Establishment of Molecular Identity Cards for Cucumis melo Cultivars Using SSR Markers

Twenty-four representative melon varieties and six parental cultivars were examined in this study. Among 159 pairs of simple sequence repeat (SSR) primers, 18 SSR core primers with rich polymorphic information, a large number of genotypes, and the ability to distinguish different melon varieties were selected. A total of 113 genotypes were detected among the 30 experimental materials, with an average of 6.28 genotypes for each pair of primers. The polymorphic information content was on average 0.6807, ranging from 0.5618 to 0.7885. Specific bands of the primers for the 30 experimental materials were analyzed, and by combining different primer loci, all 30 varieties were identified. Unique barcodes for molecular identity cards for the 30 experimental materials were established using the fingerprints formed with this SSR marker system. Each variety has a unique identity card that can be applied for the registration of the newly bred varieties, the protection of breeders’ rights, and the authenticity of breeds after promulgation of the new Seed Law of the People’s Republic of China.

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Genetic Diversity and DNA Fingerprints of Three Important Aquatic Vegetables by EST-SSR Markers

Scientific Reports ◽

10.1038/s41598-019-50569-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Xingwen Zheng ◽

Teng Cheng ◽

Liangbo Yang ◽

Jinxing Xu ◽

Jiping Tang ◽

...

Keyword(s):

Genetic Diversity ◽

High Frequency ◽

Phylogenetic Trees ◽

Expressed Sequence Tag ◽

Polymorphic Information Content ◽

Molecular Identity ◽

Sacred Lotus ◽

Identity Cards ◽

Expressed Sequence ◽

Simple Sequence

Abstract Twenty-two sacred lotus (Nelumbo nucifera), 46 taros (Colocasia esculenta) and 10 arrowheads (Sagittaria trifolia) were used as materials and combined with EST-SSR (expressed sequence tag-simple sequence repeats) primers developed by our laboratory. Core primers were screened from a large number of primers that were able to distinguish all materials with a high frequency of polymorphisms. Six pairs, twenty pairs and three pairs of core primers were screened from sacred lotus, taro, and arrowhead, respectively. The SSR fingerprints of these three important aquatic vegetables, producing 17-, 87- and 14-bit binary molecular identity cards, respectively, were separately determined by using the core primers. Since there were few core primers of sacred lotus and arrowhead, 3 and 9 primer pairs with higher polymorphic information content (PIC), respectively, were selected as candidate primers. These core and candidate primers were used to identify the purities of No.36 space lotus, Shandong 8502 taro and Wuhan arrowhead, which were 93.3% (84/90), 98.9% (89/90) and 100.0% (90/90), respectively. The fingerprints, displayed as binary molecular identification cards of three important aquatic vegetables, were obtained, and their purity was successfully determined with EST-SSR labeling technology. Phylogenetic trees were also constructed to analyze the genetic diversity of 22 sacred lotus, 46 taros and 10 arrowheads. This study classifies and identifies germplasm resources and is an important reference to test the authenticity and variety purity of other aquatic vegetables in the future.

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Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.8 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

K. T. Ramya ◽

A. Vishnuvardhan Reddy ◽

M. Sujatha

Keyword(s):

Genetic Distance ◽

Polymorphic Information Content ◽

Distance Matrix ◽

Coefficient Matrix ◽

Male Sterile ◽

Breeding Lines ◽

Genetic Distance Matrix ◽

Ssr Primers ◽

Fertility Restorers ◽

Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

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Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

10.21203/rs.3.rs-1204134/v1 ◽

2022 ◽

Author(s):

Huiling Wang ◽

Kuan Yang ◽

Liwei Guo ◽

Lifen Luo ◽

Chi He ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Yunnan Province ◽

Polymorphic Information Content ◽

Polyacrylamide Gel Electrophoresis ◽

Panax Notoginseng ◽

Expected Heterozygosity ◽

Ssr Primers ◽

Polymorphic Microsatellite ◽

Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

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Analysis of genetic diversity, population structure and linkage disequilibrium in Iranian wheat landraces using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262115000684 ◽

2016 ◽

Vol 15 (4) ◽

pp. 327-334 ◽

Cited By ~ 2

Author(s):

Elham Zarei Abbasabad ◽

Seyed Abolghasem Mohammadi ◽

Mohammad Moghaddam ◽

Mohammad Reza Jalal Kamali

Keyword(s):

Population Structure ◽

Linkage Disequilibrium ◽

Ssr Marker ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Genome Wide ◽

Geographical Regions ◽

Q Matrix ◽

Wheat Landraces ◽

Simple Sequence

AbstractPopulation structure and linkage disequilibrium (LD) were investigated in a set of 395 bread wheat landraces including 154 spring, 193 winter, two facultative wheat and 46 unknown growth type collected from different geographical regions of Iran. A total of 53 microsatellite markers distributed in three genomes of wheat were assayed for polymorphism. The 312 polymorphic alleles were served to estimate population structure and analyse the genome-wide LD. The number of alleles ranged from 2 to 18 with an average of 5.89 alleles/locus. Mean of polymorphic information content was 0.6 with a range of 0.15–0.86 and gene diversity varied from 0.16 to 0.88 with an average of 0.64. The population of landraces was highly structured and based on distance-and model-based cluster analyses the 395 landraces were assigned into eight subpopulations: SG1–SG8. Population structure estimates based on simple sequence repeat (SSR) marker data were quantified in a Q matrix and used in calculation of LD between pair of markers. A low overall LD level found in 12–13% (166) of the SSR marker pairs showed significant pairwise LD in r2 ≥ 0.01 and P ≤ 0.001 and six pair showed r2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

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Genetic diversity analysis of soybean (Glycine max (L.) Merr.) genotypes making use of SSR markers

Australian Journal of Crop Science ◽

10.21475/ajcs.19.13.07.p1638 ◽

2019 ◽

pp. 1113-1119

Author(s):

Keitumetse Kujane ◽

Moosa M Sedibe ◽

Alina Mofokeng

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Molecular Data ◽

Dna Ladder ◽

Ssr Primers ◽

Soybean Genotypes ◽

Glycine Max L ◽

Simple Sequence ◽

Selection Of

In this study, we aimed to investigate the genetic diversity and polymorphism among 30 soybean genotypes maintained by the ARC using simple sequence repeat (SSR) markers. Soybean genotypes were characterized using 20 SSR primers. DNA was extracted using the standard cetyl trimethylammonium bromide method and amplified using PCR. Allele size was determined via comparison with a 100 base pair (bp) DNA ladder. Molecular data were analyzed, and a dendrogram and matrix were generated using GGT 2.0 software. A total of 216 alleles with an average of 10.8 alleles per locus were detected. The allele sizes ranged between 2 and 33 bp with an average of 18.7 bp. The polymorphic information content among genotypes varied from 0.85 (Satt001) to 0.75 (Satt43) with an average of 0.716, and heterozygosity ranged from 0.87 to 0.78 with an average of 0.7485. The most diverse genotypes were B 66 S 31, 69S 7, and R5-4-2 M, which indicated the efficiency of the SSR markers for the detection of genetic diversity. The results of the current study revealed the diversity among the soybean genotypes tested, which might aid breeders in the future in the selection of parents for breeding.

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SSR markers for identification of purity of melon hybrids

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s147923620800243x ◽

2008 ◽

Vol 5 (3) ◽

pp. 223-229 ◽

Cited By ~ 3

Author(s):

Li Ju-Fen ◽

Ma Guo-Bin ◽

Xu Ling

Keyword(s):

Ssr Markers ◽

Cucumis Melo ◽

Field Tests ◽

Hybrid Purity ◽

Ssr Primers ◽

Hybrid Seeds ◽

Polymerase Chain ◽

Parental Lines ◽

Hybrid Lines ◽

Simple Sequence

AbstractThe hybrid purity of melon (Cucumis melo L.) was tested by polymerase chain reaction (PCR) assay based on simple sequence repeat (SSR) markers in two F1 melon hybrids (‘Dongfangmi 1’ and ‘Dongfangmi 2’) and their parental lines. Twelve pairs of SSR primers for ‘Dongfangmi 1’ and three pairs for ‘Dongfangmi 2’ were selected. Results showed that self-inbred seeds were effectively distinguished from F1 hybrid seeds using these SSR primers, a finding that was consistent with the results recorded from field tests. ‘Dongfangmi 1’ and ‘Dongfangmi 2’ were identified from their parental lines, and seven other uterine hybrid lines by multiplex primers MS48+MS60 and MS4+MS20, respectively. Contamination of F1 hybrid seeds caused by self-inbred and other unknown pollens can be effectively and more reliably detected by PCR assays with multiplex SSR primers.

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UJI POLIMORPIK DAN HETEROZIGOSITAS PADA PROGENI F4 KEDELAI (Glycine max (L.) Merril) TAHAN SALIN DENGAN MENGGUNAKAN MARKA SSR (Simple Sequence Repeats)

Jurnal Agrotek Lestari ◽

10.35308/jal.v5i2.2229 ◽

2020 ◽

Vol 5 (2) ◽

Author(s):

Evi Julianita Harahap ◽

Rosmayanti Rosmayanti ◽

Diana Sofia Hanafiah

Keyword(s):

Glycine Max ◽

Simple Sequence Repeats ◽

Ssr Marker ◽

Specific Primers ◽

Allele Number ◽

Map Construction ◽

Expected Heterozygosity ◽

Ssr Primers ◽

Glycine Max L ◽

Simple Sequence

SSR marker has some merits such as quickness, simplicity, rich polymorphism and stability, thus being widely applied in genetic diversity analysis, molecular map construction and gene mapping. the purpose of this study was to determine polymorpic test and heterozygosity in F4 soybean (Glycine max (L.) Merril) progeni saline resistant characters using SSR (Simple Sequence Repeats) markers. This research was conducted in Biomolecular Laboratory, Socfindo Seed Production Laboratory (SSPL), Kebun Bangun Bandar Village Martebing District Dolok Masihul Regency Serdang Bedagai on December-May 2017. The number of samples were used 44. The five SSR primers (QS080465, QS1101, QS1112, QS100011, and Sat_091) used were specific primers, with a band pattern that was clearly visible around one or two bands. The percentage of polymorphic primers (PLP) of these three populations is high, all populations with a PLP of 100% of the saline resistant character. The effective allele number (Ne) of 7,160 for the progeny population is lower than the number of observed alleles (Na) of 10,000 which means that many progeny individuals are homozygous. The expected heterozygosity (He) value of 0.854 in the progeny population was higher than the observed heterozygosity (Ho) value of 0.027. The overall average observed heterozygosity (Ho) was 0.009 lower than the overall expected heterozygosity (He) of 0.61. This means that each character has a low heterozygosity.Keywords: Progeny F4, soybean, SSR, saline resistant, polymorphic, heterozygosity

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Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04860-19 ◽

2020 ◽

Vol 145 (4) ◽

pp. 228-235

Author(s):

Qing Shen ◽

Hua Bian ◽

Hai-yan Wei ◽

Li Liao ◽

Zhi-yong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Diversity Index ◽

Polymorphic Information Content ◽

Principal Component ◽

Sequence Repeat ◽

Similarity Coefficients ◽

Seashore Paspalum ◽

Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

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Genetic Diversity of a Natural Population of Akebia trifoliata (Thunb.) Koidz and Extraction of a Core Collection Using Simple Sequence Repeat Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.716498 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yicheng Zhong ◽

Yue Wang ◽

Zhimin Sun ◽

Juan Niu ◽

Yaliang Shi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Simple Sequence Repeat ◽

Core Collection ◽

Polymorphic Information Content ◽

Germplasm Conservation ◽

Sequence Repeat ◽

Information Index ◽

Molecular Identity ◽

Simple Sequence

Understand genetic diversity and genetic structure of germplasm is premise of germplasm conservation and utilization. And core collection can reduce the cost and difficulty of germplasm conservation. Akebia trifoliata (Thunb.) Koidz is an important medicinal, fruit and oil crop, particularly in China. In this study, 28 simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure of 955 A. trifoliata germplasms, determine their molecular identity and extract a core collection. The genetic diversity of the 955 germplasms was moderately polymorphic. The average number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), Shannon’s information index (I∗), and polymorphic information content (PIC) were 3.71, 0.24, 0.46, 0.81, and 0.41, respectively. Four subpopulations were identified, indicating a weak genetic structure. A 955 germplasms could be completely distinguished by the characters of s28, s25, s74, s89, s68, s30, s13, s100, s72, s77, and s3. And each germplasm’s molecular identity was made up of eleven characters. The core collection was composed of 164 germplasms (17.2% of 955 total germplasms in the population) and diversity parameters differed significantly from those of a random core collection. These results have implications for germplasm conservation. At the same time, based on the results, the 955 germplasm could be better used and managed.

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Genetic diversity between improved banana diploids using canonical variables and the Ward-MLM method

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2012001000010 ◽

2012 ◽

Vol 47 (10) ◽

pp. 1480-1488 ◽

Cited By ~ 4

Author(s):

Valquíria Martins Pereira ◽

Cristine Vanz Borges ◽

Lívia Pinto Brandão ◽

Larissa Santos Oliveira ◽

Cintia Paula Feitosa Souza ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Marker ◽

Block Design ◽

Agronomic Characteristics ◽

Canonical Variables ◽

Ssr Primers ◽

Ward Clustering ◽

Using Data ◽

Simple Sequence ◽

Relative Similarity

The objective of this work was to estimate the genetic diversity of improved banana diploids using data from quantitative analysis and from simple sequence repeats (SSR) marker, simultaneously. The experiment was carried out with 33 diploids, in an augmented block design with 30 regular treatments and three common ones. Eighteen agronomic characteristics and 20 SSR primers were used. The agronomic characteristics and the SSR were analyzed simultaneously by the Ward-MLM, cluster, and IML procedures. The Ward clustering method considered the combined matrix obtained by the Gower algorithm. The Ward-MLM procedure identified three ideal groups (G1, G2, and G3) based on pseudo-F and pseudo-t² statistics. The dendrogram showed relative similarity between the G1 genotypes, justified by genealogy. In G2, 'Calcutta 4' appears in 62% of the genealogies. Similar behavior was observed in G3, in which the 028003-01 diploid is the male parent of the 086079-10 and 042079-06 genotypes. The method with canonical variables had greater discriminatory power than Ward-MLM. Although reduced, the genetic variability available is sufficient to be used in the development of new hybrids.

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