Background: Currently 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. Results: In 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 ESTSSRs 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 2k30) 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. Conclusion: This 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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Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

We developed a genetic linkage map of sweetpotato using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers and a mapping population consisting of 202 individuals derived from a broad cross between Xushu 18 and Xu 781, and mapped quantitative trait loci (QTL) for the storage root dry-matter content. The linkage map for Xushu 18 included 90 linkage groups with 2077 markers (1936 AFLP and 141 SSR) and covered 8,184.5 cM with an average marker distance of 3.9 cM, and the map for Xu 781 contained 90 linkage groups with 1954 markers (1824 AFLP and 130 SSR) and covered 8,151.7 cM with an average marker distance of 4.2 cM. The maps described herein have the best coverage of the sweetpotato genome and the highest marker density reported to date. These are the first maps developed that have 90 complete linkage groups, which is in agreement with the actual number of chromosomes. Duplex and triplex markers were used to detect the homologous groups, and 13 and 14 homologous groups were identified in Xushu 18 and Xu 781 maps, respectively. Interval mapping was performed first and, subsequently, a multiple QTL model was used to refine the position and magnitude of the QTL. A total of 27 QTL for dry-matter content were mapped, explaining 9.0–45.1 % of the variation; 77.8 % of the QTL had a positive effect on the variation. This work represents an important step forward in genomics and marker-assisted breeding of sweetpotato.

A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato

SUMMARY

Sweetpotato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) is one of the most important pathogens of sweetpotato (Ipomoea batatas L.). It can reduce yields by 50% by itself and cause various synergistic disease complexes when co-infecting with other viruses, including sweetpotato feathery mottle virus (SPFMV; genus Potyvirus, family Potyviridae). Because no sources of true resistance to SPCSV are available in sweetpotato germplasm, a pathogen-derived transgenic resistance strategy was tested as an alternative solution in this study. A Peruvian sweetpotato landrace ‘Huachano’ was transformed with an intron-spliced hairpin construct targeting the replicase encoding sequences of SPCSV and SPFMV using an improved genetic transformation procedure with reproducible efficiency. Twenty-eight independent transgenic events were obtained in three transformation experiments using a highly virulent Agrobacterium tumefaciens strain and regeneration through embryogenesis. Molecular analysis indicated that all regenerants were transgenic, with 1–7 transgene loci. Accumulation of transgene-specific siRNA was detected in most of them. None of the transgenic events was immune to SPCSV, but ten of the 20 tested transgenic events exhibited mild or no symptoms following infection, and accumulation of SPCSV was significantly reduced. There are few previous reports of RNA silencing-mediated transgenic resistance to viruses of Closteroviridae in cultivated plants. However, the high levels of resistance to accumulation of SPCSV could not prevent development of synergistic sweet potato virus disease in those transgenic plants also infected with SPFMV.

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RNA silencing-mediated resistance to a crinivirus (Closteroviridae) in cultivated sweetpotato (Ipomoea batatas L.) and development of sweetpotato virus disease following co-infection with a potyvirus

Sweetpotato is the seventh most important food crop in the world. It is mainly used for human food, animal feed, and for manufacturing starch and alcohol. This crop, a highly heterozygous, generally self-incompatible, outcrossing polyploidy, poses numerous challenges for the conventional breeding. Its productivity and quality are often limited by abiotic and biotic stresses. Gene engineering has been shown to have the great potential for improving the resistance to these stresses as well as the nutritional quality of sweetpotato. To date, an Agrobacterium tumefaciens-mediated transformation system has been developed for a wide range of sweetpotato genotypes. Several genes associated with salinity and drought tolerance, diseases and pests resistance, and starch, carotenoids and anthocyanins biosynthesis have been isolated and characterized from sweetpotato. Gene engineering has been used to improve abiotic and biotic stresses resistance and quality of this crop. This review summarizes major research advances made so far in improving agronomically important traits by gene engineering in sweetpotato and suggests future prospects for research in this field.

https://www.jstage.jst.go.jp/article/jsbbs/67/1/67_16126/_pdf

Improvement for agronomically important traits by gene engineering in sweetpotato.

Sweetpotato is grown throughout the year in Mozambique but drought affects storage root yield and biomass productivity. The objectives of this research were to estimate the impact of genotype × environment interactions (G × E) in sweetpotato and select genotypes based on drought indices such as geometric mean, percent yield reduction, drought sensitivity index and harvest index. A total of 58 clones were evaluated during the dry season of 2006, 2008 and 2009. Two treatments were applied for this multi-year trial: full irrigation and without irrigation at the middle of root initiation growth stage. The field layout was a randomized complete block design with three replications. ‘Jonathan’, ‘Resisto’ and ‘Tanzania’ were the check cultivars in each treatment. Storage root and vine yields were recorded at harvest in the trials. Harvest index was computed from the yield data. The analysis of variance, regression and the additive main effects multiplicative interaction (AMMI) analyses, plus phenotypic coefficient of variation and ecovalence were used for dissecting the G × E and assessing the stability of each clone. Treatment, genotype × treatment and genotype × year (G × Y) interactions had highest contributions to the variation in storage root yield observed among clones. The stability of harvest index was significantly correlated with the absolute AMMI’s IPCA1 and IPCA2 values for storage root yield. Cultivar performance varied within treatments. Four clones had significantly higher storage root yield (t ha−1) than ‘Tanzania’, the best check cultivar under drought. In conclusion, storage root yield (t ha−1) was negatively affected by drought and G × Y interaction. Harvest index stability and the geometric mean may be key to identify clones with storage root yield stability and high storage root yield under both treatments. At least two environments should be used at early breeding stages to consider harvest index in the early breeding cycle.

/pdf/genotype-environment-interaction-and-selection-for-drought-yaw3by08g6.pdf

Genotype × environment interaction and selection for drought adaptation in sweetpotato (Ipomoea batatas [L.] Lam.) in Mozambique

Establishment of molecular linkage maps using SRAP markers in sweet potato.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1479236204000178

Regeneration of sweet potato transgenic plants with oryzacystatin-I (OCI) gene

In Vitro Selection and Identification of Drought-tolerant Mutants of Sweet Potato

Genetic diversity of 48 sweetpotato landraces, randomly sampled from 4 regions (Anhui, Fujian, Henan and Guangdong)in China, was analyzed using RAPD, ISSR and AFLP markers. Both 30 RAPD and 14 ISSR primers and 9 AFLP primer combinations generated 227, 249 and 260 polymorphic bands, respectively. AFLPs were better than RAPDs and ISSRs in terms of the number of polymorphic bands detected and the experimental stability. These three molecular markers revealed the similar results that Chinese landraces possess high genetic diversity, and the genetic variation of Guangdong landraces was significantly (at 0.01 level) higher than that of the landraces from other three regions. These results support the hypothesis that China was the secondary center of sweetpotato diversity and also showed that Guangdong was the earliest region where sweetpotato was introduced to China. In this study, the combined RAPDs, ISSRs and AFLPs dataset appeared to be appropriate in resolving the sweetpotato varietal relationships. These landraces can be divided into two groups by UPGMA cluster based on genetic distances, one mainly includes 8 landraces from Guangdong, and another consists of the remaining landraces from Guangdong and landraces from the other three regions. Thus, the utilization of Guangdong landraces should be specially considered in sweetpotato breeding.

Analysis of genetic diversity of sweetpotato landraces in China

The present study exhibits amplified fragment length polymorphism (AFLP) molecular marker for sex identification in Broussonetia papyrifera . Based on nine selective amplification primer combinations, 230 bands were produced and the E -AGG/M-CAA combination was found to be a male-specific AFLP marker. Subsequently, this male-specific AFLP fragment was sequenced and converted into a sequence tagged site (STS) marker. Based on STS sequence, two primers, MADB-1 and MADB-2 (Male-Associated DNA from B. papyrifera ), were designed to verify the specificity of the fragment. The results indicate that common homology sequence is existed in both male and female plants while one of the bands amplified via MADB-2 primer was solely present in male individuals at high annealing temperature up to 66°C. Finally, MADB-2 primer was introduced to amplify another 16 plants and it revealed that this primer could be used as a convenient, efficient, reliable, and low-cost molecular marker for sex identification in B. papyrifera . Keywords: Broussonetia papyrifera , AFLP, STS, male-specific marker

/pdf/identification-of-a-male-specific-amplified-fragment-length-4lrjoty970.pdf

Liu Qingchang

Papers

Establishment of molecular linkage maps using SRAP markers in sweet potato.

Regeneration of sweet potato transgenic plants with oryzacystatin-I (OCI) gene

In Vitro Selection and Identification of Drought-tolerant Mutants of Sweet Potato

Analysis of genetic diversity of sweetpotato landraces in China

Identification of a male-specific amplified fragment length polymorphism (AFLP) marker in Broussonetia papyrifera