Development of Novel Coconut Ssr Markers Derived From Genome-Wide Bioinformatics Prediction

Abstract In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSR markers are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers. A total of 7,139 novel SSR markers were derived from the genome assembly of coconut ‘Catigan Green Dwarf’ (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. OligoAnalyzer-tool was also employed using the following desired parameters: %GC: 40–60%; minimum ΔG value for hairpin loop: -0.3 kcal/mol; minimum ΔG value for self-dimer: -0.9 kcal/mol; and minimum ΔG value for hetero-dimer: -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using ‘Catigan Green Dwarf’ (CATD), ‘Laguna Tall’ (LAGT), ‘West African Tall’ (WAT), and SYNVAR (LAGT x WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes. The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.

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Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon)

Plant Genetic Resources ◽

10.1017/s1479262116000332 ◽

2016 ◽

Vol 15 (6) ◽

pp. 566-569

Author(s):

Jiankun Xie ◽

Meng Zhang ◽

Jia Sun ◽

Fantao Zhang

Keyword(s):

Ssr Markers ◽

Wild Rice ◽

Pcr Amplification ◽

Oryza Rufipogon ◽

Sequencing Technology ◽

Cultivated Rice ◽

Genic Ssr ◽

Genome Wide ◽

Dongxiang Wild Rice ◽

Simple Sequence

AbstractDongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

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Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

Canadian Journal of Plant Science ◽

10.1139/cjps-2015-0250 ◽

2016 ◽

Vol 96 (5) ◽

pp. 808-818 ◽

Cited By ~ 4

Author(s):

Neil Hobson ◽

Habibur Rahman

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Low Cost ◽

Pak Choi ◽

Genome Wide ◽

A Genome ◽

Wide Range ◽

Genetic Pools ◽

High Level ◽

Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

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Molecular characterization of China aster (Callistephus chinensis (L.) Nees) genotypes using SSR markers

Israel Journal of Plant Sciences ◽

10.1163/22238980-bja10037 ◽

2021 ◽

pp. 1-10

Author(s):

Veluru Bhargav ◽

Rajiv Kumar ◽

Anuradha Sane ◽

T. Manjunatha Rao ◽

T. Usha Bharathi ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Ssr Markers ◽

Crop Improvement ◽

Flower Color ◽

Target Populations ◽

Genome Wide ◽

China Aster ◽

Simple Sequence

Abstract Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement.

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Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

10.21203/rs.3.rs-40696/v1 ◽

2020 ◽

Author(s):

Lei Zhu ◽

Hua yu Zhu ◽

Yan man Li ◽

Xiang bin Wu ◽

Jin tao Li ◽

...

Keyword(s):

Genetic Diversity ◽

Comparative Genomics ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Motif Length ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Ssr Loci ◽

Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

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citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement

Genes ◽

10.3390/genes11121486 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1486

Author(s):

Naveen Duhan ◽

Manish Meshram ◽

Cristian D. Loaiza ◽

Rakesh Kaundal

Keyword(s):

Ssr Markers ◽

Molecular Breeding ◽

Crop Improvement ◽

Variety Identification ◽

Germplasm Characterization ◽

Citrus Species ◽

Genome Wide ◽

Genomic Regions ◽

Chromosome Scaffold ◽

Simple Sequence

Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. Citrus is the world’s most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1–6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.

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Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)

Science Progress ◽

10.1177/00368504211035597 ◽

2021 ◽

Vol 104 (3) ◽

pp. 003685042110355

Author(s):

Hai-feng Tian ◽

Qiao-mu Hu ◽

Zhong Li

Keyword(s):

Genetic Diversity ◽

Capillary Electrophoresis ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Breeding Population ◽

Monopterus Albus ◽

Polymorphic Ssrs ◽

Genome Wide ◽

Swamp Eel ◽

Simple Sequence

Objectives: Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. Methods: The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. Results: A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. Conclusions: The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes ( FIS = 0.155) in one breeding population provide baseline information for future breeding program.

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Isolation and characterization of SSR sequences from the genome and TAC clones of common wheat using the PCR technique

Genome ◽

10.1139/g06-001 ◽

2006 ◽

Vol 49 (5) ◽

pp. 432-444 ◽

Cited By ~ 1

Author(s):

Michiya Koike ◽

Kanako Kawaura ◽

Yasunari Ogihara ◽

Atsushi Torada

Keyword(s):

Ssr Markers ◽

Common Wheat ◽

Genomic Dna ◽

Genomic Library ◽

Artificial Chromosome ◽

Triticum Aestivum L ◽

Pcr Screening ◽

Artificial Chromosomes ◽

Isolation And Characterization ◽

Simple Sequence

We have developed the 2-step PCR method, a kind of suppression PCR procedure, to isolate simple sequence repeats (SSRs) from common wheat (Triticum aestivum L.) in a more convenient manner. This system requires neither genomic library screening nor the SSR-enrichment procedure. As a result, we designed 131 primer pairs based on isolated SSRs from not only genomic DNA, but also transformation-competent artificial chromosome (TAC) clones. It has been demonstrated that 34 of the 131 SSR markers developed were polymorphic among 8 wheat lines. Four of 34 polymorphic SSR markers were derived from TAC clones, indicating that this method could be applied to the targeted development of unique SSR markers in large genomic DNA libraries such as those composed of bacterial artificial chromosomes (BACs). A considerable number of isolated SSR clones had similarities with part of several long terminal repeats of retrotransposons (LTR-RTs) identified in various Triticeae genome sequences. Most of those SSRs showed smear amplification profiles, suggesting that a considerable number of dysfunctional SSRs originating from repetitive DNA components, especially LTR-RTs, might exist in the common wheat genome.Key words: common wheat, simple sequence repeat (SSR), PCR screening, LTR-retrotransposon, TAC clone.

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