Sequence characterization of microsatellites in diploid and polyploid Ipomoea

 The objectives of the present study were to evaluate the inheritance and nucleotide sequence profiles of microsatellite genetic markers in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] and its putative tetraploid and diploid ancestors, and to test possible microsatellite mutation mechanisms in polyploids by direct sequencing of alleles. Sixty three microsatellite loci were isolated from genomic libraries of I. batatas and sequenced. PCR primers were designed and used to characterize microsatellite loci in two hexaploid I. batatas populations, a tetraploid Ipomoea trifida population, and a diploid I. trifida population. Nine out of the sixty three primer pairs tested yielded a clearly discernible, heritable banding pattern; five showed Mendelian segregation. All other primer pairs produced either smeared banding patterns, which could not be scored, or no bands at all in I. batatas. All of the primers which produced discernible banding patterns from I. batatas also amplified products of similar size in tetraploid and diploid I. trifida accessions. The sequence analysis of several alleles in the three species showed differences due to mutations in the repeat regions consistent with small differences in the repeat number. However, in some cases insertions/deletions and base substitutions in the microsatellite flanking regions were responsible for polymorphisms in both polyploid and diploid species. These results provide strong empirical evidence that complex genetic mechanisms are responsible for SSR allelic variation in Ipomoea. Four I. batatas microsatellite loci showed polysomic segregation fitting tetraploid segregation ratios. To our knowledge this is the first report of segregation ratios for microsatellites markers in polyploids. Received: 4 January 1999 / Accepted: 4 January 1999     

Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas,Convolvulaceae) complex

• Genome size evolution and its relationship with pollen grain size has been investigated in sweet potato (Ipomoea batatas), an economically important crop which is closely related to diploid and tetraploid species, assessing the nuclear DNA content of 22 accessions from five Ipomoea species, ten sweet potato varieties and two outgroup taxa.
• Nuclear DNA amounts were determined using flow cytometry. Pollen grains were studied using scanning and transmission electron microscopy.
• 2C DNA content of hexaploid I. batatas ranged between 3.12–3.29 pg; the mean monoploid genome size being 0.539 pg (527 Mbp), similar to the related diploid accessions. In tetraploid species I. trifida and I. tabascana, 2C DNA content was, respectively, 2.07 and 2.03 pg. In the diploid species closely related to sweet potato e.g. I. ×leucantha, I. tiliacea, I. trifida and I. triloba, 2C DNA content was 1.01–1.12 pg. However, two diploid outgroup species, I. setosa and I. purpurea, were clearly different from the other diploid species, with 2C of 1.47–1.49 pg; they also have larger chromosomes. The I. batatas genome presents 60.0% AT bases.
• DNA content and ploidy level were positively correlated within this complex. In I. batatas and the more closely related species I. trifida, the genome size and ploidy levels were correlated with pollen size. Our results allow us to propose alternative or complementary hypotheses to that currently proposed for the formation of hexaploid Ipomoea batatas.

     

Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics

Erianthus arundinaceus is not only an important germplasm resource for sugarcane breeding but also a potential bioenergy plant. Making clear the distribution of the chromosome ploidy of wild E. arundinaceus in china is the premise of the research and utilization of this species. Therefore, the objectives of this study were to determine the ploidy level and DNA content of the 55 E. arundinaceus accessions using flow cytometry and to identify the correlation between ploidy and phenotypic traits. Among the 55 accessions, four tetraploids and 51 hexaploids were identified. The four tetraploids originated from Mengma Yunnan, Shuangjiang Yunnan, Gaozhou Guangdong and Chengle Sichuan. The mean DNA content was 4.82 pg/2C for the tetraploid and 7.30 pg/2C for the hexaploid plants. The ploidy was negatively correlated with cellulose content and positively correlated (P<0.05) with plant height, stem diameter, leaf width, dry weight per plant, fresh weight per plant and hemicellulose content. However, ploidy was not correlated with leaf length, tiller number and the ratio of dry weight and fresh weight. This study will be useful for revealing the distribution of the ploidy of wild E. arundinaceus in Chin, traits markers analysis, and utilization of this species, such as cultivar improvement and sugarcane breeding in the future.     

Meiotic pairing as an indicator of genome composition in polyploid prairie cordgrass (<Emphasis Type="Italic">Spartina pectinata</Emphasis> Link)

The existence of neopolyploidy in prairie cordgrass (Spartina pectinata Link) has been documented. The neohexaploid was discovered coexisting with tetraploids in central Illinois, and has been reported to exhibit competitiveness in the natural environment. It is hypothesized that the natural tetraploid cytotype produced the hexaploid cytotype via production of unreduced gametes. Meiosis I chromosome pairing was observed in tetraploid (2n?=?4x?=?40), hexaploid (2n?=?6x?=?60), and octoploid (2n?=?8x?=?80) accessions and the percentage of meiotic abnormality was determined. Significant differences in meiotic abnormality exist between tetraploid, hexaploid, and octoploid cytotypes. An elevated incidence of abnormal, predominantly trivalent pairing in the neohexaploid suggests that it may possess homologous chromosomes in sets of three, in contrast to the tetraploid and octoploid cytotypes, which likely possess homologous chromosomes in sets of two. Abnormal chromosome pairing in the hexaploid may result in unequal allocation of chromosomes to daughter cells during later stages of meiosis. Chromosome pairing patterns in tetraploid, hexaploid, and octoploid cytotypes indicate genome compositions of AABB, AAABBB, and AABBA′A′B′B′, respectively.     

Genetic diversity and relationships of sweetpotato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat (ISSR) and restriction analysis of chloroplast DNA

Genetic diversity and relationships of 40 accessions of Ipomoea, representing ten species of series Batatas, were examined using ISSR markers and restriction-site variation in four non-coding regions of chloroplast DNA. A total of 2071 ISSR fragments were generated with 15 primers in these accessions and, on average, 52 bands per accession were amplified. Most of the primers contained dinucleotide repeats. The ISSR fragments were highly polymorphic (62.2%) among the 40 accessions studied. Restriction analysis of chloroplast (cp) DNA revealed 47 informative restriction-site and length mutations. Phylogenetic analyses of ISSR and cpDNA datasets generally revealed similar relationships at the interspecific level, but the high polymorphism of ISSRs resulted in a better separation of intraspecific accessions. However, the combined ISSR and cpDNA dataset appeared to be appropriate in resolving both intra- and interspecific relationships. Of the species examined, I. trifida was found to be the most closely related to cultivated sweetpotato, the hexaploid I. batatas, while I. ramosissima and I. umbraticola were the most distantly related to I. batatas within the series. Ipomoea triloba, hitherto considered to be one of the ancestors of sweetpotato, was only distantly related to sweetpotato based on ISSR similarity index. Received: 4 January 1999 / Accepted: 27 September 1999     

Revisiting meiotic pairing in wheat synthetics in relation to the evolution of the meiotic system in wheat

A large panel of hexaploid wheat synthetics was developed. Their tetraploid parents consisted of either four extracted wheat tetraploids (ETWs) or four natural present-day tetraploids, and their diploid parents consisted of twenty accessions of Aegilops tauschii. Analysis of meiotic behaviour of the synthetics showed that chromosome pairing is highly variable and depends on the progenitor. The meiotic behaviour in the four ETWs was compared to that of the natural tetraploid wheats. It appears there was no evolution at the hexaploid level of the meiotic genes carried by the A and B genomes. We also reach the conclusion that the neo-allohexaploids at the origin of present-day wheat had a meiotic behaviour close to that of the present-day hexaploid wheat. It is likely that other neo-hexaploids with an impaired meiosis were formed, but they had no future due to their more or less rapid disappearance due to increasing aneuploidy level and structural changes, mainly Robertsonian translocations.     

Use of Ipomoea trifida germ plasm for sweet potato improvement. 3. Development of 4x interspecific hybrids between Ipomoea batatas (L.) Lam. (2n=6x=90) and I. trifida (H.B.K) G. Don. (2n=2x=30) as storage-root initiators for wild species

Summary More than 28,000 pollinations were carried out between 5 Ipomoea batatas and 41 diploid I. trifida accessions of diverse origins to obtain 4x interspecific hybrids. From the resultant 730 seeds, 248 plants were finally obtained. Ploidy level determination of the progeny showed unexpected results: 52 individuals were hexaploid, 5 were pentaploid, 190 were tetraploid, as expected, and one was not determined. The existence of 5x and 6x progenies from 6x x 2x crosses not only confirmed the presence of 2n gametes but also their successful function in gene flow between ploidy levels and polyploidization within this genus. The progeny and their cultivated parents were planted in an observation field. The cultivated parents produced 0.49 kg/plant or less. Most 4x progenies did not produce storage roots or had very poor yields; nonetheless, and despite their cultivated parents' poor yields, 8 genotypes yielded between 0.81 and 1.50 kg/plant.A new scheme, using the 4x interspecific hybrids, is proposed for evaluating 2x and 4x wild accessions of the section Batatas to which the sweet potato belongs. Other possible uses of the 4x hybrids in breeding and genetics of the sweet potato are also discussed.     

Genetic diversity in a world germplasm collection of tall fescue

Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.     

Why only tetraploid Solidago gigantea (Asteraceae) became invasive: a common garden comparison of ploidy levels

Many studies have compared the growth of plants from native and invasive populations, but few have considered the role of ploidy. In its native range in North America, Solidago gigantea Aiton (Asteraceae) occurs as a diploid, tetraploid and hexaploid, with considerable habitat differentiation and geographic separation amongst these ploidy levels. In the introduced range in Europe, however, only tetraploid populations are known. We investigated the growth performance and life history characteristics of plants from 12 European and 24 North American (12 diploid, 12 tetraploid) populations in a common garden experiment involving two nutrient and two calcium treatments. Twelve plants per population were grown in pots for two seasons. We measured 24 traits related to leaf nutrients, plant size, biomass production and phenology as well as sexual and vegetative reproduction. Native diploid plants had a higher specific leaf area and higher leaf nutrient concentrations than native tetraploids, but tetraploids produced many more shoots and rhizomes. Diploids grown with additional calcium produced less biomass, whereas tetraploids were not affected. European plants were less likely to flower and produced smaller capitulescences than North American tetraploids, but biomass production and shoot and rhizome number did not differ. We conclude that a knowledge of ploidy level is essential in comparative studies of invasive and native populations. While clonal growth is important for the invasion success of tetraploid S. gigantea, its potential was not acquired by adaptation after introduction but by evolutionary processes in the native range.     

Phytogeographical studies ofCalamagrostis sachalinensis (Gramineae)

Chromosome numbers were determined on 223 collections ofCalamagrostis sachalinensis from 18 localities in Japan. The plants were found to be tetraploid (2n=28), hexaploid (2n=42) or octoploid (2n=56). A few collections were found to include one or two B-chromosomes. The tetraploid collections were made from central Honshu and Mt. Apoi in Hokkaido, while the hexaploids and the octoploids were detected in many localities. Pollen examination of these collections showed that the tetraploids with but one exception have good pollen and the hexaploids and the octoploids have no pollen or have bad pollen with stainability less than 10%. With the help of pollen examination of a number of herbarium specimens, the distribution of the tetraploids and that of the assemblage of the hexaploids and octoploids were delineated. Morphological studies indicated that the tetraploid, hexaploid and octoploid plants can not be separated in gross and spikelet morphology and that the tetraploids in central Honshu and those in Mt. Apoi are significantly different in leaf features. It was concluded thatC. sachalinensis represents an apo-amphimictic complex, which includes the following four races: 1) tetraploid, amphimictic, having thin leaf blades 5–10 mm broad and growing on the subalpine conifer forest belt and the conifer forest-alpine ecotone in the mountains of central Honshu; 2) tetraploid, amphimictic, having hard leaf blades 2–6 mm broad and growing on the stony, arid and exposed alpine belt on Mt. Apoi in Hokkaido; 3) hexaploid, mainly apomictic, the most variable ecologically, widely distributed; 4) octoploid, mainly apomictic, frequent in the upper montane to alpine belts, probably widely distributed.     

Survey of genome sequences in a wild sweet potato,Ipomoea trifida (H. B. K.) G. Don

Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either ‘core candidates’ (common to the two lines) or ‘line specific’. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences. A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log₂ ratio of >1 and CNV size >1,000 bases). The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.     

Components of Yield in Diploid, Tetraploid and Hexaploid Wheats (Triticum spp.)

Twenty-nine accessions of Triticum including ancestral diploidsand primitive and modern tetraploid and hexaploid froms wereexamined for differences in yield components. Mean whole plant and main shoot harvest index for the ploidygroups exhibited significant (P < 001) increascs from thediploids to the tetraploids and from the tetraploids to thehexaploids. Mean biological yield per plant for the ploidy groupsincreased significantly (P < 001) from the diploid to thehexaploid but declined significantly (P < 001) from thetetraploid to the hexaploid level. There were marked reductions in shoot number and percentageof infertile shoots per plant and increases in grain numberper spikelet and grain size from diploid what (Triticum monococcum)to the early tetraploids. Yield component variation in early and recent Australian wheatsrevealed that the semi-dwarf (gibberellininsensitive) wheatswere significantly higher in whole plant and main shoot harvestindex over normal height (gibberellin-sensitive) wheats. Triticum aestivum, wheat, Aegilops spp, harvest index, polyploidy, yield components, evolution     

A new cytotype of Jacobaea vulgaris (Asteraceae): frequency,morphology and origin

Jacobaea vulgaris subsp. vulgaris (syn. Senecio jacobaea subsp. jacobaea) constitutes an intricate polyploid complex distributed in Europe. Four cytotypes have been reported in this species, three with euploid (diploid, tetraploid and octoploid; 2n=20, 40 and 80) and one with aneuploid (2n=32) chromosome numbers. Here we report that the diploid chromosome number (2n=20) reported from Bulgaria is due to misidentification with Jacobaea aquatica. On the other hand, we have discovered a new, hexaploid (2n=6x=60) cytotype within J. vulgaris subsp. vulgaris using flow cytometry. The new cytotype occurs within four sympatric populations of otherwise tetraploid and octoploid plants in Pannonia (one locality in the eastern Czech Republic and two localities in southwestern Slovakia) and in Podillya (one locality in western Ukraine). The frequency of hexaploid individuals within 76 studied populations is very low (only 10 of 693 analysed plants), and hexaploids probably represent hybrids between tetraploid and octoploid plants. Three mixed populations with hexaploid plants were subjected to detailed morphological and pollen fertility analyses. Multivariate morphometric analysis reveals partial separation of tetraploid and octoploid plants, whereas hexaploid individuals are similar in morphology to octoploids. In comparison with tetraploids, octoploids and hexaploids exhibit slightly longer ray florets, involucral bracts and tubular florets and more hairy outer achenes. Hexaploid plants display larger pollen grains and lower pollen fertility compared to tetraploids and octoploids.     

Isolation and identification of Triticeae chromosome 1 receptor-like kinase genes (Lrk10) from diploid, tetraploid, and hexaploid species of the genus Avena.

The DNA sequence of an extracellular (EXC) domain of an oat (Avena sativa L.) receptor-like kinase (ALrk10) gene was amplified from 23 accessions of 15 Avena species (6 diploid, 6 tetraploid, and 3 hexaploid). Primers were designed from one partial oat ALrk10 clone that had been used to map the gene in hexaploid oat to linkage groups syntenic to Triticeae chromosome 1 and 3. Cluster (phylogenetic) analyses showed that all of the oat DNA sequences amplified with these primers are orthologous to the wheat and barley sequences that are located on chromosome 1 of the Triticeae species. Triticeae chromosome 3 Lrk10 sequences were not amplified using these primers. Cluster analyses provided evidence for multiple copies at a locus. The analysis divided the ALrk EXC sequences into two groups, one of which included AA and AABB genome species and the other CC, AACC, and CCCC genome species. Both groups of sequences were found in hexaploid AACCDD genome species, but not in all accessions. The C genome group was divided into 3 subgroups: (i) the CC diploids and the perennial autotetraploid, Avena macrostachya (this supports other evidence for the presence of the C in this autotetraploid species); (ii) a sequence from Avena maroccana and Avena murphyi and several sequences from different accessions of A. sativa; and (iii) A. murphyi and sequences from A. sativa and Avena sterilis. This suggests a possible polyphyletic origin for A. sativa from the AACC progenitor tetraploids or an origin from a progenitor of the AACC tetraploids. The sequences of the A genome group were not as clearly divided into subgroups. Although a group of sequences from the accession 'SunII' and a sequence from line Pg3, are clearly different from the others, the A genome diploid sequences were interspersed with tetraploid and hexaploid sequences.     

The origin and meiotic behaviour of hexaploid northern wheatgrass (Agropyron dasystachyum)

The occurrence of hexaploid (2n = 6x = 42) forms in some otherwise natural tetraploid populations of Agropyron dasystachyum (2n = 4x = 28) was cytologically detected and studied. The hexaploid plants are morphologically similar to the tetraploids except for a small reduction in the anther size. The general survey of chromosome numbers of natural Northern Wheatgrass (A. dasystachyum 2n = 4x = 28) populations derived from eight different regions of Alberta indicated that the occurrence of hexaploid variants was not restricted to a single locality. A comparative study of chromosome pairing in the natural and the synthetic hexaploids revealed that the naturally occurring 42-chromosomed plants of A. dasystachyum originated as a result of fertilization between unreduced (SSHH) and the natural (SH) gametes, both coming from the tetraploid form of A. dasystachyum. Based on chromosome pairing, the genomes of the natural hexaploid A. dasystachyum have been designated as SSSHHH. The natural hexaploids appear to intercross among themselves and also with tetraploids producing euploid and aneuploid hybrids. The possible evolutionary significance of these findings is briefly discussed.     

Genetic characterization of Paspalum notatum accessions by AFLP markers

Paspalum notatum Flügge is a warm-season forage grass with sexual diploid and apomictic tetraploid races. Genetic improvement was achieved in out-breeding diploids. The acquisition of artificial sexual tetraploids has raised the possibility of performing crosses and plant improvement at the tetraploid level. The objective of our study was to obtain a genetic and cytoembryological characterization of a germplasm collection of P. notatum, including 31 accessions from seven countries of America and 11 experimentally obtained genotypes. Morphology of mature gametophytes was observed to assess the mode of reproduction of the accessions. A total of 1342 AFLP fragments were generated across the 42 genotypes and from two reference taxa: P. urvillei and P. procurrens. AFLP data were converted into a binary matrix and similarity relationships were established. The genetic distance among all the accessions showed a maximum value of 0.36. In addition, eleven AFLP fragments were observed exclusively in apomictic plants, which could be linked to genomic regions implicated in the control of apospory.     

Evidence for autoploid evolution in the artemisia ludoviciana complex of the Pacific Northwest

TheArtemisia ludoviciana complex of the Northwest is considered to be an intervarietal autoploid complex on the basis of evidence obtained from cytogenetic analysis. The evidence includes the occurrence of chromosomal races within all but two of the inclusive taxa, the degree and constancy of multivalent formation in the polyploid races, and the high degree of homology among the genomes of the various taxa as demonstrated by the pairing relationships in the F₁ progeny. Both triploid and tetraploid progeny were produced in diploid-tetraploid crosses, and the tetraploid offspring were fully as fertile as the natural tetraploids. The triploids, on the other hand, produced very few viable pollen grains. The production of tetraploid offspring in interracial crosses could provide a mechanism for gene flow from the diploid to the tetraploid population. With the observation of both diploid and tetraploid populations ofA. douglasiana, in addition to the well-known hexaploid, a reasonable doubt is cast upon the putative amphidiploid origin of the hexaploid via hybridization betweenA. suksdorfii andA. ludoviciana.     

Breeding barriers at a diploid–hexaploid contact zone in <Emphasis Type="Italic">Aster amellus</Emphasis>

Polyploidization is an important mechanism of sympatric speciation, but few studies have addressed breeding barriers between polyploids and their diploid progenitors in the field, and the available data have been mainly obtained from diploid-tetraploid contact zones. In contrast to diploid-tetraploid complexes, hybridization between diploid and hexaploid individuals may lead to viable fertile tetraploid offspring, and thus the interactions between these ploidy levels can be more complex. We investigated the breeding barriers operating between diploid and hexaploid individuals of Aster amellus at a contact zone in Central Europe to understand the absence of hybrids (i.e., tetraploids) and mixed populations. Phenological segregation, assortative mating mediated by pollinators and crossing ability were assessed under natural and controlled conditions in diploid and hexaploid populations growing in close proximity. The results revealed low levels of reproductive isolation (RI) due to flowering phenology (RI = 11–45%) and pollinator behavior (RI = 17%), so that pollen transfer between diploids and hexaploids is possible. In contrast, almost complete reproductive isolation was observed due to a series of post-pollination barriers that significantly reduced the production of offspring from inter-cytotype crosses (RI = 99.9%), even though some tetraploids were detected in seeds and seedlings. We conclude that the absence of tetraploids at the contact zone is probably due to a combination of several factors, including spatial segregation, strong post-pollination barriers (such as gametic isolation, low viability of tetraploid seeds and/or inability of tetraploid plants to reach the flowering stage), and to a lesser extent, temporal and behavioral segregation. Future studies should explore the fitness of tetraploids and the effect of different traits on the reproductive success and fitness of each cytotype. This will enable a fuller understanding of the dynamics and mechanisms acting in contact zones.