Sequence characterization of microsatellites in diploid and polyploid Ipomoea (original) (raw)
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PLOS ONE
To better define the sweetpotato polyploidy, we sought to reconstruct phylogenies of its subgenomes based on hybridization networks that could trace reticulate lineages of differentiated homoeolog triplets of multiple single-copy genes. In search of such homoeolog triplets, we distinguished cDNA variants of 811 single-copy Conserved Ortholog Set II (COSII) genes from two sweetpotato clones into variation partitions specified by corresponding homologs from two I. trifida lines, I. tenuissima and I. littoralis using a phylogenetic partition method, and amplicon variants of the COSII-marker regions from 729 of these genes from two sweetpotato clones into putative homoeoallele groups using haplotype tree and the partition methods referenced by corresponding homologs from I. tenuissima. These analyses revealed partly or completely differentiated expressed-homoeologs and homoeologs from a majority of these genes with three important features. 1. Two variation types: the predominant interspecific variations (homoeoalleles), which are non-randomly clustered, differentially interspecifically conserved or sweetpotato-specific, and the minor intraspecific ones (alleles), which are randomly distributed mostly at non-interspecifically variable sites, and usually sweetpotato-specific. 2. A clear differentiation of cDNA variants of many COSII genes into the variation partition specified by I. tenuissima or I. littoralis from that by I. trifida. 3. Three species-homolog-specified and one sweetpotato-specific variation partitions among 293 different COSII cDNAs, and two or three out of the four partitions among cDNA variants of 306 COSII genes. We then constructed hybridization networks from two concatenations of 16 and 4 alignments of 8 homologous COSII cDNA regions each, which included three taxa of expressed homoeologs in a triple-partition combination from the 16 or 4 sweetpotato COSII genes and 5 taxa each of respective cDNA homologs from the three sweetpotato relatives and I. nil, and inferred a species tree embodying both networks. The species tree predicted close-relative origins of three partly differentiated sweetpotato subgenomes.
Phylogenetic Relationships of the Sweetpotato [Ipomoea batatas (L.) Lam.]
Journal of the American Society for Horticultural Science. American Society for Horticultural Science
Twenty-four accessions of Ipomoea, representing 13 species of section Batatas and the outgroup species I. gracilis and I. pes-caprae were analyzed for restriction fragment length polymorphisms. Polymorphisms were detected by probing Southern blots of restriction enzyme-digested genomic DNA with 20 low or moderate copy number sequences isolated from an I. batatas CV. Georgia Red genomic library. Data were analyzed cladistically and phenetically. Ipomoea trifida, I. tabascana, and collection K233 are, of the materials examined, the most closely related to sweetpotato (I. batatas). Ipomoea littoralis, the only Old World species in the section, is a sister species to I. tiliacea. Ipomoea littoralis, I. umbraticola, I. peruviana, I. cynanchifolia, and I. gracilis are shown to be diploid (2n = 2x = 30). In contrast, I. tabascana is tetraploid (2n = 4x = 60). The intrasectional relationships of section Batatas species and the role of tetraploid related species in the evolution of the cultivated I. batatas are discussed.
Plant Science, 2006
The distribution and organization of 5S and 18S-5.8S-26S (18S) rDNA were studied in 10 varieties of hexaploid Ipomoea batatas, five accessions of tetraploid Ipomeoa trifida, and six related species (five diploids, I. trifida, I. triloba, I. tiliacea, I. leucantha and I. setosa and one tetraploid, I. tabascana), by using fluorescence in situ hybridization (FISH). The FISH data obtained indicated that polyploidization was followed by decrease in the number of 18S rDNA loci in higher ploidy level and provided evidence for major genomic rearrangements and/or diploidization in polyploid I. batatas. Among the five diploid species examined, I. trifida appeared to be the most closely related to I. batatas. By contrast, I. leucantha was closed to I. tiliacea, but both species were distant from sweet potato. I. triloba and I. setosa were distantly related to the rest of Ipomoea batatas complex. The close relationship between I. trifida and I. batatas was also demonstrated by the presence of one 18S and CMA marker in these two chromosome complements only. Based on chromosome morphology, tetraploid I. trifida appeared to be more closely related to sweet potato than I. tabascana. Taking all data obtained in this study, I. trifida might be the progenitor of I. batatas, and I. tabascana, interspecific hybrid between these two species.
Molecular genotyping of sweet potato (Ipomoea batatas L. Lam) accessions using microsatellites
for genetic diversity using five microsatellite markers. The results showed that the polymorphic SSR loci revealed diverse relationship among the sweet potato cultivars, which was grouped into four major clusters by unweighted pair group method analysis (UPGMA) method. Cluster analysis showed a Jaccard coefficient ranging from 0.0 to 3.0 indicating high genetic diversity. The primers detected a total of 18 alleles and the number of alleles per locus was 4 for IBR-19, IBR-286, IBR-297 and 3 for IBR-16 and IBR-242 with an average of 3.67 alleles per locus. The polymorphic information content (PIC) of the markers varied from 0.35 to 0.72 with an average of 0.497. Marker IBR-19 revealed the highest PIC of 0.72, while marker IBR-297 had the lowest PIC of 0.35. Observed heterozygosity ranged from 0.32 to 0.89 with a mean of 0.675 across the five SSR loci. The results from the Analysis of molecular variance (AMOVA) which was used to quantify the diversity level and genetic relationship among the thirty sweet potato accessions indicated that a high diversity was mostly distributed within the populations for sweet potato accessions (75.12%) and (15.67%) among the populations.
Genetic Resources and Crop Evolution, 2002
Comparative analyses of genetic diversity and phylogenetic relationshipsof sweetpotato (Ipomoea batatas (L.) Lam.) and its wildrelatives in Ipomoea series Batataswere conducted using amplified fragment length polymorphism (AFLP) and sequencedata from the internal transcribed spacer (ITS) region of the ribosomal DNA. LowITS divergence among thirteen species of ser. Batatasresulted in poorly resolved relationships. More variable AFLP characters werefound to be more efficient in characterizing genetic diversity and phylogeneticrelationships at both intra- and interspecific levels within ser.Batatas. Highly informative AFLP fingerprints of 36accessions representing 10 species of ser. Batatas weregenerated using only six primer combinations. Of the species examined,I. trifida was found to be the mostclosely related to I. batatas, whileI. ramosissima andI. umbraticola were the most distantlyrelated to I. batatas. The highlypolymorphic AFLP markers are a valuable tool in assessing genetic diversity andphylogenetic relationships of sweetpotato and its wild relatives.
CTAB methods for DNA extraction of sweetpotato for microsatellite analysis
Scientia Agricola, 2009
Microsatellite markers have proved to be useful in genetic diversity assessments of sweetpotato (Ipomoea batatas) but practical DNA extraction methods to ensure good quality and quantity DNA for these studies are yet to be established. This study compares the efficiency of three modified methodologies for DNA extraction of six sweetpotato landraces using the CTAB extraction buffer in regard to quantity and purity of DNA quantification and microsatellite band patterns. All methodologies yielded satisfactory results, but the method based in leaf tissue macerated in liquid nitrogen was deemed more adequate because of its simplicity and lower cost. However, the method based in dry leaf tissue was considered more advantageous, first because elicits practicability in the plant acquisition and drying process, especially when the collection is performed in situ, and also because its simplicity makes possible the cold storage of the dry, ground samples for future DNA extractions.
Simple Sequence Repeats (SSRs) in Sweetpotato [Ipomoea batatas (L.) Lam.]
HortScience
Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of sweetpotato [Ipomoea batatas (L.) Lam.]. Screening of the library with five oligonucleotide probes, including; (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 142 positive colonies among ≈12,000 recombinants. Automated DNA sequencing revealed the presence of simple, compound, perfect, and imperfect SSRs. Five homologous PCR primer pairs were synthesized commercially and used to screen 30 sweetpotato clones for the occurrence of SSR polymorphisms. All primer pairs produced an amplification product of the expected size and detected polymorphisms among the genotypes examined. The potential for the use of SSRs as genetic markers for sweetpotato germplasm characterization is discussed.