Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers

Yang, Xinsun; Su, Wen‐Jin; Wang, Lianjun; Lei, Jian; Chai, Shasha; Liu, Qingchang

doi:10.1016/s2095-3119(14)60794-2

Cited by 39 publications

(40 citation statements)

References 26 publications

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“…Molecular techniques have been widely adopted as powerful tools for germplasm characterization, cultivar identification, phylogenetic studies, and diversity analysis in many crop plants [8]. In sweet potato studies, molecular markers have been used to evaluate the phylogenetics and germplasm to study the origin of sweet potato and its dissemination [9].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

Lee

et al. 2019

Agronomy

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Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the germplasm collection of the National Agrobiodiversity Center (NAC). Eight of the nine cpSSR showed polymorphisms, while Ibcp31 did not. The number of alleles per locus ranged from two to four. In general, the Shannon index for each cpSSR ranged from 0.280 to 1.123 and the diversity indices and unbiased diversity ranged from 0.148 to 0.626, and 0.210 to 0.627, respectively. Results of the median-joining network showed 33 chlorotypes in 558 sweet potato accessions. In factor analysis, 558 sweet potato accessions were divided into four clusters, with clusters I and II composed only of the sweet potato accessions from Korea, Japan, Taiwan, and the USA. The results of this study confirmed that the genetic diversity of the female parents of sweet potato accessions conserved at the NAC is low and therefore more sweet potato accessions need to be collected. These results will help to establish an efficient management plan for sweet potato genetic germplasms at the NAC.

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Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

Lee

et al. 2019

Agronomy

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“…Generally, SSR markers are distributed in both transcribed and non-coding sequences referred to as EST-and genomic-SSRs respectively. With the advantages of being co-dominant, PCR-based, highly polymorphic, chromosome-speci c, reproducible and consistent [42] compared to other molecular markers, SSR markers have been widely used in many genetic and molecular-based studies in sweetpotato including variety identi cation, genetic diversity analysis and construction of linkage maps [19][20][21]. Although several studies have reported the use of SSR markers in sweetpotato, most of them evolved from investigating transcriptome libraries and ESTs.…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, SSR analyses may present false-positive results that can cause overlapped SSRs or null alleles [17] and polymerase slippage during DNA replication [18]. In sweetpotato, SSR markers are utilized extensively for the construction of genetic maps, diversity analysis, and variety identi cation [19][20][21]. They are widely distributed in both transcribed and non-coding sequences, generally described as expressed sequence tag (EST)-and genomic-SSRs respectively [22].…”

Section: Development and Characterization Of Simplementioning

confidence: 99%

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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“…The analysis of RAPD generated polymorphic bands showed variations in the number, length, and intensity of the resulting bands. Yang et al (2015), PCR-RAPD are widely distributed throughout the eukaryotic genomes in coding and non-coding regions. Their random genome distribution and use with low quality DNA have resulted in extensive use in the determination of genetic diversity, germplasm fingerprinting, genetic linkage mapping, and phylogenetic studies of sweet potato.…”

Section: E a Bmentioning

confidence: 99%

Anatomical profile and genetic variability of sweet potato (Ipomoea batatas) cultivars in Banyumas, Central Java, based on RAPD markers

et al. 2020

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Abstract. Samiyarsih S, Fitrianto N, Azizah E, Herawati W, Rochmatino. 2020. Anatomical profile and genetic variability of sweet potato (Ipomoea batatas) cultivars in Banyumas, Central Java, based on RAPD markers. Biodiversitas 21: 1755-1766. Indonesia has developed a food consumption diversification based on local sources. Sweet potato (Ipomoea batatas) is one of the tubers of carbohydrate sources in addition to wheat, rice, corn, potatoes, and cassava. It has a wide distribution, and high cultivars diversity produces a high variation on its morphology, anatomy, and genetic modification. The objectives of this research were to investigate the anatomical profile and genetic variability of eight sweet potatoes (Ipomoea batatas) cultivars found in Banyumas, Central Java, Indonesia. Anatomical profile was observed by the embedding method and subjected to analysis of variance. DNA amplification using Random Amplified Polymorphic DNA (RAPD) method with 10 primers, namely OPA-1, OPA-2, OPA-3, OPA-4, OPA-9, OPA-11, OPA-13, OPA-15, OPA-16, and OPA-18. The result of the anatomical study showed that eight sweet potato cultivars have significantly different (p<0.05) variation in leaf anatomical profile. RAPD primers produced 52 amplified fragments varying from 100 to 1300 bp in size, and 90.40% of the amplification bands were polymorphic. The genetic similarity level is ranged from 0.37 to 0.93. Two unspecific groups were forming at a coefficient of 55% from the dendrogram. The first group consisted of one cultivar, Cangkuang, and the second group consisted of seven cultivars Antin, Ungu Tua, Borobudur, Sukuh, Sari, Beta, and Kidal. The nearest relationships cultivars were Borobudur, and Ungu Tua had the highest similarity coefficient of 93%, and the lowest similarity found in Cangkuang and Antin with a coefficient of 37%. The range of genetic distance of eight cultivars was from 0.37-0.93. Implementation of the research would particularly useful for the identification and evaluation of the genetic improvement of sweet potato cultivars.

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Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers

Cited by 39 publications

References 26 publications

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

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

Anatomical profile and genetic variability of sweet potato (Ipomoea batatas) cultivars in Banyumas, Central Java, based on RAPD markers

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