Genetic Diversity of Angelica gigas Nakai Collected in Korea using Genome-Wide SSR Markers

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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Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

10.1101/2021.08.23.457289 ◽

2021 ◽

Cited By ~ 1

Author(s):

Wanling Yang ◽

Yuanwei Fan ◽

Yong Chen ◽

Gumu Ding ◽

Hu Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Stress Responses ◽

Wild Rice ◽

Diversity Index ◽

Oryza Rufipogon ◽

Coding Sequences ◽

Genome Wide ◽

Ssr Loci ◽

Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

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Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

10.1101/723544 ◽

2019 ◽

Cited By ~ 1

Author(s):

Gisele Kanzana ◽

Yufei Zhang ◽

Tiantian Ma ◽

Wenxian Liu ◽

Fan Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Target Genes ◽

Stress Conditions ◽

Biotic And Abiotic Stress ◽

Marker Assisted Breeding ◽

Map Construction ◽

Expected Heterozygosity ◽

Genome Wide ◽

Precursor Mirnas

AbstractSSR markers are commonly used for many genetic applications, such as map construction, fingerprinting and genetic diversity analysis due to their high reproducibility, levels of polymorphism and abundance. As endogenous, small RNAs, miRNAs have essential roles in plant development and gene expression under diverse stress conditions, including various biotic and abiotic stress conditions. In the present study, we predicted 110 pre-miRNAs sequences from 287 precursor miRNAs and used them as queries for SSR marker development. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other gramineae and non-gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. In this study, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The results showed that this miRNA-based microsatellite marker system can be very useful for genetic diversity and marker-assisted breeding studies.

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Genome-wide SSR Markers in Bottle Gourd: Development, Characterization, Utilization in Assessment of Genetic Diversity of National Genebank of India and Synteny With Other Related Cucurbits

10.21203/rs.3.rs-990222/v1 ◽

2021 ◽

Author(s):

Bhawna Bonthala ◽

Manjusha Verma ◽

M Z Abdin ◽

Lalit Arya ◽

Chithra D Pandey ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Bottle Gourd ◽

Map Construction ◽

Phylogenetic Studies ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Tetranucleotide Repeats ◽

Nucleotide Repeats

Abstract Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance,informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding geneticimprovement, cultivar identification and phylogenetic studies. Next generation sequencing has revolutionizedthe approaches for discovery, assessment and validation of molecular markers. We conducted a genome wideanalysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Ofwhich 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for anin depth genetic diversity and population structure analysis of 96 accessions from the National Genebank ofIndia. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%),further 21.03%, 9.6% and 4.3% of di-, penta- and hexa- nucleotide repeats in the bottle gourd genome. Syntenyof SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber(93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers providea valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, genediscovery and for breeding in bottle gourd and other cucurbits species.

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Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers

Tree Genetics & Genomes ◽

10.1007/s11295-015-0953-z ◽

2015 ◽

Vol 11 (6) ◽

Cited By ~ 21

Author(s):

Qingwen Liu ◽

Yue Song ◽

Lun Liu ◽

Mingyue Zhang ◽

Jiangmei Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Core Genome ◽

Genome Wide

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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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Development of genome-wide SSR markers in melon with their cross-species transferability analysis and utilization in genetic diversity study

Molecular Breeding ◽

10.1007/s11032-016-0579-3 ◽

2016 ◽

Vol 36 (11) ◽

Cited By ~ 11

Author(s):

Huayu Zhu ◽

Luqin Guo ◽

Pengyao Song ◽

Feishi Luan ◽

Jianbin Hu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genome Wide ◽

Genetic Diversity Study ◽

Diversity Study

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Genome Wide SSR Development and Their Application in Genetic Diversity Analysis in Wax Gourd

10.21203/rs.3.rs-147921/v1 ◽

2021 ◽

Author(s):

Qianmei Hu ◽

Haiping Wang ◽

Biao Jiang ◽

Huayu Zhu ◽

Xiaoming He ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Molecular Mapping ◽

Draft Genome ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Benincasa Hispida ◽

Wax Gourd

Abstract Background: Wax gourd (Benincasa hispida Cong., 2n=2x=24) is one of the most important winter vegetables of the Cucurbitaceae family. There are only limited markers available for this crop and the draft genome of wax gourd provides a powerful tool for SSR marker development.Results: In this study, we developed genome-wide SSR markers from wax gourd genome and characterized their distribution and frequency of different motifs and repeats. A total of 52,431 microsatellites from wax gourd genome were identified, of which 39,319 SSR markers were developed. 1,152 non-wax gourd SSR markers were selected from cucumber, melon, watermelon and pumpkin to test their transferability in wax gourd. 580 SSR markers could be transferable in wax gourd, and 42 of them were detected with polymorphic in 11 tested accessions of wax gourd. In addition, 11 good polymorphic transferrable SSR markers and 21 SSR markers of wax gourd were selected to investigate the genetic diversity and population structure of 129 wax gourd accessions. 112 alleles were detected by these 32 SSR markers. The result of population structure showed that the 129 wax gourd accessions were divided into two main populations, and the genetic diversity analysis separated them into two clusters. Conclusions: The large number of wax gourd SSR markers developed in this study provides a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection (MAS) in wax gourd.

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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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