Screening of Applicable SSR Molecular Markers Linked to Creeping Trait in Crape Myrtle

Creeping plants have unique ornamental value because they have more branches and flowers and the creeping trait is rare in crape myrtle (Lagerstroemia indica L.). In this study, the first filial generation (F1) population was derived from Lagerstroemia fauriei Koehne (standard) and L. indica “Creole” (creeping) and the backcross1 (BC1) population was derived from the backcross of F1 individual S82 (creeping) and L. fauriei. The segregation of the creeping trait was analyzed for 174 seedlings of the BC1 population to examine the linkage relationship between simple sequence repeat (SSR) molecular markers and the creeping trait. Creeping genes were screened using bulked segregant analysis combined with 322 SSR primers, which were detected with good polymorphism. The results show that two SSR markers (S364 and LYS12) were detected, with genetic distances of 23.49 centimorgan (cM) and 25.86 cM from the loci controlling the plant opening angle trait and the branching angle trait, respectively. The accuracy rate for phenotypic verification using S364 and LYS12 was 76.51% and 74.14%, respectively. Our results provide basic information for the molecular marker-assisted selective breeding and cloning of the creeping gene to improve architecture diversity in the breeding of crape myrtle.

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Bulked Segregant Analysis Identifies Molecular Markers Linked to Melampsora medusae Resistance in Populus deltoides

Phytopathology ◽

10.1094/phyto.2000.90.9.1039 ◽

2000 ◽

Vol 90 (9) ◽

pp. 1039-1042 ◽

Cited By ~ 27

Author(s):

G. M. Tabor ◽

T. L. Kubisiak ◽

N. B. Klopfenstein ◽

R. B. Hall ◽

H. S. McNabb McNabb

Keyword(s):

Molecular Markers ◽

Leaf Rust ◽

Populus Deltoides ◽

Bulked Segregant Analysis ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

Resistance Locus ◽

The North ◽

Melampsora Medusae ◽

Central United States

In the north central United States, leaf rust caused by Melampsora medusae is a major disease problem on Populus deltoides. In this study we identified molecular markers linked to a M. medusae resistance locus (Lrd1) that was segregating 1:1 within an intraspecific P. deltoides family (C9425DD). Previous field results were confirmed in the controlled environment of a growth chamber through an excised whole-leaf inoculation method. Using bulked segregant analysis we identified two random amplified polymorphic DNA (RAPD) markers (OPG10340 and OPZ191800) that are linked to Lrd1. Based on segregation in a total of 116 progeny, the genetic distances between OPG10340 and OPZ191800 and the resistance locus were estimated as 2.6 and 7.4 Haldane centimorgans (cM), respectively. Multipoint linkage analyses strongly suggest the most likely order for these loci is Lrd1, OPG10340, and OPZ191800. These markers may prove to be instrumental in the eventual cloning of Lrd1, as well as for marker-assisted selection of leaf-rust resistant genotypes.

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Molecular evaluations of thirty one clones of poplar based on RAPD and SSR molecular markers

Genetika ◽

10.2298/gensr1403985s ◽

2014 ◽

Vol 46 (3) ◽

pp. 985-1001 ◽

Cited By ~ 1

Author(s):

M.K. Singh ◽

N.B. Singh ◽

S. Thakur ◽

P.K. Naik

Keyword(s):

Genetic Variation ◽

Molecular Markers ◽

Selective Breeding ◽

Analysis Of Molecular Variance ◽

Ssr Primers ◽

The World ◽

The Mean ◽

Relationship Of ◽

Management And Conservation ◽

Selective Breeding Programme

Poplar is an important tree species valued all over the world for its wood importance. Despite limited knowledge of the levels of genetic diversity and relatedness, their cultivation as a source of plywood is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for selective breeding programme, genetic analysis of 31 genotypes was performed using RAPD and SSR molecular markers. Twenty six RAPD primers and 14 SSR primers amplified a total of 236 and 85 scoreable bands of which 86.44% and 86.02% were polymorphic. The mean coefficient of gene differentiation (Gst) was 0.388 and 0.341 indicating that 61.2% and 65.9% of the genetic variation resided within the populations. Analysis of molecular variance (AMOVA) indicated that majority of genetic variation (94.6% using RAPD and 89% using SSR) occurred among genotypes, while the variation between the three groups (categorized as tall, medium and small plants height) was 5.4% (using RAPD and 11% (using SSR). The dendrogram obtained from NJ and STRUCTURE analysis revealed splitting of genotypes into four clusters with clear distinction between short, medium and tall height genotypes, indicated that genetic differentiations measure with respect to RAPD and SSR. However, both the markers were equally useful in providing some understanding about the genetic relationship of different genotypes of poplar that are important in the conservation and exploitation of poplar genetic resources.

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Genetic diversity and molecular markers of five snapper species

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001210 ◽

2007 ◽

Vol 4 (1) ◽

pp. 39-46 ◽

Cited By ~ 2

Author(s):

Liu Li ◽

Liu Chu-Wu

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Simple Sequence Repeats ◽

Microsatellite Loci ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

The Other ◽

Information Contents ◽

The Mean ◽

Simple Sequence

AbstractIn order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

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Development of SSR markers via de novo transcriptome assembly in Akebia trifoliata (Thunb.) Koidz

Genome ◽

10.1139/gen-2019-0068 ◽

2019 ◽

Vol 62 (12) ◽

pp. 817-831

Author(s):

Juan Niu ◽

Yujuan Wang ◽

Yaliang Shi ◽

Xiaofei Wang ◽

Zhimin Sun ◽

...

Keyword(s):

Molecular Markers ◽

De Novo ◽

Transcriptome Assembly ◽

Trinucleotide Repeats ◽

Genetic Identification ◽

De Novo Transcriptome ◽

Geographical Patterns ◽

Ssr Primers ◽

River Line ◽

Simple Sequence

Owing to its high nutritive, economic, and medicinal values, Akebia trifoliata has received increased attention, making worthy of being used as a new fruit crop for further domestication and commercialization in China. However, molecular research of A. trifoliata has lagged as investigations of its genomic resources and molecular markers are rare. In this study, a cDNA library of A. trifoliata leaves was sequenced using the Illumina NovaSeq. 6000 sequencing system. In total, 101 417 transcripts, 63 757 unigenes, and 9494 simple sequence repeats were assembled and identified from the transcriptome datasets. The majority of the SSRs were di- and trinucleotide repeats. Length and number of SSR motifs ranged from 15 to 66, and 5 to 48 bp, respectively. Of which, the A/T mononucleotide motif and AG/TC and CT/GA dinucleotide motifs were the most abundant. Furthermore, 100 SSR primers were randomly selected to validate amplification and polymorphism, and 88 A. trifoliata accessions were definitively distinguished by 49 primers. With the Qinling mountains and Huaihe River line as the boundaries, the northern and southern accessions were clustered into different groups, but no clear geographical patterns (city or origin) were observed in the southern accessions. These newly identified molecular markers may provide a foundation for the genetic identification and diversity analysis and marker-assisted selection breeding in species of Akebia.

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Identification of SSR marker associated with rust resistance in cowpea (Vigna unguiculata L.) using bulk segregant analysis

Legume Research - An International Journal ◽

10.18805/lr.v39i1.8861 ◽

2016 ◽

Vol 39 (1) ◽

Author(s):

M. S. Uma ◽

Niranjan Hegde ◽

Shailaja Hittalmani

Keyword(s):

Molecular Markers ◽

Ssr Markers ◽

Rust Resistance ◽

Bulked Segregant Analysis ◽

Rust Disease ◽

Ssr Primers ◽

Single Marker ◽

Significant Regression ◽

Resistant Genotypes ◽

Selection Of

Bulked segregant analysis was undertaken to tag gene(s) controlling rust resistance using molecular markers in cowpea, to permit rapid selection of superior desirable rust resistant genotypes in the breeding program. For this purpose, the C-152, cultivated variety with high yielding, semi determinate plant type, good protein content and highly rust susceptible was crossed with genotype IC202778, the landrace from Himachal Pradesh, India having determinate, semi spreading and rust resistant characters. The parental genotypes were analyzed with 92 SSR markers for detection of polymorphism and only 13 markers showed polymorphism between the parents. Using each of these 13 SSR primers, we carried out bulked segregate analysis on F2 plants representing two extremes of rust disease resistance and susceptible trait. Three SSR markers VuUGM02, VuUGM08 and VuUGM19 were found to be associated with rust resistance. This was further confirmed through selective genotyping. The co-segregation data on these molecular markers and rust resistance on F2 plants were analysed by means of single-marker linear regression approach. Significant regression suggested linkage between VuUGM02 and rust resistance gene.

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Studies on Genetic Diversity of Selected Population of Hybrid Scallop Chlamys farreri（♀）× Patinopecten yessoensis（♂） by Microsatellites Markers

Journal of Molecular Biology Research ◽

10.5539/jmbr.v5n1p39 ◽

2015 ◽

Vol 5 (1) ◽

pp. 39 ◽

Cited By ~ 1

Author(s):

Biao Wu ◽

Aiguo Yang ◽

Ningning Cheng ◽

Xiujun Sun ◽

Zhihong Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Selective Breeding ◽

Chlamys Farreri ◽

Patinopecten Yessoensis ◽

Microsatellites Markers ◽

Expected Heterozygosity ◽

Ssr Primers ◽

Two Populations ◽

Simple Sequence

The growth superiority of hybrid scallop Chlamys farreri (♀) × Patinopecten yessoensis (♂), as the following successive generation selection have been reported. However, the data about the genetic diversity in those population remains unexplored. In this study, the genetic structure analysis of F1, F2 and F3 were conducted by PCR with 10 Simple Sequence Repeats (SSR) primers. It showed that a total of 68 alleles were detected, and the number of alleles per locus ranged from 3 to 11, Polymorphism Information Content (PIC) per locus ranged from 0.4729 to 0.8429. And, the average observed heterozygosity (Ho) of the three populations were 0.6100, 0.6975 and 0.7750, while the average expected heterozygosity (He) were 0.7607, 0.7751 and 0.7379 respectively. Fst values among the three populations were also low (Fst<0.05) which suggested low genetic differentiation between each two populations. In all, those data indicated the genetic structure challenge caused by hybridization and selection, supplying a new angle to understand artificial selective breeding.

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Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

Journal of Bioresource Management ◽

10.35691/jbm.1202.0205 ◽

2021 ◽

Vol 8 (4) ◽

pp. 86-94

Author(s):

Jaleel Ahmad ◽

Muhammad Baber ◽

Wajid Nazeer ◽

Sana Hamdullah ◽

Aleena Ahmad Somroo

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Gene Diversity ◽

Molecular Genetic ◽

Genetic Distances ◽

Genetic Studies ◽

Molecular Genetic Basis ◽

Ssr Primers ◽

Minimum Genetic Distance ◽

Simple Sequence

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

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Simple Sequence Repeats (SSR) Marker Screening Related to Orange Fleshed Sweet Potato F1 Genotype Resistance against Scab (Sphaceloma batatas Saw.)

KnE Life Sciences ◽

10.18502/kls.v2i6.1050 ◽

2017 ◽

Vol 2 (6) ◽

pp. 279

Author(s):

Nurfitriani Rista ◽

Fitri Widiantini ◽

Anna Aina Roosdab ◽

Endah Yulia ◽

Agung Karuniawanb

Keyword(s):

Molecular Markers ◽

Sweet Potato ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Pcr Analysis ◽

Resistant Variety ◽

Resistant Varieties ◽

Ssr Primers ◽

Orange Fleshed Sweet Potato ◽

Simple Sequence

Orange fleshed sweet potato contains high beta carotene as vitamin A precursor. However, its production is limited by the presence of scab disease caused by Sphaceloma batatas Saw. The disease is able to cause yield loss up to 60%. Best controlling method is using resistant varieties. However, the development of resistant varieties are involving long procedures which is time consuming. The long procedure of resistance varieties selection can be shorted cut using molecular markers such as SSR (Simple Sequence Repeats). Specific SSR markers for sweet potato resistance against scab has not been found. This study aimed to screen SSR molecular markers which were related to resistance to scab. The study used 5 resistant genotypes, 5 susceptible genotypes, and 6 SSR primers. PCR analysis showed that those SSR primers were polymorphic. Furthermore, the biplot analysis result demonstrated that several markers allele were related to plant resistance against scab. This finding indicated that these particular SSR markers can be used in sweet potato breeding program as marker assisted selection to develop resistant variety against scab disease. Keywords: Sphaceloma batatas; orange fleshed sweet potato; SSR markers.

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GENETIC DIVERSITY OF HONEYBEE (APIS MELLIFERA ADANSONII) IN IJEBU ENVIRONAS REVEALED BY SIMPLE SEQUENCE REPEAT (SSR) MARKERS

African Journal of Science and Nature ◽

10.46881/ajsn.v10i0.180 ◽

2020 ◽

Vol 10 ◽

pp. 77

Author(s):

Mistura Temitope Adeleke ◽

Oladunni Nimota Adekunle ◽

Folarin Ojo Owagboriaye ◽

Adebola Olayemi Odeseye ◽

Kemi Sarah Oyedele ◽

...

Keyword(s):

Genetic Diversity ◽

Apis Mellifera ◽

Simple Sequence Repeat ◽

Gene Diversity ◽

Genetic Distances ◽

Sequence Repeat ◽

Ogun State ◽

Ssr Primers ◽

Apis Mellifera Adansonii ◽

Simple Sequence

Honeybee Apis mellifera adansonii, dominant honey producing species in Nigeria was subjected to genetic variability studies using Simple Sequence Repeat (SSR) in other to provide the baseline data in Nigeria. Nine (9) Simple Sequence Repeats (SSR) primers were used to assess the genetic diversity in Two (2) worker bees each collected from 22 colonies found in the four apiaries in Ijebu environs of Ogun State. Data collected were subjected to analysis and results showed that six (6) out of nine primers produced 80 reproducible, polymorphic bands while the remaining three (3) were monomorphic. Gene diversity (H ) in total population and magnitude of differentiation among T populations (FST) was 0.430 and 0.340, respectively. Analysis of Molecular Variance (AMOVA) partitioned the total genetic variation as 70% within, 30% among populations. The cluster analysis showed that Ipari-Oke 3 and Odo-Epo 1-8 populations diverged from others which showed they are closer in genetic distances while Ipari-Oke 1 and Odo-Epo 2-5 were newly observed subcluster which represents another subspecies. In conclusion, genetic variations existed amongst the honey worker bees populations in Ogun State.

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Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽

10.3390/plants10071386 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1386

Author(s):

Soyun Kim ◽

Keunho Yun ◽

Han Yong Park ◽

Ju Young Ahn ◽

Ju Yeon Yang ◽

...

Keyword(s):

Molecular Markers ◽

Raphanus Sativus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cosmetic Industry ◽

Natural Colorants ◽

Health Promoting ◽

Primer Sets ◽

Red Radish ◽

Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

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