Don LaBonte

Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation

BackgroundThe number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) generating a database for the sweetpotato root transcriptome using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous and initiating storage roots; (2) comparing the expression profiles of initiating storage roots and fibrous roots, using the Illumina Genome Analyzer to sequence cDNA libraries of the two root types and map the data onto the root transcriptome database.ResultsUse of the 454-Roche platform generated a total of 524,607 reads, 85.6% of which were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database. A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change). The Illumina-based differential expression results were validated for nine putative genes using quantitative real-time PCR. The differential expression profiles indicated down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots, and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, data indicated delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.ConclusionsThis study adds a valuable resource of sweetpotato root transcript sequences to available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel transcripts related to storage root initiation identified in this study provide a starting point for further investigation into the molecular mechanisms underlying this process.

Molecular marker variability for southern root-knot nematode resistance in sweetpotato

Amplified fragment length polymorphism (AFLP) marker profiles for individuals in two F1 populations of sweetpotato [Ipomoea batatas (L.) Lam] were used in association studies to identify AFLP markers suitable for identification of plants possessing a resistant reaction to southern root-knot nematode race 3 [Meloidogyne incognita (Kofoid and White) Chitwood]. Population one consisted of 48 half-sib genotypes developed at the Louisiana State University (LSU) AgCenter. The second population consisted of 54 full-sibs developed by the East African and International Potato Center (CIP) sweetpotato breeding programs. Results for plant nematode resistance indicate a bimodal distribution among the genotypes for the LSU population and a normal distribution for the CIP population. Using analysis of molecular variance (AMOVA) at P < 0.001 and two multivariate analysis techniques i.e logistic regression and discriminant analysis, 5 and 4 AFLP markers that had a strong and significant association with respect to the resistance trait were selected for the LSU and CIP populations, respectively. A comparative analysis of the power of discriminant analysis models for southern root-knot nematode resistance class prediction achieved 88.78% (LSU) and 88.04% (CIP) classification efficiencies.

Determining paternity in polyploids : Hexaploid simulation studies

The breeding of new sweet potato varieties is a highly inefficient process, confounded by incompatibility, poor fertility, open-pollination and hexaploidy. Upwards of 12–20 lines are combined in open pollinated nurseries based on horticulturally important characteristics. After several years of selection most progeny can be traced back to just 3 or 4 maternal lines. A method that would identify the paternal parent of superior progeny would enable breeders to combine parents that exhibit superior combining ability in more efficient, smaller nurseries. The objective of this work is to explore by means of computer simulation the application of genealogy reconstruction techniques on hexaploid individuals based on co-dominant marker data. The progeny obtained from each female parent is categorically assigned to each male with non-zero exclusion probability based on its paternity likelihood. Computer simulations show that even with polysomic segregation types, it is possible to discriminate between putative parents with few errors or mis-assignments. The number of loci scored for a 10 parent population should not be less than 20 in the case of 3 alleles per locus, and no more than 10 loci for a five allele model. An increment in the number of alleles or loci increases the discriminatory power with the number of alleles yielding a far more important effect than the number of loci. This study also demonstrates the feasibility of using simulations to determine the minimum requirements, i.e. number of loci to be genotyped, for unambiguous parentage allocation in polyploids.

INFLUENCE OF DROUGHT STRESS ON SWEETPOTATO RESISTANCE TO SWEETPOTATO WEEVIL, CYLAS FORMICARIUS (COLEOPTERA: APOINIDAE), AND STORAGE ROOT CHEMISTRY

Abstract The effect of drought stress on the resistance of sweetpotato roots to sweetpotato weevil (SPW), Cylas formicarius (Fab.), was studied in 1997 and 1998 in two genotypes (“Beauregard” and “Excel”) with different SPW susceptibility. Storage roots produced under drought or normal conditions were tested for adult feeding, oviposition, larval survival and pupal weight in the laboratory under no-choice and free-choice test conditions. The levels of sweetpotato resin glycoside and caffeic acid in the periderm tissue of the roots were also determined. Drought-stressed roots received significantly more SPW eggs under no-choice and free-choice conditions and more feeding punctures under free-choice conditions than non-stressed roots in 1997. Larval survival rate was significantly lower on drought-stressed roots. A significant drought effect on feeding, oviposition and larval survival was absent in 1998. Drought stress had no effect on sweetpotato resin glycosides content in both years, but significantly reduced the content of caffeic acid in 1997. Genotype had a significant effect on SPW feeding in 1997 and on feeding and oviposition in 1998 under free-choice test conditions, where Beauregard was preferred for both feeding and oviposition. Beauregard also supported a significantly higher larval survival rate compared with Excel. Resin glycosides or caffeic acid contents were similar for the two genotypes in 1997, while higher level of resin glycosides was detected in Excel than in Beauregard in 1998. The interaction between drought stress and genotype was significant for adult feeding under free-choice conditions and for larval survival, indicating a different response between the two genotypes.

Detection of Ty1-copia-like reverse transcriptase sequences in Ipomoea batatas (L.) Poir.

Abstract Ty1-copia-like sequences were PCR amplified from sweetpotato [Ipomoea batatas (L.) Poir.] L87-95 genomic DNA samples by using Ty1-copia reverse transcriptase-specific primers. PCR fragments within the expected size range were isolated, cloned, and sequenced. Inferred amino acid sequences of two randomly selected cloned fragments were found to be highly homologous to Ty1-copia-like reverse transcriptase sequences in the GenBank database. Subsequent sequencing of an additional 22 cloned fragments revealed a high level of reverse transcriptase sequence diversity (sequence divergence ranged from 2% to 73%). Southern blot hybridization analysis indicated that these sequences are present in the genome of I. batatas and taxonomic relatives in high copy numbers. PCR amplification from leaf cDNA obtained from a sweetpotato clone using Ty1-copia reverse transcriptase-specific primers yielded a Ty1-copia-like fragment. This is the first known report of the presence of genomic, and putatively expressed, Ty1-copia-like reverse transcriptase sequences in I. batatas.

EFFECT OF SWEETPOTATO GENOTYPE, STORAGE TIME AND PRODUCTION SITE ON FEEDING AND OVIPOSITION BEHAVIOR OF THE SWEETPOTATO WEEVIL, CYLAS FORMICARIUS (COLEOPTERA: APOINIDAE)

The effect of sweetpotato genotype, storage time and production site on Cylas formicarius (Fab.) feeding and oviposition was investigated. Sweetpotato genotype had a significant effect on feeding and oviposition rates in both no-choice and choice arenas. Beauregard and Centennial were uniformly susceptible across all age groups. W-250 had the least number of feeding punctures and eggs at 7 and 25 days after harvest. At 85 days after harvest, W-244 had the least number of feeding punctures and eggs, while W-250 was not significantly different from Beauregard and Centennial. Roots of the same genotype grown in different locations differed in the number of feeding punctures and eggs. These results suggest that antixenosis is responsible for at least part of the sweetpotato weevil resistance. Storage time and production sites appeared to affect the expression of the resistance, but the outcomes depended on the genotypes.

Multivariate selection of AFLP markers associated with β-carotene in sweetpotatoes

A population that consisted of F1 half-sibs and their parents was replicated in field plantings to generate roots to identify AFLP molecular markers and compare statistical models for selection of trait-linked markers using β-carotene content as the grouping variable. Genotypes were grouped into high and low β-carotene classes based on hierarchical cluster analysis. Association parameters between the high and low phenotypic classes of β-carotene and molecular marker profiles were made using logistic regression and discriminant analysis. Logistic regression selected 8 markers less that were associated with β-carotene content compared to discriminant analysis. Further analysis showed that logistic regression achieved 100% correct classification with the 9 markers selected compared to 17 markers that were required by discriminant analysis thus making logistic regression more efficient than discriminant analysis. Logistic regression based on Frequentist hypothesis testing differs from Bayesian based discriminant analysis. This difference may account for the percent correct classification observed.

Adventitious root primordia formation and development in stem nodes of 'Georgia Jet' sweetpotato, Ipomoea batatas.

UNLABELLED • PREMISE OF THE STUDY Yield in sweetpotato is determined by the number of storage roots produced per plant. Storage roots develop from adventitious roots (ARs) present in stem cuttings that serve as propagation material. Data on the origin of sweetpotato ARs and the effect of nodal position on AR establishment and further development are limited.• METHODS We anatomically described root primordium initiation using stem sections and measured number of root primordia formed at different nodal positions using light microscopy and correlated nodal positions with AR number and length 14 d after planting (DAP).• KEY RESULTS Primordia for ARs initiate at the junction of the stem pith ray and the cambium, on both sides of the leaf gap, and they are well developed before emerging from the stem. The number of ARs that develop from isolated stem nodes 14 DAP corresponded to the number of AR primordia detected inside the stem. The total length of established roots at nodes 9-13 from the apex is about 2-fold longer than at nodes 5-8.• CONCLUSIONS Nodal position (age) has a significant effect on the developmental status and number of root primordia inside the stem, determining the number and length of ARs that have developed by 14 DAP. Adventitious roots originating from nodes 9-13 possess similar AR systems and develop better than those originating from younger nodes 3-8. The mechanism regulating AR initiation in nodes is discussed. This system can serve for studying the effect of environmental conditions on AR initiation, development, and capacity to form storage roots.

Effect of Nitrogen on Resistance of Sweet Potato to Sweetpotato Weevil (Coleoptera: Curculionidae) and on Storage Root Chemistry

Abstract The effects of nitrogen fertilizer on sweet potato, Ipomoea batatas (L.) Poir., resistance to the sweetpotato weevil, Cylas formicarius elegantulus (Summers), was studied. Adult weevil feeding and oviposition preference, larval survival, and pupal weight were used as measures of sweet potato resistance. Sweet potato resin glycosides and caffeic acid concentrations in the periderm tissue of storage roots also were measured. Sweet potato genotypes (Beauregard, Excel, W-244, W-250, and Sumor) with varying levels of resistance to sweetpotato weevil were grown in the field under three nitrogen regimes (0, 45, and 135 kg N/ha). Harvested storage roots were evaluated in the laboratory for feeding and oviposition activity of sweetpotato weevil female adults under no-choice and choice test conditions. Larval survival rate and pupal weight were determined by rearing the insects individually on storage root sections. Nitrogen level had a significant effect on the number of eggs deposited, but not on the number of feeding punctures. Sweetpotato weevils laid fewer eggs on plants with the highest level of nitrogen. Nitrogen levels did not significantly affect larval survival and pupal weight. Genotype had a significant effect on feeding, oviposition, and larval survival. Beauregard had higher levels of feeding, oviposition, and larval survival compared with the other genotypes. No interaction effects between nitrogen and genotype were significant. Resin glycosides and caffeic acid concentrations were significantly different among genotypes and between years. Nitrogen levels significantly affected the concentrations of caffeic acid in 1997.

Effects of Previous Insect Feeding Injury to Sweet Potato on Resistance to Sweet Potato Weevil (Coleoptera: Curculionidae) and Storage Root Chemistry

The effects of root and foliage feeding on sweet potato resistance to sweet potato weevil, Cylas formicarius (F.), and on the levels of resin glycoside and caffeic acid in sweet potato storage root...