Genetic diversity assessment of Tanzanian sweetpotato genotypes using simple sequence repeat markers

Ngailo, Stephan; Shimelis, Hussein; Sibiya, Julia; Amelework, Beyene; Mtunda, K.

doi:10.1016/j.sajb.2015.08.001

Cited by 33 publications

(28 citation statements)

References 30 publications

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“…There have been many recent studies on the genetic diversity of sweetpotato collection around the world, including Africa (Elameen et al, 2008;Kagimbo et al, 2018;Ngailo et al, 2016;Selaocoe et al, 2019;Tumwegamire et al, 2011;Zawedde et al, 2015), Asia (Fajardo et al, 2002;He et al, 2006;Luo et al, 2016;Rahajeng and Rahayuningsih, 2017;Soegianto et al, 2011;Su et al, 2017;Zhang et al, 2014) , 2008;Zhang et al, 2000), and North America (Jarret and Austin, 1994;Rodriguez-Bonilla et al, 2014;Wadl et al, 2018). From these studies, it has been generally accepted that there is an abundance of genetic diversity in sweetpotato germplasm collections worldwide (Gichuki et al, 2003;Gr€ uneberg et al, 2015;Su et al, 2017;Wadl et al, 2018;Yang et al, 2015); however, smaller geographic collections may show a narrower range of genetic diversity due to inbreeding or other factors (Elameen et al, 2008;Hao et al, 2007;Meng et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

Jackson¹,

Harrison²,

Jarret³

et al. 2020

horts

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During 2012–14, 737 sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS) sweetpotato germplasm collection were evaluated for several phenotypic leaf and plant characteristics, and a photographic record of each accession was made. Data were prepared for placement in the USDA, ARS Germplasm Resources Information Network (GRIN) database and the sweetpotato ontology. The parameters recorded for each genotype were canopy coverage, vine length, general leaf outline, leaf lobing, shape of the central leaf lobe, number of leaf points, leaf petiole length, leaf width, leaf length, leaf width × length, and leaf width/length (aspect ratio). The data indicate that there is wide genetic diversity for vegetative phenotypic characteristics within the USDA, ARS sweetpotato germplasm collection. This study provides important phenotype information for the USDA, ARS sweetpotato collection that has been lacking and can be used for curation of the collection and by researchers and breeders working with this important global food crop.

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Section: Discussionmentioning

confidence: 99%

Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

Jackson¹,

Harrison²,

Jarret³

et al. 2020

horts

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“…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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“…Past researches on rice have enhanced the development of hundreds of microsatellite markers and a genetic map comprising so many markers for documentation and characterization. In crop species, this approach has recently been used (Ngailo et al, 2016;Rodriguez-Bonilla et al, 2014;Yada et al, 2015;Yang et al, 2015). In Bangladesh, nine soybean cultivars were identified through microsatellite markers, which have provided distinctiveness and will perhaps be protective (Islam et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Simple sequence repeat (SSR) marker-based DNA fingerprinting of some varieties of rice (Oryza sativa L.) released in Nigeria

Ishaq¹,

Ehirim²,

Nwanyanwu³

et al. 2019

Afr. J. Biotechnol.

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Over time, precise, specific and rapid identification of variety have been achieved via fingerprinting with molecular markers. In this research, 13 out of 45 screened simple sequence repeat (SSR) markers were employed to fingerprint 27 rice varieties (22 are commercially released while five are suspected duplicates from the hands of marketers with different names) in Nigeria. The SSR primer pairs (13) were polymorphic and were found to generate 81 allele distinct reproducible bands with an average of 6.233 bands per primer pair. Primer RM400 had the highest allelic frequency of 0.94 resulting from 20 alleles. The polymorphic information content (PIC) values of each primer pair ranged between 0.31 and 0.93 with an average of 0.54. The unweighted pair group method with arithmetic (UPGMA) cluster analysis helped to separate the 27 varieties into 13 major groups indicating wide range of diversity. A large number of the closely related varieties were identified by means of the fingerprinting on the basis of the polymorphic SSR primer pairs. The findings showed a broad genetic variation among the test varieties giving a first-hand insight on how related some of the commercially released varieties are and also disproving the duplicity suspected from the materials with marketers.

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Genetic diversity assessment of Tanzanian sweetpotato genotypes using simple sequence repeat markers

Cited by 33 publications

References 30 publications

Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

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

Simple sequence repeat (SSR) marker-based DNA fingerprinting of some varieties of rice (Oryza sativa L.) released in Nigeria

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