Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers

Cervantes-Flores, J.C.; Yencho, G. Craig; Kriegner, Albert; Pecota, Kenneth V.; Faulk, Maria A.; Mwanga, R.O.M.; Sosinski, Bryon

doi:10.1007/s11032-007-9150-6

Cited by 100 publications

(118 citation statements)

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“…Molecular markers have great potential to speed up the process of developing improved cultivars. Although several sweetpotato genetic maps have been published [2-4], the existing maps do not have sufficient markers to be highly useful for genetic studies. Thus, there is a great need for development of novel markers.…”

Section: Introductionmentioning

confidence: 99%

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

et al. 2011

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BackgroundCurrently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.ResultsIn this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.ConclusionThis study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

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Section: Introductionmentioning

confidence: 99%

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

et al. 2011

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“…In this species, several non-integrated maps have been published (Ukoskit and Thompson, 1997;Kriegner et al, 2003;Cervantes-Flores et al, 2008;Chang et al, 2009;Monden et al, 2015;Shirasawa et al, 2017), with three publications reporting information on homologous chromosomes without actually integrating the maps. In two publications, this information was based on markers that had a dosage of two (duplex) in one parent and zero (nulliplex) in the other (2x0 markers), and markers with a dosage three (triplex) in one parent and zero in the other (3x0 markers; (Ukoskit and Thompson, 1997;Cervantes-Flores et al, 2008)). Others have identified homologous chromosomes based on alignment to a reference genome (Shirasawa et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic mapping in polyploids

Bourke¹

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“…The tuberous roots are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for its breeding, because despite its importance, this hexaploid crop is difficult to breed owing to the complexity of its genetics and the lack of genomic resources [10][11]. Traditionally, phenotypic markers have been used to provide descriptors for identifying sweet potato cultivars [12], but they are unreliable owing to their paucity and vulnerability to environmental influence.…”

Section: Introductionmentioning

confidence: 99%

“…The amplified fragment length polymorphism (AFLP) technique developed in 1995 [20] is based on the selective PCR amplification of small restriction fragments (80-400 bp) from a total digest of genomic DNA. In sweet potato, AFLP markers have been used to study genetic linkage maps [13,21] and to assess genetic diversity [22]. Expressed sequence tags (ESTs) can be used as a cost-effective and valuable source for the development of molecular markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs).…”

Section: Introductionmentioning

confidence: 99%

Characterization and Development of EST-SSR Markers in Sweet Potato (<em>Ipomoea batatas</em> (L.) Lam)

Kim

et al. 2016

Preprint

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According to statistics from the Food and Agriculture Organization, the world population will increase to about 91 million (Asia 51 million, Africa 19 million). A rise in the world's population means an increased need for food. However, climate change has caused desertification and unpredictable weather, creating problems in the supply and demand of food. Sweet potato (Ipomoea batatas) is an alternative to solving the food problem, as it is one of the world's most important food crops, especially in developing countries. The tuberous roots of sweet potato are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for breeding this crop. Recently, molecular markers developed for sweet potato have demonstrated good potential for use in genetic selection. In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of fullsequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.

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Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers

Cited by 100 publications

References 53 publications

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

Genetic mapping in polyploids

Characterization and Development of EST-SSR Markers in Sweet Potato (<em>Ipomoea batatas</em> (L.) Lam)

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