RAPD重建的大豆属植物的亲缘关系

利用８种ＲＡＰＤ引物（ＯＰＨ－２、ＯＰＨ－３、ＯＰＨ－５、ＯＰＨ－１２、ＯＰＨ－１５、ＯＰＨ－１６、ＯＰＨ－１８和ＯＰＨ－２０）对大豆属的２１份植物材料,其中包括Ｇｌｙｃｉｎｅ亚属的１０个种和Ｓｏｊａ亚属的３个种,进行了基因组指纹图谱构建。通过对获得的基因组指纹图谱的量化分析,利用Ｕｎｗｅｉｇｈｔｅｄｐａｉｒｇｒｏｕｐｗｉｔｈｍａｔｈｅｍａｔｉｃａｖｅｒａｇｅ（ＵＰＧＭＡ）对大豆属中的各个种进行了亲缘关系重建。重建的亲缘关系表明：Ｇ．ｔｏｍｅｎｔｅｌｌａ种中存在３种不同的进化类型,其分化距离已大于某些种种间的分化距离,它们可能是被形态遮蔽的３个种。Ｓｏｊａ亚属内３个种的分化关系同前人的研究推断相同,其亲缘关系很近,这一结果支持将这３个种归并为一个种的观点。但是重建的亲缘关系未能显示出大豆属两个亚属的划分格局。     

用SSR分子标记研究大豆属种间亲缘进化关系

利用SSR标记技术对大豆属11个种37份材料的遗传多样性进行分析,不同位点在种间的等位基因数为6－29,平均生个位点15．9个等位基因,Soja亚属的等位基因数是Glycine亚属的71．5％,并且Glycine亚属种间指纹 谱的差异大于Soja亚属种间的指纹图谱,SSR等位基因的主成分分析结果表明,大豆属中的Glycine亚属和Soja亚属的分类界限是比较明确的,利用第一主成分和第二主成分可较明显地区分开Glycine 亚属的分类界限是比较明显的,利用第一主成分和第二主成分可较明显地区分开Glycine亚属和Soja亚属,通过UPGMA方法构建了大豆属11个种的遗传进化关系,Soja亚属中G.max,G.soja和G.gracilis3个种在系统分化树上界限是比较明显的,由此看来这3个种是独立存在的。     

Systematic Status of the Glycine tomentella and G. tabacina Species Complexes (Fabaceae) Based on ITS Sequences of Nuclear Ribosomal DNA

Glycine was reconstructed based on nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA to examine the systematic status of the G. tomentella and G. tabacina species complexes. Rooted at the subgenus Soja (2 species, 7 accessions), parsimony analysis was conducted for 17 species (31 accessions) of the subgenus Glycine, including 9 and 6 populations of G. tomentella s.l. and G. tabacina s.l., respectively. The nrlTS phytogeny indicated polyphyly of G. tomentella s.l. as well as G. tabacina s.l. In the G. tomentella species complex, larger legumes, narrower leaflets, and deflexed indumentum hairs differentiated G. dolichocarpa from G. tomentella s.s. The tetraploid G. dolichocarpa (2n=80) and aneuploid G. tomentella (2n= 38) represented independent lineages from another clade of the remaining diploid (2n=40) and tetraploid species with a DD genome type. Tetraploid G. tabacina (2n=80) was closely related to G. dolichocarpa instead of the diploid G. tabacina (2n=40) with a BB genome type. The nrlTS phytogeny suggested allopolyploidy of G. dolichocarpa and of the tetraploid G. tabacina, both of which possibly share a common parental species with an AA genome type. Their phylogenetic affinity also indicated biased inheritance of the nrDNA ITS and a possible dominant role of the AA genome. Phylogenetically, G. dolichocarpa and allotetraploid G. tabacina should be recognized as distinct species. Received 12 February 2001/ Accepted in revised form 17 August 2001     

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.     

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.     

Phylogeny of 12 species of genusGlycine Willd. reconstructed with internal transcribed region in nuclear ribosomal DNA

The ITS-Is of 24 accessions belong to 10 species of subgenusGlycine, and 2 species of subgenusSoja of genusGlycine were amplified, cloned and sequenced. According to the homology of the sequences, the phylogeny of the 24 accessions were reconstructed. The reconstructed dendrogram showed that there were some divergent genomic types found in the previously classified species, such asG. tomentella, G. canescens andG. tabacina, and they might be some cryptic species by morphologic analysis.     

Polymerase chain reaction detect polymorphisms and trait association in soybean

Five sets of synthetic oligonucleotide (20-to 24-mers containing no intenal repeats) primers of known gene sequences [yellow lupin nodule specific (hydroxyl) proline-rich protein, pearl millet alcohol dehydrogenase, Pisum sativum heat shock proteins, Drosophila homeobox, and tRNA] were used to differentiate 73 soybean accessions, including 56 Glycine max (L.) Merr. and 17 G. soja Zucc. & Sieb. The amplified genetic markers revealed polymorphic bands for most genotypes studied. The χ²-analyses of the results showed that several fragments produced with these gene primers were associated non-randomly with resistance to Phytophothora, maturity, seed size, flower colour, seed coat colour, seed hilum colour, growth type, and leaf shape. These markers appear to be valuable for differentiation of G. max and G. soja species and genotypes within these species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogeny of 12 species of genusGlycine Willd. reconstructed with internal transcribed region in nuclear ribosomal DNA

The ITS-Is of 24 accessions belong to 10 species of subgenusGlycine, and 2 species of subgenusSoja of genusGlycine were amplified, cloned and sequenced. According to the homology of the sequences, the phylogeny of the 24 accessions were reconstructed. The reconstructed dendrogram showed that there were some divergent genomic types found in the previously classified species, such asG. tomentella, G. canescens andG. tabacina, and they might be some cryptic species by morphologic analysis. Project supported by the Chinese Academy of Sciences     

Cloning and comparative analysis of the gene encoding diacylglycerol acyltransferase from wild type and cultivated soybean

Diacylglycerol acyltransferase (DGAT), as an important enzyme in triacylglycerol synthesis, catalyzes the final acylation of the Kennedy pathway. In the present study, the GmDGAT gene was cloned from Glycine max by using AtDGAT as a query to search against the soybean EST database and the rapid amplification of cDNA ends (RACE) method. Allelic genes were also isolated from 13 soybean accessions and the divergence of the deduced amino acid sequences were compared. The comparison reveals that although GmDGAT is a highly conserved protein, several differences of insertion/deletion were identified in the N-terminal region of the GmDGATs from various soybean accessions. In the C-terminal regions, a single amino acid mutation specific to both G. max and G. soja was also found. The GmDGAT genomic sequences were further cloned and the number and size of exons in the DGAT genomic sequence were very similar among different plant species, whereas the introns were more diverged. These results may have significance in elucidating the genetic diversity of the GmDGAT among the soybean subgenus.     

A REAPPRAISAL OF THE SUBGENUS GLYCINE

The genus Glycine Willd. is divided into three subgenera, Glycine Willd., Soja (Moench) F. J. Herm., and Bracteata Verdc. Six species are currently recognized in the subgenus Glycine: G. canescens F. J. Herm., G. clandestina Willd., G. falcata Benth., G. latrobeana (Meissn.) Benth., G. tabacina (Labill.) Benth., and G. tomentella Hayata. Distribution of the subgenus extends from south China to Tasmania and includes several Pacific islands. A collection of these species was examined cytologically and morphologically in an attempt to evaluate existing variability between and within taxa. Chromosome counts confirmed G. canescens, G. clandestina and G. falcata to be diploid with 2n = 40. Both tetraploids (2n = 80) and diploids were found in G. tabacina, the latter restricted to Australia. Glycine tomentella accessions were primarily tetraploid, but several collections from New South Wales, Australia, were found to be aneuploid with 78 chromosomes. One collection was aneuploid at the diploid level with 38 chromosomes. Meiosis appeared normal in the aneuploids with regular bivalent formation. Several accessions previously identified as G. tomentella were diploid. Seed of G. latrobeana was not available for analysis. Numerical techniques in the form of cluster analysis and principal components analysis were applied to morphological data on vegetative and inflorescence characters obtained from each collection. Numerical analysis grouped the accessions essentially according to current species delimitations with some exceptions. Glycine tabacina specimens from Taiwan approached G. clandestina in several characteristics. The diploid G. tomentella specimens formed a separate cluster and appeared morphologically distinct from the remaining taxa.     

Genetic structure of Glycine canescens,a perennial relative of soybean

Summary Allozyme variation as detected by starch gel electrophoresis was used to assess the extent and spatial organization of genetic variation across the entire range of Glycine canescens sensu lato. Eleven enzyme systems were assayed in 116 accessions of this taxon and 102 alleles were detected at a total of 31 loci. Eighty-one percent of loci were polymorphic. Most of this variation occurred between and very little within accessions. Three major groupings were detected. These groupings (groups 1, 2, and 3) also differed with respect to mean seed size and their geographic distribution. A further ten accessions stood out from these distinct groups. These accessions were most closely related to group 3 but were variable among themselves. In general, they were collected from highly dissected terrain, often in the remote interior of the continent. A final group of 18 problematic accessions (group X), originally tentatively identified as G. canescens on morphological grounds, was shown to be isozymically distinct from this species and was reclassified as one form of the polytypic species G. clandestina.     

Fine-scale phylogenetic structure and major events in the history of the current wild soybean (Glycine soja) and taxonomic assignment of semi-wild type (Glycine gracilis Skvortz.) within the Chinese subgenus Soja

Wild and cultivated species of soybeans have coexisted for 5000 years in China. Despite this long history, there is very little information on the genetic relationship of Glycine soja and G. max. To gain insight into the major events in the history of the subgenus Soja, we examined 20 simple sequence repeat (SSR) markers of a large number of accessions (910). The results showed no significant differences between wild and semi-wild soybeans in genetic diversity but significant differences between G. soja and G. max. Ancestry and cluster analyses revealed that semi-wild soybeans should belong to the wild category and not to G. max. Our results also showed that differentiation had occurred not only among G. soja, G. gracilis, and G. max but also within G. soja and within G. gracilis. Glycine soja had 3 clear genetic categories: typical small-seeded (≤2.0 g 100-seed weight), dual-origin middle-seeded (2.0-2.5 g), and large-seeded plants (2.51-3.0 g). These last were genetically close to G. gracilis, their defining some traits having been acquired mainly by introgression from soybeans. Small-seeded G. gracilis (3.01-3.5 g) were genetically different from larger seeded ones (from 3.51 to 4.0 to over 10 g). Seed size predominated over seed coat color in evolutionary degree. Typical and large-seeded G. soja were found to have 0.7% and 12% introgressive cultivar genes, respectively. The genetic boundary of G. gracilis was at the range of 2.51-3.0 g of G. soja. In the great majority of wild accessions, traits such as white flowers, gray pubescences, no-seed bloom, and colored seed coats were likely introgressive from domesticated soybeans.     

Incongruence in the diploid B-genome species complex of Glycine (Leguminosae) revisited: histone H3-D alleles versus chloroplast haplotypes.

Variation at the single-copy nuclear locus histone H3-D was surveyed in the diploid B-genome group of Glycine subgenus Glycine (Leguminosae: Papilionoideae), which comprises three named Australian species and a number of distinct but as yet not formally recognized taxa. A total of 23 alleles was identified in the 44 accessions surveyed. Only one individual was clearly heterozygous, which is not surprising given the largely autogamous breeding system of subgenus Glycine. Alleles differed by as many as 19 nucleotide substitutions, nearly all in the three introns; length variation was minimal. Phylogenetic analysis identified two shortest allele trees with very little homoplasy, suggesting that recombination has been rare. Both topological and data set incongruence were statistically significant between histone H3-D allele trees and trees inferred from chloroplast DNA haplotypes previously described from these same accessions. Whereas the distribution of H3-D alleles agrees well with morphologically based taxonomic groupings, chloroplast DNA haplotype polymorphisms transgress species boundaries, suggesting that the chloroplast genome is not tracking taxic relationships. Divergences among chloroplast DNA haplotypes involved in such transgressive patterns appear to be more recent than speciation events, suggesting hybridization rather than lineage sorting.     

Construction and comparison of three reference‐quality genome assemblies for soybean

We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.     

Genomic diversity and multiple origins of tetraploid (2n = 78, 80) Glycine tomentella.

Among 15 wild perennial species of the genus Glycine Willd. subgenus Glycine, G. tomentella is exceptional. It is composed of four cytotypes (2n = 38, 40, 78, 80), is diverse in morphological features, and covers a wide geographical area. The objectives of this study were to uncover the genomic diversity in 78- and 80-chromosome cytotypes through a multidisciplinary approach, using cytogenetic, biochemical, and molecular methods, to verify previously identified isozyme groupings and to determine their possible origins. The cytogenetic observations, total seed protein and protease inhibitor profile comparisons, and the phylogenetic analysis of restriction fragment length polymorphisms identified three distinct groups (T1, T5, T6) among aneutetraploid (2n = 78) and four distinct groups (T2, T3, T4, T7) among tetraploid (2n = 80) G. tomentella accessions. The groupings were congruent with those of isozyme analysis. Tetraploid accessions from Indonesia were assigned to a new group, T7, based on the present study. Morphology, cytology, and seed protein banding patterns of synthetic tetraploids indicated that the T1 and T5 group aneutetraploids were composed of D3D3EE and AAEE genomes, respectively, and the T2 group tetraploid accessions consisted of AAD3D3 genomes. Various groups within the 78- and 80-chromosome G. tomentella were suggested to have originated in Australia by allopolyploidization, most likely through multiple independent events.     

Genomic diversity in aneudiploid (2n = 38) and diploid (2n = 40) Glycine tomentella revealed by cytogenetic and biochemical methods.

Of the 15 perennial species of the subgenus Glycine Willd., G. tomentella Hayata is unique in that it has four cytotypes (2n = 38, 40, 78, and 80) and a wide range of geographical distributions. The objective of this study was to uncover the genomic diversity among accessions of aneudiploid (2n = 38) and diploid (2n = 40) G. tomentella based on crossability rate, hybrid seed and seedling viability, meiotic chromosome pairing of F1 hybrids, and seed protein and protease inhibitor profiles. Aneudiploid and diploid G. tomentella accessions were divided into two (D1 and D2) and three [D3(A,B,C), D4, and D5] groups, respectively, based on previous isozyme studies. Crossability rate, intergenomic hybrid viability, degree of chromosome pairing, total seed protein profiles, and trypsin and chymotrypsin inhibitor banding patterns confirmed the isozyme grouping with minor disagreements. A consistent variation was not observed among the aneudiploid accessions in any method of analysis used in this study. Similarly, cytogenetic analysis and the total seed protein profiles did not show dissimilarity among the accessions from Papua New Guinea (PNG; the D3 group) and north of Mitchell River in Northern Queensland [N.Qld(n)]. However, trypsin and chymotrypsin inhibitor analysis revealed that the PNG accessions were distinctly different from N.Qld(n) accessions. The D4 and D5 group accessions were clearly distinguishable by both cytogenetic and biochemical methods. Thus, this study indicates the presence of four genomic groups among G. tomentella (2n = 38, 40) accessions, including the aneudiploids D1 and D2 in one group and diploids in three groups (D3, D4, and D5). These findings will be useful in further genome analysis and add to our present understanding of the biosystematics of the genus Glycine.     

Sequence variation of non-coding regions of chloroplast DNA of soybean and related wild species and its implications for the evolution of different chloroplast haplotypes

Soybean chloroplast DNAs (cpDNAs) are classified into three types (I, II and III) based on RFLP profiles. Type I is mainly observed in cultivated soybean (Glycine max), while type II and type III are frequently found in both cultivated and wild soybean (Glycine soja), although type III is predominant in wild soybean. In order to evaluate the diversity of cpDNA and to determine the phylogenetic relationship among different chloroplast types, we sequenced nine non-coding regions of cpDNA for seven cultivated and 12 wild soybean accessions with different cpDNA types. Eleven single-base substitutions and a deletion of five bases were detected in a total of 3849 bases identified. Five mutations distinguished the accessions with types I and II from those with type III, and seven were found in the accessions with type III, independently of their taxa. Four species of the subgenus Glycine shared bases that were identical to those with types I and II at two of the five mutation sites and shared bases that were identical to those with type III at the remaining three sites. Therefore, the different cpDNA types may not have originated monophyletically, but rather may have differentiated from a common ancestor in different evolutionary directions. A neighbor-joining tree resulting from the sequence data revealed that the subgenus Soja connected with Glycine microphylla which formed a distinct clade from Clycine clandestina and the tetraploid cytotypes of Glycine tabacina and Glycine tomentella. Several informative length mutations of 54 to 202 bases, due to insertions or deletions, were also detected among the species of the genus Glycine. Received: 16 December 1999 / Accepted: 12 February 2000     

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.     

Resistance of Glycine species and various cultivated legumes to the soybean aphid (Homoptera: Aphididae)

The soybean aphid, Aphis glycines Matsumura, is a new pest of soybean, Glycine max (L.) Merr., in North America. It has become widespread on soybean in North America since it was first identified in the Midwest in 2000. Species of Rhamnus L. (buckthorn) are the primary hosts of A. glycines, and soybean is known as a secondary host. There is limited information about the secondary host range of A. glycines. Aphid colonization on various legume hosts was compared in choice experiments. Aphid colonization occurred on species in the genus Glycine Wild. No colonization occurred on Lablab purpureus (L.) Sweet, Lens culinaris Medik, Phaseolus vulgaris L., Pisum sativum L., or species of Vicia L. and Vigna Savi. Colonization was limited or aphids were transient on species of Medicago L., Phaseolus L., and Trifolium L. There were significant differences in aphid colonization among Medicago truncatula accessions with numbers ranging from 7 to 97 aphids per plant. Six Glycine soja Sieb. & Zucc. accessions were as resistant as G. max accessions to A. glycines; these may represent novel sources of A. glycines resistance not found in G. max. Antibiosis was found to play a large role in the expression of resistance in three of the G. soja accessions. Results of this study indicated that G. max and G. soja were the best secondary hosts of A. glycines; however, its secondary host range may include other leguminous species. Therefore, A. glycines did not seem to have a highly restricted monophagous secondary host range.     

Genomes,multiple origins,and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences

Relationships among the various diploid and polyploid taxa that comprise Glycine tomentella have been hypothesized from crossing studies, isozyme data, and repeat length variation for the 5S nuclear ribosomal gene loci. However, several key questions have persisted, and detailed phylogenetic evidence from homoeologous nuclear genes has been lacking. The histone H3-D locus is single copy in diploid Glycine species and has been used to elucidate relationships among diploid races of G. tomentella, providing a framework for testing genome origins in the polyploid complex. For all six G. tomentella polyploid races (T1-T6), alleles at two homoeologous histone H3-D loci were isolated and analyzed phylogenetically with alleles from diploid Glycine species, permitting the identification of all of the homoeologous genomes of the complex. Allele networks were constructed to subdivide groups of homoeologous alleles further, and two-locus genotypes were constructed using these allele classes. Results suggest that some races have more than one origin and that interfertility within races has led to lineage recombination. Most alleles in polyploids are identical or closely related to alleles in diploids, suggesting recency of polyploid origins and spread beyond Australia. These features parallel the other component of the Glycine subgenus Glycine polyploid complex, G. tabacina, one of whose races shares a diploid genome with a G. tomentella polyploid race.