Development of Polymorphic Genic SSR Markers  by Transcriptome Sequencing in the Welsh Onion  (Allium fistulosum L.)

Yang, Liuyi; Wen, Changlong; Zhao, Hong; Liu, Qianchun; Yang, Jingjing; Liu, Lecheng; Wang, Yongqin

doi:10.3390/app5041050

Cited by 15 publications

(8 citation statements)

References 41 publications

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“…In agreement with our current study, Wang et al [28] identi ed AAT/ATT as the most dominant SSR motif in sweetpotato. Similarly, Yang et al [6] identi ed AAAT/ATTT as the most frequent repeat motif among tetranucleotides in Welsh onion. However, previous studies identi ed AG/CT, AAG/CTT, and AT/TA motifs as the most dominant motif types in sweetpotato [47], con icting with our ndings.…”

Section: Discussionmentioning

confidence: 93%

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Zhang

Amoanimaa-Dede

2020

Preprint

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Background: Sweetpotato is a multifunctional root crop with many essential nutrients and bioactive compounds. Due to its genetic complexity and lack of genomic resources, efficient genetic studies, and cultivar development lags far behind other major crops. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweetpotato. Results: To further explore new SSR markers and accelerate its use in sweetpotato genetic studies, genome-wide characterization and development of SSR markers were performed using the recently published genome of sweetpotato cultivar, Taizhong6. In this study, a set of 2,431 primer pairs were developed from 133,727 SSRs identified in the sweetpotato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. 50% of the 100 randomly selected primer pairs amplified 251 alleles and the average number of alleles was 5.02 alleles per locus with a range of 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweetpotato materials into four clusters at a similarity coefficient of 0.68. Conclusion: The SSR markers currently developed will provide valuable genetic resources for germplasm identification, genetic diversity analysis, and functional genomics studies in sweetpotato and related species.

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Section: Discussionmentioning

confidence: 93%

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Zhang

Amoanimaa-Dede

2020

Preprint

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“…Since NGS technology allows cost-effective and higher throughput genome sequencing, it has been universally applied for many crop species, including Allium fistulosum L., Sesamum indicum L., and Vicia sativa subsp. Sativa [ 35 , 36 ]. Recently, a study on the development of 18 polymorphic microsatellite markers for A. sinensis using NGS technology has been reported although it was focused on species identification [ 37 ].…”

Section: Resultsmentioning

confidence: 99%

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Gil

Kim

et al. 2017

Genes

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Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

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“…The advancement of next-generation sequencing has generated scores of datasets for many plant species that provide useful genomic materials for developing efficient molecular markers for genetic analyses [27]. Recently, technological advancement in high throughput DNA sequencing offers new information to accelerate the development of molecular markers.…”

Section: Discussionmentioning

confidence: 99%

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweet potato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Amoanimaa-Dede¹,

Zhang²,

Su³

et al. 2020

Preprint

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The genetic complexity and the lack of genomic resources in sweet potato make genetic improvement extremely challenging. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweet potato. To explore new SSR markers and accelerate its use in sweet potato, we developed a set of 2,431 primer pairs from 133,727 SSRs identified in the sweet potato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. Out of the 100 randomly selected primer pairs, 50% produced clear bands and amplified 251 alleles. On average, the number of alleles was 5.02 per locus for values ranging from 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweet potato materials into four clusters at a similarity coefficient of 0.68 showing no relationship between the genotypes and the geographic sources of germplasm. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, and accelerate studies on genetic diversity in sweet potato and related species.

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Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)

Cited by 15 publications

References 41 publications

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweet potato [Ipomoea batatas L. (Lam) cv. Taizhong6]

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