markers. The key objective was to examine whether the genomic data could provide value over information obtained from just quantitative trait data. Significant genetic variation was found among seed sources and among families within seed sources for most quantitative traits. The ratio of variance among seed sources to variance among families within seed sources, based on variances estimated from quantitative trait data, varied from 0.1% (height at 9 months) up to 75.2% (bark thickness). Equivalent ratios estimated from the AMOVA on SSR loci data were similar for height (ages 24 and 36 months) and also pilodyn penetration at 36 months, but not for 9-month height or 36-month bark thickness. From 48 SSR loci examined, the genetic differentiation coefficient (among seed sources) was 0.086, indicating low genetic differentiation among seed sources. While overall genetic diversity in the trial population examined was high, the levels within the different seed sources varied markedly. Prior to this study, genetic distances among families from the three exotic seed sources (from domesticated Indian populations) in the trial, along with their genetic distances from, and relatedness to, families from five natural stand seed sources (Australian) in the trial were unknown. The SSR loci data removed uncertainties and revealed that the exotic sources increased the breadth of genetic origins represented in the trial population—information that could not have been obtained from just the quantitative trait data.

scholarly journals Genetic Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Aissam EL FINTI ◽  
Driss TALIBI ◽  
Mouhamed SIDKI ◽  
Abdelhamid E. MOUSADIK
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Opuntia Ficus Indica ◽  
Distance Analysis ◽  
Reference Collection ◽  
Ssr Loci ◽  
Set Up ◽  
Genetic Distance Analysis ◽  
Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

scholarly journals Analysis of Genetic Diversity within Nepalese Maize Populations Using SSR Markers

1970 ◽  
Vol 11 ◽  
pp. 1-8 ◽  
Author(s):  
Dil Bahadur Gurung ◽  
Maria Luz C George ◽  
Quirino D Dela Cruz
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Maize Breeding ◽  
Maize Populations ◽  
Maize Varieties ◽  
Ssr Loci ◽  
Average Gene ◽  
Hybrid Maize

Information on genetic diversity and relationships among breeding materials is necessary for hybrid maize breeding. Four open-pollinated varieties were analyzed using SSR markers to determine the genetic diversity within the varieties. In each variety, 15 individuals were genotyped with 30 SSR markers. Average heterozygosity percentage of the varieties was 45.07%, ranging from 35.23% in Rampur Composite to 54.64% in Khumal Yellow, indicating the higher level of heterozygosity in these two varieties. An average PIC value across all the polymorphic SSR loci was 0.50; which ranged from 0.47 in Manakamana-2 to 0.52 in Khumal Yellow and Arun-4. At the genotype level, the range was from 0.07 in umc1161 to 0.84 in umc1136. The total number of alleles detected was 415 for 30 SSR markers in 60 genotypes. The unique and common alleles detected respectively were 27 and 71. The average number of alleles per locus was 3.45 among the varieties, ranging from 3.21in Manakamana-2 to 3.76 in Khumal Yellow. Average gene diversity across the varieties was 0.54 and ranged from 0.51 in Manakamana-2 to 0.56 in Khumal Yellow and Arun-4. The genetic similarity coefficient of all individuals among the varieties was seen at 0.35.The MRD values were higher between Arun-4 and Manakamana-2 (0.290) and low between Khumal Yellow and Rampur Composite (0.221). Estimate of genetic distances among the varieties showed that Rampur Composite, Khumal Yellow, and Manakamana-2 were closely related sharing the similar genetic backgrounds, whereas Arun-4 was genetically more distantly related. Efforts are being made for the development and evaluation of inbred lines from these distantly related maize varieties for developing high yielding maize hybrids. Key Words: genetic diversity; maize hybrid; SSR markers DOI: 10.3126/njst.v11i0.4082Nepal Journal of Science and Technology 11 (2010) 1-8

scholarly journals Genetic Diversity Analysis and F2 Population Development for Breeding of Long Juvenile Trait in Soybean

2018 ◽  
Vol 14 (1) ◽  
pp. 11 ◽  
Author(s):  
I Made Tasma ◽  
N. P. Mega Gena Yani ◽  
Rosliana Purwaningdyah ◽  
Dani Satyawan ◽  
Kristianto Nugroho ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Segregation Ratio ◽  
Genetic Distances ◽  
Day Length ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
F2 Population ◽  
Soybean Genotypes ◽  
The Usa

<p>Genetic diversity analysis using molecular markers is an important step for selecting appropriate parents in a soybean breeding program. The aims of this study were to (1) analyze genetic diversity of 29 soybean genotypes assessed with 27 SSR markers for selecting appropriate parents and (2) develop F2 populations to be used for breeding long juvenile (LJ) trait in soybean to<br />be cultivated in short photoperiod condition. The soybean genotypes used consisted of 11 Indonesian soybean genotypes and 18 genotypes introduced from the USA. F2 populations were developed by crossing Grobogan with three introduced genotypes carrying LJ character. The PIC values of the 27 SSR markers ranged from 0.87 to 0.96. Cluster analysis resulted in three main<br />clusters at coefficient similarity of 0.76. The five LJ introduced accessions and the nine Indonesian genotypes showed high genetic distances and are useful as parent pairs for developing breeding populations. The F1 progeny phenotypic<br />performances of the cross far exceeded the performaces of both parents. Three F2 populations were developed by crossing the distantly related soybean genotypes. The F2 populations were verified by using SSR markers and it was found that they segregated in a 1:2:1 ratio confirming the segregation ratio of codominant SSR markers. The F2 populations should be useful for breeding LJ characters to improve soybean productivity in low latitude tropical countries such as Indonesia, which has day length of approximately 12 h all year round.</p>

scholarly journals Genetic diversity and population structure of rice stripe virus in China

2009 ◽  
Vol 90 (4) ◽  
pp. 1025-1034 ◽  
Author(s):  
Tai-Yun Wei ◽  
Jin-Guang Yang ◽  
Fu-Long Liao ◽  
Fang-Luan Gao ◽  
Lian-Ming Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Yunnan Province ◽  
Southwest China ◽  
Eastern China ◽  
Rice Stripe Virus ◽  
Genetic Distances ◽  
Geographical Regions ◽  
Strong Negative Selection ◽  
Recent Outbreak

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

scholarly journals Molecular Characterization and Similarity Relationships among Flue-Cured Tobacco (Nicotiana tabacum L.) Genotypes Using Simple Sequence Repeat Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 247
Author(s):  
Soheila GHOLIZADEH ◽  
Reza DARVISHZADEH ◽  
Babak ABDOLLAHI MANDOULAKANI ◽  
Iraj BERNOUSI ◽  
Seyed Reza ALAVI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Allele Number ◽  
Nicotiana Tabacum L ◽  
Ssr Loci ◽  
Actual Degree ◽  
Similarity Relationships

Characterization of genetic diversity has long been a major goal in tobacco breeding programs. Information on genetic diversity is essential for a rational use of genetic resources. In the present study, the genetic variation among 72 flue-cured tobacco genotypes was evaluated using microsatellite markers (SSRs). A set of 104 alleles was generated at 30 SSR loci. The mean number of alleles per locus (na) and the effective allele number (ne) were 3.467 and 2.358, respectively. The expected heterozygosity ranged from 0.29 to 0.75 with average of 0.54. Several methods were used to construct the similarity matrices and dendrograms. The co-phenetic correlation coefficient, which is a measure of the correlation between the similarities represented on the dendrograms and the actual degree of similarity, was calculated for each dendrogram. Among the different methods, the highest value (r=0.76368) was observed for the UPGMA created based on Jaccard’s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccard’s similarity coefficient ranged from 0.08 to 0.84, suggesting the presence of high molecular genetic variability among the studied tobacco genotypes. Based on UPGMA clustering method all studied flue-cured tobacco genotypes, except for ‘Glustinusa Rasht’, were placed in three distinct groups. We observed an obvious heterotic pattern in the studied flue-cured germplasm corresponding to genetic distances and classification dendrogram, which persuades exploitation of heterosis in flue-cured tobaccos.

scholarly journals Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8038
Author(s):  
Yanli Xiong ◽  
Wenhui Liu ◽  
Yi Xiong ◽  
Qingqing Yu ◽  
Xiao Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Western China ◽  
Tibet Plateau ◽  
Group Method ◽  
Breeding Strategies ◽  
Population Genetic Differentiation ◽  
Principal Coordinates ◽  
Geographical Regions ◽  
Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

scholarly journals Genetic Diversity and Origin of Weedy Rice (Oryza sativa f. spontanea) Populations Found in North-eastern China Revealed by Simple Sequence Repeat (SSR) Markers

2006 ◽  
Vol 98 (6) ◽  
pp. 1241-1252 ◽  
Author(s):  
Q. CAO ◽  
B.-R. LU ◽  
H. XIA ◽  
J. RONG ◽  
F. SALA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Eastern China ◽  
Weedy Rice ◽  
Sequence Repeat ◽  
North Eastern ◽  
Simple Sequence

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.)

2014 ◽  
Vol 12 (S1) ◽  
pp. S118-S120 ◽  
Author(s):  
Rajeev Varshney ◽  
Mahendar Thudi ◽  
Hari Upadhyaya ◽  
Sangam Dwivedi ◽  
Sripada Udupa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Ssr Markers ◽  
Quality Criteria ◽  
Specific Information ◽  
Wide Range ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Diversity Studies

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

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