Sweetpotato Germplasm Collection Research Articles

First report of sweepoviruses infecting Ipomeas batatas L. cultivars and landraces in Trinidad.

Root crops, referred to as ground provisions in the Caribbean, are traditional staples in Trinidad. One widely consumed example is sweet potato (Ipomeas batatas L.). The crop is mainly produced by subsistence farming which together with imports from neighboring Caribbean countries meet domestic demand (Singh et al. 2008). The Central Experiment Station, situated in the eastern part of Trinidad, maintains a sweet potato germplasm collection comprising both imported and locally-sourced landraces for cultivar development and distribution of propagules. In May 2017 chlorosis and leaf curling symptoms, typically associated with sweepoviruses, were observed on imported cultivars, Centennial, Jewel, 86 BM 31, TIB 313, TIB 8 21 1, and S128, and the landraces, Kick Up Jenny, John, and Carrot. Leaf samples from these nine symptomatic plants were collected for analysis, along with samples from the asymptomatic landrace, Chickenfoot. Total nucleic acids were extracted (Sharma et al. 2008) and the samples were assayed by PCR using degenerate primers SPG1 and SPG2 (Li et al. 2004) that target the replication associated protein gene (ORF C1), a highly conserved region of sweepoviruses. Amplicons of 912-bp were obtained from two of the nine symptomatic plants (TIB 8 21 1, Kick Up Jenny), but not from the asymptomatic Chickenfoot. The same samples were assayed by PCR amplification using primers SpvF and SpvR (Avelar 2015) which are specific to a highly conserved 632-bp region of the coat protein gene (ORF V1) of sweet potato leaf curl virus (SPLCV). All 10 samples tested positive for SPLCV, including the asymptomatic landrace, Chickenfoot. The ORF V1 PCR products from three of the 10 samples, namely Chickenfoot, TIB 8 21 1, and Kick Up Jenny, were cloned and sequenced (two clones per sample). Comparison of the sequences (GenBank accession nos. OR882007 [Chickenfoot], OR913125 [TIB 8 21 1] and OR913126 [Kick Up Jenny]) identified up to 4% nt sequence variability between samples. In BLASTn analysis, they were most closely related to the SPLCV isolate China:Sichuan (GenBank accession no. KJ013557), sharing 94 to 98% nt identity. Total nucleic extracts from one representative sample (TIB 8 21 1) was used as template for rolling circle amplification (RCA, TempliPhi Amplification Kit, GE Healthcare Life Sciences, Piscataway, NJ, USA). Digestion of the RCA product with StuI (Thermo Scientific, MA, USA) yielded ~2.8 kb DNA fragments indicative of monomeric full length genomes. Digested fragments were cloned, completely sequenced and deposited in GenBank under the accession nos. OR866202 (2,821 nts) and OR866203 (2,828 nts). Two species of sweepoviruses were detected. In BLASTn analysis, OR866202 showed 95% nt identity with sweet potato golden vein associated virus (SPGVaV) US:MS:1B-3 (GenBank accession no. HQ333143.1) which is a recombinant virus comprised of SPLCV and sweet potato leaf curl Georgia virus (SPLCGV) (Zhang and Ling 2011) and in BLASTx analysis OR866202 was most similar (92-99%) to SPLCV isolates from Brazil (GenBank accession nos. ACI23475.1, AGW16179.1, ACY79479.1), Peru (GenBank accession no. ACY79466.1) and China (GenBank accession nos. ACY79439.1). OR866203 shared 96% nt identity with SPLCV China:Henan25(8):2012 (GenBank accession no. KF040465.1) in BLASTn analysis and BLASTx analysis revealed ≥ 94% aa sequence identity with SPLCV from Brazil (GenBank accession nos. ACI23475.1, AGW16179.1, ADZ96559.1), Peru (GenBank accession no. ACY79479.1), China (GenBank accession no. ACY79466.1). and Spain (GenBank accession no. QWQ56365.1). Both Trinidad isolates also showed 90-96% nt identity with SPLCV from Korea (GenBank accession no.s KT992061.1, KT992064.1, unpublished). This is the first detection of sweepoviruses in Trinidad. SPGVaV has been reported in Brazil, the United States and Korea (Kil et al. 2014), while SPLCV has been described in other Caribbean islands, including Cuba, Jamaica, Puerto Rico, St. Vincent (Cuellar et al. 2015), and Barbados (Alleyne et al. 2019), as well as several countries in South America. Although Koch's postulates were not completed, our findings suggest that sweet potato crops in Trinidad harbor sweepoviruses, notwithstanding efforts to distribute pathogen-free materials and, in some instances, the apparent absence of visible symptoms on infected plants. Further studies on the management and impact of these viruses are necessary, including their prevalence in the sweet potato production regions of Trinidad.

Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection.

Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.

Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato (I. batatas) Germplasm Collection.

The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.

Screening of sweetpotato germplasm collections for sweetpotato weevil (Cylas spp.) resistance in Tanzania

Weevil damage caused by sweetpotato weevil (Cylas spp.) is a major constraint to sweetpotato production in Tanzania due to a lack of improved varieties with durable resistance. The objective of this study was to screen sweetpotato germplasm collections for weevil resistance and to select the best parents to be used in resistance breeding. Field studies involving 96 sweetpotato genotypes were conducted at two weevil hotspot sites in Western Tanzania using a 12 x 8 lattice design with three replications at each site. Data collected included yield and yield related traits, weevil reaction and weevil damage score. The tested genotypes differed significantly (P < 0.01) for sweetpotato storage root number, root weight, root infestation and root damage score. Weevil infestation on storage roots significantly (P ≤0.05) correlated with total root number (r = 0.38) and weevil damage score (r = 0.79). Marketable root weight and total root weight were significantly correlated with infested root weight each with r = 0.45. The study identified nine sweetpotato genotypes expressing resistance and 10 genotypes with moderate resistance to weevil. Five genotypes including Magunhwa, Chuchu ya Nesi, Rugomoka, Tumauma and New Kawogo were selected with weevil resistance and desirable yield and yield-related traits. These genotypes can be used in future weevil resistance breeding programs of sweetpotato in Western Tanzania or related agro-ecologies.

Identification and Control of Latent Bacteria in in vitro Cultures of Sweetpotato [Ipomoea batatas (L.) Lam

Bacterial microorganisms which are latent in in vitro cultures can limit the efficiency of in vitro methods for the conservation of genetic resources. In this study we screened 2,373 accessions from the in vitro sweetpotato germplasm collection of the International Potato Center in Lima, Peru for bacteria associated with plantlets in tissue culture through a combination of morphological methods and partial 16S rDNA sequencing. Bacteria were detected in 240 accessions (10% of the accessions screened) and we were able to isolate 184 different bacterial isolates from 177 different accessions. These corresponded to at least nineteen Operational Taxonomic Units (OTUs) of bacteria, belonging to the genera Sphingomonas, Bacillus, Paenibacillus, Methylobacterium, Brevibacterium, Acinetobacter, Microbacterium, Streptomyces, Staphylococcus, and Janibacter. Specific primers were developed for PCR based diagnostic tests that were able to rapidly detect these bacteria directly from tissue culture plants, without the need of microbial sub-culturing. Based on PCR screening the largest bacterial OTUs corresponded to a Paenibacillus sp. closely related to Paenibacillus taichungensis (41.67%), and Bacillus sp. closely related to Bacillus cereus (22.22%), and Bacillus pumilus (16.67%). Since in vitro plant genetic resources must be microbe-free for international distribution and use, any microbial presence is considered a contamination and therefore it is critical to clean all cultures of these latent-appearing bacteria. To accomplish this, plantlets from in vitro were transferred to soil, watered with Dimanin® (2 ml/l) weekly and then reintroduced into in vitro. Of the 191 accessions processed for bacterial elimination, 100% tested bacteria-free after treatment. It is suspected that these bacteria may be endosymbionts and some may be beneficial for the plants.

Assessment of the genetic diversity of sweetpotato germplasm collections for protein content

Sweetpotato [Ipomoea batatas (L.) Lam.] is a relatively cheap source of nutrients for humans in most developing countries, including those in sub-Saharan Africa. Breeding for essential quality traits is an important goal of sweetpotato breeding programs. This may include root protein content (RPC), since protein-energy malnutrition is a common problem worldwide. The objective of this study was to quantify the genetic diversity in RPC present among sweetpotato accessions maintained in the genebank of the Agricultural Research Council (ARC) of South Africa in order to characterize and select the most promising clones for breeding. Both, Dumas combustion and Near-infrared Spectroscopy (NIRS) were used to determine RPC for a diverse set of accessions. In addition, total root yield and dry matter content were determined and root flesh colour recorded. Data was subjected to standard analysis of variance. A total of 227 sweetpotato accessions (53 introduced accessions, 18 local cultivars, 24 local landraces and 132 ARC breeding lines) were screened for total RPC, and a large variation was observed. As measured by the Dumas combustion, RPC values varied from 2.65 to 6.45% on a dry weight basis (dwb). RPC estimated by NIRS ranged from 0.68 to 11.51%. The NIRS proved to be an efficient and quick tool that can be useful in sweetpotato breeding programs towards selecting for quality traits such as RPC. A total of 31 medium to high yielding accessions with high, intermediate and low RPC were selected for genetic analysis and breeding for enhanced nutrition. Some promising germplasm included the local informal market cultivar ‘Impilo’ (orange-fleshed) at 6.18%, and the breeding line ‘2012-29-4’, seed imported from Mozambique, at 6.45%. NIRS values for ‘Tanzania’ and ‘Maria Angola’ were promising. The study is one of only a few that provides protein data for a large set of sweetpotato accessions from various parts of the world and is useful for sweetpotato breeding programs. Future work can focus on the determination of the concentrations of individual amino acids.

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

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.

Phenotypic analysis of leaf colours from the USDA, ARS sweetpotato (Ipomoea batatas) germplasm collection

AbstractLeaf colour characteristics of 730 sweetpotato,Ipomoea batatas(L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the USDA sweetpotato germplasm collection were evaluated during 2012–2014. Colorimetry data for the abaxial and adaxial leaf surfaces were recorded using a tristimulus colorimeter and the CIE 1976 L*a*b* and CIE L*C*h* colour spaces. Most accessions (725 of 730 PIs) had dark-to-medium green leaves, but two PIs had totally purple leaves, and three PIs had yellow or yellow-green (chartreuse) leaves. For mature, field-grown green leaves, values for the red-green coordinate (a*) averaged −12.4 for the adaxial and −10.4 for the abaxial leaf surface. Values for the blue-yellow coordinate (b*) averaged 17.2 for the adaxial and 17.3 for the abaxial leaf surface. Hue angle (h*) for green leaves averaged 120.9° for the adaxial and 126.2° for the abaxial leaf surface. Colour saturation (Chroma, C*) averaged 21.3 for the adaxial and 20.2 for the abaxial leaf surface. Lightness (L*) averaged 35.4 for the adaxial and 47.2 for the abaxial leaf surface of green leaves. Late in the season, over one-half (53.9%) of the 730 PIs showed some level of purple pigmentation in the leaf lamina. Late-season purple leaves were collected and colour coordinates were recorded for 118 PIs grown in the field. For purple leaves, values for a*, b*, C*, L* and h* averaged 2.3, 6.2, 7.9, 28.2 and 64.4° for the adaxial surface and −1.0, 12.7, 13.9, 43.1 and 87.0° for the abaxial leaf surface, respectively.

Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly.

Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East – Pacific Islands) to 0.110 (Australia – South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species.

Color analysis of storage roots from the USDA, ARS sweetpotato (Ipomoea batatas) germplasm collection

The United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit in Griffin, GA maintains the United States germplasm collection for Ipomoea spp. (Convolvulaceae). During 2012–2014, 737 sweetpotato, Ipomoea batatas (L.) Lam., plant introductions (PI) were acquired as tissue-culture plantlets and then acclimated to greenhouse conditions at the USDA, ARS, U. S. Vegetable Laboratory (USVL), Charleston, SC. Single plants were transferred to plastic-covered plant beds to produce cuttings for replicated field trials. Storage roots were harvested from 690 PIs grown in the field and 695 PIs grown in pots. Color coordinates were obtained for each PI using a tristimulus colorimeter. Hue angle values (h*) ranged from 8.2° to 88.3° ( $$ \bar{x} $$ = 54.9°) for the periderm (peel or skin) of field-grown storage roots (n = 690 PIs) and − 9.4° (= 350.6°) to 96.2° ( $$ \bar{x} $$ = 51.3°) for pot-grown roots (n = 695 PIs). The red–green coordinate (a*) ranged from 0.8 to 30.7 ( $$ \bar{x} $$ = 12.8) for the periderm of field-grown roots and − 2.0 to 44.9 ( $$ \bar{x} $$ = 16.1) for pot-grown roots. The yellow–blue coordinate (b*) ranged from 2.8 to 33.1 ( $$ \bar{x} $$ = 19.4) for the periderm of field-grown roots and − 7.4 to 38.1 ( $$ \bar{x} $$ = 19.3) for pot-grown roots. Color saturation (chroma, C*) ranged from 13.7 to 35.8 ( $$ \bar{x} $$ = 24.9) for the periderm of field-grown roots and 14.9–45.5 ( $$ \bar{x} $$ = 29.3) for pot-grown roots. Lightness (white–black, L*) ranged from 32.6 to 81.7 ( $$ \bar{x} $$ = 54.6) for the periderm of field-grown roots and 32.1–88.2 ( $$ \bar{x} $$ = 64.0) for pot-grown roots. Hue angles ranged from − 13.1° (= 346.9°) to 100.9° ( $$ \bar{x} $$ = 80.9°) for the stele (flesh) of field-grown storage roots (n = 672 PIs) and − 29.9° to 103.5° ( $$ \bar{x} $$ = 81.6°) for pot-grown roots (n = 676 PIs); a* ranged from − 5.6 to 35.0 ( $$ \bar{x} $$ = 8.0) for the stele of field-grown roots and − 6.0 to 41.0 ( $$ \bar{x} $$ = 7.6) for pot-grown roots; and b* ranged from − 7.7 to 56.1 ( $$ \bar{x} $$ = 34.6) for the stele of field-grown roots and − 12.6 to 56.1 ( $$ \bar{x} $$ = 31.8) for pot-grown roots. C* ranged from 12.7 to 65.8 ( $$ \bar{x} $$ = 37.2) for the stele of field-grown roots and 8.9–65.7 ( $$ \bar{x} $$ = 34.5) for pot-grown roots; and L* ranged from 27.8 to 91.1 ( $$ \bar{x} $$ = 77.7) for the stele of field-grown roots and 28.2–91.9 ( $$ \bar{x} $$ = 80.4) for pot-grown roots. There were significant relationships between stele color (h*) and percent dry matter, with orange stele having a significantly lower % dry matter ( $$ \bar{x} $$ = 25.6%, n = 183) compared with roots with cream/white stele ( $$ \bar{x} $$ = 30.8%, n = 373). There appears to be wide genetic diversity for root color characteristics for the United States sweetpotato germplasm collection.

Adaptation to mid-season drought in a sweetpotato (Ipomoea batatas [L.] Lam) germplasm collection grown in Mozambique

Abstract Drought has negative effects on sweetpotato production. Two experiments with two watering treatments (irrigated and water-stressed) were conducted at Umbeluzi Research Station in 2015. The objectives were to (i) determine response of 48 sweetpotato germplasms to mid-season drought, (ii) determine best traits for improvement of storage root yield under mid-season drought and (iii) assess the selection criteria for identifying drought tolerance in sweetpotato germplasms. The irrigated and water- stressed trials received 640 and 400 mm of water, respectively, throughout the season. Water stress was imposed from 30 to 70 days after planting. Each treatment had two replicates arranged in a randomized complete block design. Data collected on storage root and vine yield and derived drought tolerance indices including harvest index were subjected to analysis of variance in R. Sweetpotato germplasms with high storage root yield under mid-season drought were associated with a high harvest index. Harvest index stability and the geometric mean are key to identifying cultivars with high and stable storage root yield under both treatments. MUSGP0646-126, Irene and Ivone combined both low TOL, SSI, HI and high yield storage root yield across the treatments and over seasons. The use of drought and harvest indices is encouraged for selecting improved cultivars for varied production environments and their regular use in accelerated breeding schemes is suggested.

ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China

To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat (ISSR) markers. The mean genetic similarity coefficient, Nei's gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and five subpopulations based on neighbor-joining (NJ) clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identified. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to flesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance (AMOVA) revealed small but significant difference between white and orange-fleshed sweet potato accessions. Small but significant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.

Molecular, morphological and agronomic characterization of the sweet potato (Ipomoea batatas L.) germplasm collection from Mozambique: Genotype selection for drought prone regions

Sweet potato (Ipomoea batatas (L.) Lam) is one of the most important root crops in Mozambique, ranking in the 3rd position, after cassava and maize. Within the scope of the national and regional strategies/initiatives, we have used a multi-analysis approach to characterize the national sweet potato germplasm collection at two different levels: i) genetic, morphological and agronomic diversity; and ii) agronomic potential (storage root yield, vine weight, biomass, harvest index and dry matter content) toward drought tolerance. This collection, composed by 44 accessions, comprises 28 genotypes cultivated in three different provinces of Mozambique (Gaza, Inhambane and Zambezia), nine from other African countries (Kenya, South Africa, Uganda and Zimbabwe), one from the United States of America, and six from CGIAR research centers (IITA and CIP). According to our results, the Mozambican germplasm bank presents a high level of diversity, comparable to those from the collections of the primary centers of origin and South Africa, therefore constituting of a good source of agronomic traits for breeding. Regarding drought tolerance, six Mozambican genotypes (Admarc, Chingova, Nhacoongo-1, Xihetamakote, Nwanatuyo, and Chissicuana-2), one from Uganda (NASPOT-5), one from Zimbabwe (Moz_white), one from Kenya (SPK 004), and one from the USA (Resisto) seem to have the highest potential to be used in regions with frequent drought seasons and in future breeding programs. The results showed that such integrated analysis can be used to successfully characterize the genetic material in terms of suitability to drought-prone regions, therefore helping sweet potato crop management, with economic and food security impacts.

Detection and Classification of SPLCV Isolates in the U.S. Sweetpotato Germplasm Collection via a Real-Time PCR Assay and Phylogenetic Analysis.

The United States Department of Agriculture-Agricultural Research Service sweetpotato (Ipomoea batatas) germplasm collection contains accessions that were initially collected from various countries worldwide. These materials have been maintained and distributed as in vitro plantlets since the mid-1980s. The status of viral infection by the emerging Sweet potato leaf curl virus (SPLCV) and other Begomovirus spp. in this germplasm has yet to be determined. In order to minimize the potential distribution of virus-infected clones, all accessions in the collection were tested for SPLCV using a real-time polymerase chain reaction assay. In total, 47 of 701 accessions of in vitro plantlets tested positive for SPLCV. The presence of SPLCV detected in these materials was confirmed via biological indexing using the indicator plants I. nil and I. muricata. Symptoms appeared more rapidly on I. muricata than on I. nil. Nucleotide polymorphisms among the isolates were evaluated by sequencing the AV1 coat protein gene from 24 SPLCV-infected accessions. The results revealed that the SPLCV isolates shared high sequence identity. Ten nucleotide substitutions were identified, most of which were synonymous changes. Phylogenetic analysis was conducted on those 24 SPLCV isolates in combination with six described SPLCV species and various SPLCV strains from GenBank to evaluate the relationships among viral species or strains. The results from this analysis indicated that most of the AV1 genes derived from previously classified SPLCV species clustered together, some of which formed well-supported monophyletic clades, further supporting the current taxonomy. Overall, identification of SPLCV-infected germplasm will allow approaches to be employed to eliminate the virus from the collection and limit the distribution of infected materials.

Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces

We analysed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kinds of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Central/Caribbean America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of sweet potato germplasm collections.

Phenotypic diversity of plant morphological and root descriptor traits within a sweet potato, Ipomoea batatas (L.) Lam., germplasm collection from Tanzania

In Tanzania sweet potato ranks as the third most important crop after cassava and potato. We studied the phenotypic diversity of morphological plant and root descriptor traits in accessions of the sweet potato germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania, using phenotypic characters. A total number of 105 sweet potato accessions of different geographic origins were studied in field trials of The Sugarcane Research Institute at Kibaha Tanzania, and data were recorded for 27 phenotypic characters. Estimates of pair-wise phenotypic similarities using the Manhattan coefficient varied from 0.023 to 0.814, with a mean of 0.285. Cluster analysis was conducted using the unweighted pair group method with arithmetic mean (UPGMA) and Principal Coordinate Analysis (PCO). The clustering of phenotypic data resulted in a dendrogram which was discordant with geographic origin and AFLP data. The analysis of variance (ANOVA) revealed highly significant variation among the accessions for 21 out of the 27 characters studied. Phenotypic analyses revealed a wider range of variability than AFLP analyses. Comparison of molecular and phenotypic data using the Mantel test showed a very low correlation (r2 = 0.0007). Molecular and phenotypic classifications are discordant, and both are necessary to classify the germplasm correctly and to clarify genetic relationships among sweet potato accessions.

An Online Database of Sweetpotato Germplasm Collection in Uganda

Sweetpotato [Ipomoea batatas (L.) Lam], the world’s seventh most important crop, is widely grown and consumed as a staple food crop in Uganda. Uganda is the third largest global producer after China and Nigeria (Food and Agricultural Organization, 2007). It lies within the East African region, which is considered a secondary center of diversity for the crop where the farmers grow and maintain large numbers of different cultivars and landraces (Mwanga et al., 2001; Villordon et al., 2006). Genetic erosion threatens this diversity as a result of sweetpotato virus disease (SPVD) caused by dual infection of Sweetpotato feathery mottle virus (Potyvirus; Potyviridae) and Sweetpotato chlorotic stunt virus (Crinivirus; Closteroviridae) (Gibson et al., 1998), Alternaria bataticola blight, and African sweetpotato weevils, Cylas puncticollis Boheman and Cylas brunneus Fabricius. Farmers are also known to abandon poor-performing traditional cultivars in favor of newly developed ones released by the national breeding program (Bashaasha et al., 1995; Mwanga et al., 2001). The National Sweetpotato Program based at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda, undertook a rigorous germplasm collection, characterization, evaluation, and conservation program to mitigate sweetpotato genetic erosion and also to find superior germplasm for cultivar development in hybridization schemes. A total of 1303 accessions of sweetpotato germplasm were collected from 21 major sweetpotato-producing districts of Uganda from January to July 2005. Information about farmers’ indigenous knowledge of the cultivars was also collected. These accessions were assembled at NaCRRI and morphologically characterized using 40 standard root, vine, leaf, and flower descriptors of sweetpotato [International Potato Center (CIP), Asian Vegetable Research and Development Center, and International Board for Plant Genetic Resources, 1991] scored 90 to 100 d after planting in the field. A total of 946 morphologically distinct accessions were identified after removal of duplicates. Field evaluations were also conducted for SPVD, Alternaria blight, and yield at three sites for two seasons. Subsequently, 192 superior genotypes were selected from the germplasm evaluation of which 190 were genetically distinct on molecular characterization using 10 fluorescent-labeled simple sequence repeat markers, IB-R16 (VIC), IB-R19 (PET), IBCIP-13 (NED), IB-R03 (PET), IBCIP-9 (6-FAM), IB-S09 (NED), IB-R08 (PET), IB-R12 (NED), IB-S07 (6-FAM), and IB-S07 (PET), obtained from CIP, Lima, Peru. The database for sweetpotato germplasm collection in Uganda referred to as the ‘‘Uganda Sweetpotato Germplasm Database’’ (USGDB) is described. To our knowledge, the USGDB is the most comprehensive description of collected sweetpotato germplasm in the region. USGDB has all 946 morphologically distinct accessions fully described, including passport (accession identifiers and information recorded by collectors) data, morphological characterization, and evaluation data. This database has been made available online for public use at: http:// www.viazivitamu.org/ugasp_db/index.php. The database contains the names, accession number as assigned by collectors, geographical location (longitude and latitude), form of maintenance, and a total of 40 morphological descriptors. It further contains the total root yield, SPVD, and Alternaria bataticola blight disease resistance values for each accession. This online database is an important resource for enhancing the global exchange of sweetpotato germplasm. An online web-accessible database developed for the sweetpotato germplasm collection in Kenya called the ‘‘Viazivitamu database’’ is also available at http:// www.viazivitamu.org (Villordon et al., 2007). The Ugandan and Kenyan databases will eventually be merged and expanded to produce a comprehensive regional database of sweetpotato germplasm resources that is representative of the entire East African region after checking for duplicates in the two collections. This USGDB collection is being maintained in the screenhouse and field at NaCRRI. Some 30 accessions are being maintained in vitro at the CIP gene bank at Lima, Peru. Request for this germplasm should be directed to the National Sweetpotato Program, NaCRRI, P.O. Box 7084, Kampala, Uganda.

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.

Using GIS-Based Tools and Distribution Modeling to Determine Sweetpotato Germplasm Exploration and Documentation Priorities in Sub-Saharan Africa

Detailed information on the geographic distribution of a crop is important in planning efficient germplasm conservation strategies but is often not available, particularly for minor crops. Using germplasm collection data from Kenya, Tanzania, and Uganda, we used distribution modeling to predict the distribution of sweetpotato [Ipomoea batatas L. (Lam.)] in sub-Saharan Africa. We used a consensus modeling approach using the following algorithms: genetic algorithm for rule set prediction (GARP), maximum entropy, BIOCLIM, and DOMAIN. The predicted distribution encompasses known sweetpotato production areas as well as additional areas suited for this crop species. New geographic areas where at least three models predicted presence were in Angola, Cameroon, Central African Republic, The Congo, Democratic Republic of Congo, Gabon, Ghana, Angola, Ethiopia, Mozambique, Rwanda, and the Central African Republic. This information can be used to fill gaps in current sweetpotato germplasm collections as well as to further enhance the current presence-only based distribution model. Our approach demonstrates the usefulness of considering several models in developing distribution maps.

A WEB-ACCESSIBLE GEO-REFERENCED DATABASE OF SWEETPOTATO ACCESSIONS FOR TANZANIA AND KENYA

One of the secondary centers of genetic diversity for the sweetpotato [Ipomoea batatas (L.) Lam.] is located in Africa. We have developed a geo-referenced database of sweetpotato accessions for Tanzania and Kenya that is accessible by stakeholders and other users. Public domain base maps and other files were used to generate the underlying GIS components. DIVA-GIS was used to convert existing spreadsheet-based accession and passport data into GIS-compliant files. ALOV Map, a public domain Java application for publishing vector and raster maps, was used to provide the framework for a web-accessible GIS database. This demonstrates that the availability of publicly available software requiring minimal or flexible licensing costs provide a cost-effective alternative to institutions that are considering developing GIS databases as well as enabling web accessibility to such resources. DIVA-GIS was also used to predict potential distribution of sweetpotato germplasm in Sub-Saharan Africa using the built-in ecological niche modelling tool. We describe procedures, software, and other applications that we used to develop a publicly accessible web interface to a GIS database of sweetpotato germplasm collections in Kenya and Tanzania.