Genome Wide SSR Development and Their Application in Genetic Diversity Analysis in 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 simple sequence repeats development and their application in genetic diversity analysis in wax gourd ( Benincasa hispida )

Plant Breeding ◽

10.1111/pbr.12990 ◽

2022 ◽

Author(s):

Qianmei Hu ◽

Haiping Wang ◽

Biao Jiang ◽

Huayu Zhu ◽

Xiaoming He ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Benincasa Hispida ◽

Wax Gourd ◽

Simple Sequence

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Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers

Molecular Biology Reports ◽

10.1007/s11033-014-3304-5 ◽

2014 ◽

Vol 41 (7) ◽

pp. 4329-4339 ◽

Cited By ~ 21

Author(s):

B. Kalyana Babu ◽

Vimla Meena ◽

Vasudha Agarwal ◽

P. K. Agrawal

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Oryza Sativa ◽

Ssr Markers ◽

Oryza Sativa L ◽

Diversity Analysis ◽

Genetic Diversity Analysis

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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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Analysis of Genetic Diversity and Population Structure Using SSR Markers in Tobacco

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.850-851.1243 ◽

2013 ◽

Vol 850-851 ◽

pp. 1243-1246

Author(s):

Yan Shi Xia ◽

Pei Guo Guo ◽

Rong Hua Li ◽

Yong Hua Lü ◽

Miao Wen Qiu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Clustering Analysis ◽

Genetic Similarity ◽

Diversity Analysis ◽

Germplasm Management ◽

Genetic Diversity Analysis ◽

Group A ◽

Group B

Genetic diversity analysis and population structure can estimate genetic variation of diverse materials, and can be used in germplasm management and varietal protection. In this study, the genetic diversity and population structure for tobacco germplasm (78 cultivated tobacco accessions in China) were analyzed by using 28 SSR markers. A total of 127 alleles were detected with an average of 4.5 per locus in 78 accessions, while PIC values ranged from 0.19 to 0.89 with an average of 0.63 per marker. Based on genetic similarity, most of sun-cured and flue-cured tobacco accessions were clustered into group A and group B, respectively. A model-based structure analysis for these accessions detected two subpopulations, which were generally coincident with the clustering analysis and showed the genetic similarities were relative high for these accessions. These results revealed narrow genetic diversity for the tobacco germplasm in China.

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Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding

Frontiers in Plant Science ◽

10.3389/fpls.2021.708332 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sujata Thakur ◽

Inderjit Singh Yadav ◽

Manish Jindal ◽

Parva Kumar Sharma ◽

Guriqbal Singh Dhillon ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Breeding ◽

Draft Genome ◽

Psidium Guajava ◽

Comparative Transcriptomics ◽

Functional Markers ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Greenish Yellow ◽

Genome Wide

Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket.

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