Distribution of restriction site polymorphism within the chloroplast genome of the genus Glycine,subgenus Soja

Summary Restriction fragment length polymorphisms (RFLPs) have been used to detect intragenic sequence diversity in Glycine subgenus soja chloroplast DNA. The distribution of these RFLPs allow Glycine max and G. soja accessions to be grouped according to cytoplasmic genetic relatedness. DNA clones from mung bean chloroplast DNA were used to locate the RFLPs to specific regions of the chloroplast genome. In the course of the experiments, several previously unobserved RFLPs were also identified. At least six molecular changes were detected, including both restriction site loss or gain and insertion/deletion events. Three of the fragment polymorphisms detected are due to changes in the juncture region between one inverted repeat region and the large single-copy region. Probes detecting polymorphisms in three representative soybean genotypes were used to screen additional cultivars and Plant Introductions. The distribution of RFLP patterns in these accessions were consistent with the patterns of previously described cytoplasmic groupings, with the exception of one accession, which formed a new plastome group.     

Identification of sequence variations by PCR-RFLP and its application to the evaluation of cpDNA diversity in wild and cultivated soybeans

The diversity and maternal lineage in wild and cultivated soybeans have previously been assayed using restriction fragment length polymorphism (RFLP) and sequencing analyses of chloroplast DNA (cpDNA). Here we describe a method based on PCR-RFLP for the identification of nucleotides at four mutation sites in non-coding regions of cpDNA. Of the four sites, two were located in restriction enzyme sites and two were not. For the latter two sites, new primers were designed to artificially create restriction sites that spanned them. The PCR-RFLP method enabled us to identify nucleotides at each of the four mutation sites easily and reliably. Fifty-seven wild and sixty-seven cultivated soybeans of different origins and different cpDNA types (types I, II, and III) were assayed. All of the samples tested could be classified into four haplotypes. All of the type-I and -II accessions had the same nucleotides at each of the four mutation sites, while all of the type-III accessions, except for 3 wild ones, had nucleotides that were different from those of types I and II. A sequencing analysis revealed that the 3 wild accessions possessed other single-base variations in the non-coding regions of trnH-psbA and trnT-trnL. The results of this study suggest that the type-I and type-II chloroplast genomes form a group that is distinct from the type-III chloroplast genome. Received: 14 April 2000 / Accepted: 11 July 2000     

Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives

Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.     

5S ribosomal gene variation in the soybean and its progenitor

Summary The soybean, Glycine max and its wild progenitor, Glycine soja, have been surveyed for repeat length variation for the nuclearly encoded 5S ribosomal RNA genes. There is little variation among the 33 accessions assayed, with a common repeat length of 345 bases being typical of both taxa. A 334 base size variant was encountered in individuals from two populations of G. soja from China. The low level of variability is in marked contrast to the variation observed within and between the species of the perennial subgenus Glycine.     

Ribosomal gene variation in soybean (Glycine) and its relatives

Summary The genes encoding the 18S25S ribosomal RNA gene repeat in soybean (Glycine max) and its relatives in the genus Glycine are surveyed for variation in repeat length and restriction enzyme site locations. Within the wild species of subgenus Glycine, considerable differences in repeat size occur, with a maximum observed in G. falcata. Repeat length and site polymorphisms occur in several species, but within individual plants only single repeat types are observed. The rDNA of the cultivated soybean and its wild progenitor, G. soja are identical at the level of this study, and no variation is found in over 40 accessions of the two species. Data from rDNA mapping studies are congruent with those of previous biosystematic studies, and in some instances give evidence of divergences not seen with other approaches.     

CHLOROPLAST DNA POLYMORPHISM SUGGESTS NIGERIAN CENTER OF DOMESTICATION FOR THE COWPEA,VIGNA UNGUICULATA (LEGUMINOSAE)

Twenty-one independent chloroplast DNA polymorphisms were identified in Vigna unguiculata defining 19 different chloroplast DNA molecules (plastome types). Two plastome types, differing by a single character, were found among 32 accessions of cultivated cowpea (Vigna unguiculata ssp. unguiculata). Eighteen different plastome types were found among 26 accessions of wild cowpea (V. unguiculata ssp. dekindtiana). The very low level of chloroplast DNA diversity found in cultivated accessions relative to wild cowpea suggests that 1) the domesticated form was derived from a narrow selection of the wild germplasm and 2) chloroplast gene flow between wild and cultivated types has been very limited. Cladistic analysis of the cpDNA data generated a robust tree completely lacking homoplasy. Three wild accessions from Nigeria possessed a plastome type indistinguishable from one present in cultivated accessions, suggesting that Nigeria represents one center of domestication of the cowpea. The other plastome type within the cultivated germplasm was not found among wild accessions.     

A CHLOROPLAST-DNA PHYLOGENY OF THE WILD PERENNIAL RELATIVES OF SOYBEAN (GLYCINE SUBGENUS GLYCINE): CONGRUENCE WITH MORPHOLOGICAL AND CROSSING GROUPS

Hypotheses of evolutionary relationships among the Australian wild perennial relatives of soybean (Glycine subgenus Glycine) are based largely on patterns of meiotic pairing in intra- and interspecific experimental hybrids. This evidence has indicated a number of genome groupings within the subgenus but has not resolved most phylogenetic relationships. Restriction-endonuclease site variation of chloroplast DNA (cpDNA) within the perennial subgenus is reported here, representing a sampling of approximately 3% of the approximately 150-kilobase plastome. Seven hundred twenty-one unique restriction sites were compared within Glycine using 29 restriction endonucleases; 157 sites varied within the genus. Distance and parsimony methods using these data yielded congruent results, recognizing the existence of three major groups within subgenus Glycine: the species-rich and geographically diverse A clade consisting of G. canescens and related taxa; the B clade, which includes the stoloniferous species; and the C group, containing two species with distinctive curved pods. These results are in general agreement with hypotheses based on genome analysis; inconsistencies involve the inclusion of genetically divergent taxa such as G. falcata in well-supported plastome clades comprised of otherwise interfertile species. Such findings are not unexpected if crossing barriers are considered to be unique features of such anomalous species, paralleling their often numerous morphological and cpDNA autapomorphies. Consideration of cpDNA divergence within the three major clades of subgenus Glycine indicates that the rate of plastome evolution is uncoupled from rates of morphological or ecological diversification.     

Introgression between wild and cultivated soybeans of Japan revealed by RFLP analysis for chloroplast DNAs

Wild soybeans collected in Japan were surveyed for RFLPs of chloroplast DNA. Three haplotypes were detected in RFLPs with a cpDNA clone which contains a LSC region adjacent to the left member of IR. Most of the plants tested possessed haplotype III, and a few plants, collected mostly in southern Japan, had haplotype II. Haplotype I, which is the predominant form in modern cultivars, was detected at six sites from four widely separated regions. Our results indicate that haplotype III is predominant in wild soybean of Japan. Some of the plants having haplotype I were phenotypically intermediate between wild and cultivated soybeans, while the others possessed a seed morphology and plant architecture typical of ordinary wild soybean. The plants having haplotype I appear to be either derivatives of hybridization between wild and cultivated soybeans or relics of a direct progenitor of soybean cultivars with the haplotype I chloroplast genome.     

Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean

Soybean [ Glycine max (L.) Merr.] is one of the major crops in the world and was domesticated from a wild progenitor, Glycine soja Sieb. & Zucc., in East Asia. In order to address the questions concerning the evolution and maternal lineage of soybean, we surveyed the variation in chloroplast DNA simple sequence repeats (cpSSR) of 326 wild and cultivated soybean accessions that were collected from various Asian countries. Twenty-three variants were detected at six cpSSRs in the accessions tested. All of the variants were found in wild soybean, whereas only 14 variants existed in the cultigen. Combining the variants at the six cpSSRs gave 52 haplotypes in the former and eight haplotypes in the latter. Both analyses indicated a considerably higher genetic diversity in the wild soybean. Around 75% of the cultivated accessions tested possessed a common haplotype (no. 49), which was detected in only seven wild accessions, six from southern Japan and one from southern China. The predominant haplotype in the cultigen may therefore have originated from a rare haplotype of the wild soybean that is presently distributed in the southern areas of Japan and China. The remaining seven haplotypes in the cultigen were distributed regionally, and except for three rare haplotypes, largely overlapped with the distributions of wild accessions with the same respective haplotypes. Our results strongly suggest that the cultivated soybeans with different cpDNA haplotypes originated independently in different regions from different wild gene pools and/or hybrid swarms between cultivated and wild forms.     

CHLOROPLAST DNA POLYMORPHISM AND PHYLOGENY IN THE B GENOME OF GLYCINE SUBGENUS GLYCINE (LEGUMINOSAE)

The B genome of Glycine subgenus Glycine comprises three diploid species whose monophyly is supported by morphological, crossing, and chloroplast DNA (cpDNA) data. Previous cpDNA studies indicated low levels of divergence among these taxa and failed to resolve cladistic relationships among them. More intensive studies of cpDNA variation were initiated, using additional restriction endonucleases and accessions. Results from cladistic analyses of over 50 restriction site characters indicate that there is considerable cpDNA polymorphism within this group of species, with a minimum of 27 plastome types occurring among the 74 accessions sampled. Levels of homoplasy observed in this group are relatively high (15%) for closely related congeneric species. There is only limited congruence between plastome type and taxonomic classification based on morphological characters. Explanations for this lack of concordance include: 1) the early state of taxonomic understanding in this group, 2) lack of resolution in the cpDNA tree caused by homoplasy and the small number of synapomorphic characters, 3) introgression among these interfertile, often sympatric taxa, and 4) maintenance of ancestral cpDNA polymorphisms resulting in shared plastomes among species.     

Composite and clinal distribution of Glycine soja in Japan revealed by RFLP analysis of mitochondrial DNA

 Wild soybean (Glycine soja Sieb. et Zucc.), regarded as the progenitor of cultivated soybean [G. max (L.) Merr.], is widely distributed in East Asia. We have collected 1097 G. soja plants from all over Japan and analyzed restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA (mtDNA) in them. Based on the RFLPs detected by gel-blot analysis, using coxII and atp6 as probes, the collected plants were divided into 18 groups. Five mtDNA types accounted for 94% of the plants examined. The geographic distribution of mtDNA types revealed that, in many regions, wild soybeans grown in Japan consisted of a mixture of plants with different types of mtDNA, occasionally even within sites. Some of the mtDNA types showed marked geographic clines among the regions. Additionally, some wild soybeans possessed mtDNA types that were identical to those widely detected in cultivated soybeans. Our results suggest that the analysis of mtDNA could resolve the maternal lineage among plants of the genus Glycine subgenus Soja. Received: 16 June 1997/Accepted: 5 August 1997     

Phylogenetic relationships of the chloroplast genomes in the genus Glycine inferred from four intergenic spacer sequences

The nucleotide sequences of four intergenic spacer regions of chloroplast DNA, atpB-rbcL, trnS-trnG, rps11-rpl36, and rps3-rpl16, were analyzed in the genus Glycine. Phylogenetic analysis based on the sequence data using Neonotonia wightii as the outgroup generated trees supporting the classification of two subgenera, Soja and Glycine, and three plastome groups in the subgenus Glycine. The results were consistent with the presence of diversified chloroplast genomes within tetraploid plants of G. tabacina and G. tomentella, as well as with a close relationship between G. tomentella and G. dolichocarpa that had been suggested based on morphological analyses. Little sequence variation was found in the subgenus Soja, suggesting that G. soja rapidly expanded its distribution in East Asia. The analysis also showed that the differentiation into three plastome groups in the subgenus Glycine occurred in the early stages of its evolution, after the two subgenera diverged.     

Origin of chloroplast DNA diversity in the Andean potatoes

Summary Wide chloroplast DNA (ctDNA) diversity has been reported in the Andean cultivated tetraploid potato, Solanum tuberosum ssp. andigena. Andean diploid potatoes were analyzed in this study to elucidate the origin of the diverse ctDNA variation of the cultivated tetraploids. The ctDNA types of 58 cultivated diploid potatoes (S. stenotomum, S. goniocalyx and S. phureja), 35 accessions of S. sparsipilum, a diploid weed species, and 40 accessions of the wild or weed species, S. chacoense, were determined based on ctDNA restriction fragment patterns of BamHI, HindIII and PvuII. Several different ctDNA types were found in the cultivated potatoes as well as in weed and wild potato species; thus, intraspecific ctDNA variation may be common in both wild and cultivated potato species and perhaps in the higher plant kingdom as a whole. The ctDNA variation range of cultivated diploid potatoes was similar to that of the tetraploid potatoes, suggesting that the ctDNA diversity of the tetraploid potato could have been introduced from cultivated diploid potatoes. This provided further evidence that the Andean cultivated tetraploid potato, ssp. andigena, could have arisen many times from the cultivated diploid populations. The diverse but conserved ctDNA variation noted in the Andean potatoes may have occurred in the early stage of species differentiation of South American tuber-bearing Solanums.     

Restriction fragment length polymorphism diversity in soybean

Summary Fifty-eight soybean accessions from the genus Glycine, subgenus Soja, were surveyed with 17 restriction fragment length polymorphism (RFLP) genetic markers to assess the level of molecular diversity and to evaluate the usefulness of previously identified RFLP markers. In general, only low levels of molecular diversity were observed: 2 of the 17 markers exhibited three alleles per locus, whereas all others had only two alleles. Thirty-five percent of the markers had rare alleles present in only 1 or 2 of the 58 accessions. Molecular diversity was least among cultivated soybeans and greatest between accessions of different soybean species such as Glycine max (L.) Merr. and G. soja Sieb. and Zucc. Principal component analysis was useful in reducing the multidimensional genotype data set and identifying genetic relationships.     

Phytoalexin Production as a Chemosystematic Parameter Within the Genus Glycine

Glycine max, the cultivated soybean, has previously been shown to produce a mixture of related isoflavonoid phytoalexins called ‘glyceollins’ in response to pathogen attack. We now report the occurrence of considerable qualitative and quantitative variation in the glyceollins produced by various Glycine spp. All species exhibited highly conserved glyceollin production patterns except G. clandestina, G. tabacina and G. tomentella. These latter groups are also regarded as unsettled based on classical characters. Thus, phytoalexin production constitutes a possible basis for the classification of Glycine accessions. The cultivated soybean, G. max, produced predominantly only glyceollins I, II and III, but yielded varying proportions depending on the plant part utilized but not the agent employed to elicit their production.     

杂草稻叶绿体籼粳分化的多重PCR分析

通过分析籼稻93-11和粳稻培矮64S的叶绿体全基因组,优化和构建了籼粳分化的叶绿体分子标记ORF100和ORF29-TrnC^GCA的多重PCR。应用这个多重PCR对200余份世界各地杂草稻和其它水稻材料进行分析。结果表明:杂草稻中有明显的叶绿体籼粳分化,表现出明显的地域性,且与传统的中国栽培稻的南籼北粳能较好的对应。推测粳型杂草稻可能是栽培稻突变或粳型水稻(作母本)与其它类型水稻材料杂交而形成的。     

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     

Incongruence between chloroplast and species phylogenies in Eucalyptus subgenus Monocalyptus (Myrtaceae)

Seventy-eight polymorphic cpDNA (chloroplast DNA) characters were found in 13 closely related taxa from Eucalyptus series Amygdalinae (subgenus Monocalyptus) and seven potential outgroup taxa. The strict consensus of six cladograms generated from cpDNA data confirmed monophyly of Monocalyptus. However, cpDNA phylogeny within Monocalyptus was incongruent with taxonomic classification, being more related to geography, even when accessions were from divergent series. Monocalyptus cpDNA formed two major clades. On the island of Tasmania cpDNA was restricted to a single clade, exhibited very little variation, and was phylogenetically related to cpDNA found in central and western Victoria. In contrast, cpDNA of mainland monocalypt taxa was more variable, even within the Amygdalinae. Four out of six Tasmanian Amygdalinae species were polymorphic. The difference between cpDNA of replicates was often greater than differences between species from different series. The low level of cpDNA variation and extensive morphological intergradation between the Tasmanian endemics suggest recent speciation. However, the transfer of cpDNA through hybridization between lineages is the most likely explanation for the observed sharing of cpDNA across series. This study highlights that the geographical pattern to cpDNA variation in Eucalyptus may be an important source of information on past plant distributions in Australia.     

A single nuclear locus phylogeny of soybean based on DNA sequence

Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.     

Molecular and morphological differentiation between the crop and weedy types in velvetleaf (Abutilon theophrasti Medik.) using a chloroplast DNA marker: seed source of the present invasive velvetleaf in Japan

A comparison of chloroplast DNA (cpDNA) sequences was carried out between the crop and weed types of Abutilon theophrasti to clarify the seed source of the present weedy velvetleaf in Japan. A sequencing analysis of approx. 6% of the chloroplast genome (ca 10 kbp) detected three nucleotide substitutions, one six-base-pair insertion/deletion (indel) and one 30-base pair inversion, which distinguish two haplotypes of cpDNA. A PCR-based survey of the indel and the inversion revealed that the 93 accessions of velvetleaf collected from the world could be divided into two groups. A morphological marker (capsule color) could be used to discriminate the crop type and the weed type, and hence, along with cpDNA haplotype, to distinguish three genotypes (Type I, II, and III). All Japanese cultivars and crop accessions from other countries were Type I. Weed types were divided into Type II and III. All of the samples from the USA, and the samples taken from grain imports to Japan were Type III. Since most of the weedy types distributed in Japan were of Type III, it is argued that they were introduced as seeds in the imported grain. We also found that the Type II plants sporadically occurred in Japan. It is suggested that they originated as hybrids, with indigenous cultivars as the maternal ancestor. Such hybrids must have survived since the cessation of velvetleaf cultivation about a century ago.