Transferability of Sorghum Microsatellite Markers to Bamboo and Detection of Polymorphic Markers

The use of molecular markers for the characterization and evaluation of plant genetic resources has become a useful approach in plant genetic research. Simple Sequence Repeats (SSRs) are among the markers that are widely used in genetic diversity and parental analysis owing to their co-dominant nature, high reproducibility, abundance in the genome and transferability across species or genera. The development of these markers for a species might be costly and time consuming. Hence, screening existing markers through transferability test from closely related species or family is resource conscious. In this study, the transferability of 90 polymorphic SSR markers of sorghum to bamboo was tested and polymorphic analysis of transferable markers were performed. Nearly 62% of the tested SSRs successfully recorded amplification in at least one bamboo species of which 55% were polymorphic. These polymorphic markers detected a total of 147 alleles at an average rate of 4.7 alleles per marker. The abundant alleles account 20.4% while the common and rare alleles share 39.6 and 40 %, respectively. The result showed a relatively low degree of polymorphic information content (PIC) averaging 0.29. The gene diversity index (He) ranged from 0.21 to 0.49 with a mean of 0.37. The cluster analysis based on the polymorphic markers surfaced most of the species in accordance with their geographic origin. The complementarity of the weighted neighbour joining tree and coordinate analysis implies the representative nature of the transferred markers for the diversity analysis of bamboo species.

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Forests ◽

10.3390/f11010061 ◽

2020 ◽

Vol 11 (1) ◽

pp. 61 ◽

Cited By ~ 1

Author(s):

Chengcai Zhang ◽

Xiaohua Yao ◽

Huadong Ren ◽

Jun Chang ◽

Jun Wu ◽

...

Keyword(s):

Genetic Study ◽

Polymorphic Information Content ◽

Genetic Research ◽

Geographic Origin ◽

Pcr Amplification ◽

Genetic Studies ◽

New Development ◽

Ssr Loci ◽

Simple Sequence

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

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The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species

BMC Plant Biology ◽

10.1186/s12870-020-02792-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lingyun Liu ◽

Xifeng Fan ◽

Penghui Tan ◽

Juying Wu ◽

Hui Zhang ◽

...

Keyword(s):

Rna Sequencing ◽

Gene Function ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Average Distance ◽

Vascular Plant ◽

Geographic Origin ◽

Sequencing Analysis ◽

Genetic Characteristics ◽

Functional Studies

Abstract Background Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms. Results In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei’s (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What’s more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods. Conclusions The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.

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Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽

10.2298/gensr1503983b ◽

2015 ◽

Vol 47 (3) ◽

pp. 983-992

Author(s):

Zelmíra Balázová ◽

Andrej Trebichalský ◽

Zdenka Gálová ◽

Radomíra Hornyák-Gregáňová

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Ssr Marker ◽

Diversity Index ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Average Frequency ◽

Polymorphic Markers ◽

Average Value ◽

Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

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Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-487 ◽

2019 ◽

Author(s):

Bouri Amina ◽

Mediouni Mohammed Rida ◽

Ameur Ameur Abdelkader ◽

Udupa Sripada ◽

Gaouar Souheil Bechir Semir

Keyword(s):

Genetic Diversity ◽

Information Content ◽

Cicer Arietinum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Geographic Origin ◽

Diversity Analysis ◽

Factorial Correspondence Analysis ◽

Genetic Diversity Analysis ◽

Cicer Arietinum L

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P less than 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

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Genetic diversity in sorghum (Sorghum bicolor L. Moench) accessions using SNP based Kompetitive allele-specific (KASP) markers

Australian Journal of Crop Science ◽

10.21475/ajcs.21.15.06.p3088 ◽

2021 ◽

pp. 890-898

Author(s):

Thulo Sejake ◽

Nemera Shargie ◽

Riann Christian ◽

Assefa B. Amelework ◽

Toi J. Tsilo

Keyword(s):

Genetic Diversity ◽

Agricultural Research ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Population Analysis ◽

Geographic Origin ◽

Snp Analysis ◽

Germplasm Bank ◽

Allele Specific ◽

Kasp Markers

Genetic diversity analysis is an important component in conventional and marker-assisted breeding. The objective of this study was to assess the level of genetic diversity among 100 sorghum accessions, which were selected randomly from the Sorghum National Germplasm Bank maintained at Agricultural Research Council, South Africa. A total of 136 Kompetitive Allele-Specific PCR (KASP) markers were used in this study. The KASP markers were previously derived from single-nucleotide polymorphic (SNP) analysis of the world-wide sorghum accessions by other research groups. A total of 110 KASP markers were polymorphic and recorded an average polymorphic information content (PIC) value of 0.3, which indicated high level of discrimination of the markers. The markers had an average gene diversity and observed heterozygosity of 0.3 and 0.10, respectively. Analysis of molecular variance revealed a significantly high variation among accessions (83% and 89%) than within accessions (10% and 11%) based on breeding status and geographic origin, respectively. Genetic distance varied from 0.0 between SA0672 and SA0673, SA1282 and SA0670 to 0.57 between Hakika and SA1442 with an average mean of 0.30. The dendrogram and model-based population analysis identified three and four distinct groups in 95 sorghum accessions, respectively. These results imply the presence of genetic diversity and lack of genetic bottleneck within the National Sorghum Germplasm Bank, which could be highly relevant for sorghum breeding and germplasm maintenance

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Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia

Journal of Fungi ◽

10.3390/jof7100820 ◽

2021 ◽

Vol 7 (10) ◽

pp. 820

Author(s):

Gezahegne Getaneh ◽

Tadele Tefera ◽

Fikre Lemessa ◽

Seid Ahmed ◽

Tarekegn Fite ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Ascochyta Blight ◽

Geographic Origin ◽

Principal Component ◽

Internal Transcribed Spacer Region ◽

Pathogen Populations

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

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Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Animals ◽

10.3390/ani10061093 ◽

2020 ◽

Vol 10 (6) ◽

pp. 1093

Author(s):

Selen Yatkın ◽

Fulya Özdil ◽

Emel Özkan Ünal ◽

Serdar Genç ◽

Selçuk Kaplan ◽

...

Keyword(s):

Microsatellite Markers ◽

Likelihood Function ◽

Diversity Index ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Clustering Algorithms ◽

Structural Features ◽

Equus Asinus ◽

Genetic Diversity And Structure

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

PLoS ONE ◽

10.1371/journal.pone.0242506 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242506

Author(s):

Krisztián Frank ◽

Nóra Á. Bana ◽

Norbert Bleier ◽

László Sugár ◽

János Nagy ◽

...

Keyword(s):

Microsatellite Markers ◽

Y Chromosome ◽

Cervus Elaphus ◽

Red Deer ◽

High Throughput Sequencing ◽

Genomic Sequence ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Forensic Genetics ◽

Geographic Origin

Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

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Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Journal of Plant Pathology ◽

10.1007/s42161-021-00759-8 ◽

2021 ◽

Author(s):

Rui Zang ◽

Ying Zhao ◽

Kangdi Guo ◽

Kunqi Hong ◽

Huijun Xi ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Fusarium Oxysporum ◽

Diversity Index ◽

Gene Diversity ◽

Pcr Amplification ◽

Bitter Gourd ◽

Diseased Plant ◽

Variation Analysis ◽

Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

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