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.     

SSR marker and ITS cleaved amplified polymorphic sequence analysis of soybean × Glycine tomentella intersubgeneric derived lines

Wild perennial Glycine species are an invaluable gene resource for the cultivated soybean [Glycine max (L.) Merr., 2n=40]. However, these wild species have been largely unexplored in soybean breeding programs because of their extremely low crossability with soybean and the need to employ in vitro embryo rescue methods to produce F₁ hybrids. The objective of this study was to develop molecular markers to identify gene introgression from G. tomentella, a wild perennial Glycine species, to soybean. A selection of 96 soybean simple sequence repeat (SSR) markers was evaluated for cross-specific amplification and polymorphism in G. tomentella. Thirty-two SSR markers (33%) revealed specific alleles for G. tomentella PI 483218 (2n=78). These SSR markers were further examined with an amphidiploid line (2n=118) and monosomic alien addition lines (MAALs), each with 2n=40 chromosomes from soybean and one from G. tomentella. The results show that the use of SSR markers is a rapid and reliable method to detect G. tomentella chromosomes in MAALs. We also developed a cleaved amplification polymorphism sequence (CAPS) marker according to the sequences of internal transcribed spacer (ITS) regions in soybean and G. tomentella. Four MAALs that carry the ITS (rDNA) locus from G. tomentella were identified. The SSR and ITS-CAPS markers will greatly facilitate the introgression and characterization of gene transfer from G. tomentella to soybean.Communicated by F.J. Muehlbauer     

HYBRIDIZATION IN THE GENUS GLYCINE SUBGENUS GLYCINE WILLD. (LEGUMINOSAE,PAPILIONOIDEAE)

The genus Glycine is composed of two subgenera, Glycine and Soja. Soja includes the cultivated soybean, G. max, and its wild annual counterpart G. soja, while Glycine includes seven wild perennial species. Hybridization was carried out within and between wild perennial species of the subgenus Glycine. The success rate (pods set/flowers crossed) was 11% for intraspecific and 8% for interspecific crosses. A total of 220 F₁ hybrids was examined morphologically and cytologically where possible. Hybrids within G. canescens (2n = 40) and G. latifolia (2n = 40) were fertile as expected. Glycine clandestina (2n = 40) was morphologically separable into at least three groups, which produced fertile hybrids within each group. One cross between two groups gave vegetatively vigorous but sterile hybrids. The majority of crosses within G. tabacina (2n = 80) were fertile, except that extremely narrow-leaved forms gave sterile hybrids in combination with more usual forms. Sterility was also encountered in G. tomentella when aneuploids (2n = 78) from New South Wales, Australia, were crossed with tetraploids (2n = 80) from either Queensland, Australia, or Taiwan; crosses between the latter two populations resulted in seedling lethality. Cytological behavior of sterile hybrids followed a similar pattern, whether at the diploid or tetraploid level. The frequency of chromosome pairing was approximately half that expected if genomes showed full pairing homology. Bivalent disjunction at anaphase I was usually followed by precocious division of the majority of univalents. Telophase I and II were characterized by lagging chromosomes and micronuclei, so that resulting pollen was misshapen and sterile. Chromosome pairing data from sterile intraspecific hybrids at the tetraploid level may indicate a polyphyletic origin of tetraploids, whereby different diploid populations were involved in their formation. Similarly, chromosome pairing in sterile intraspecific diploid hybrids may indicate that the various diploid groups arose independently of one another. Both 40- and 80-chromosome forms are fully diploidized, however, and if they are of ancient origin, divergence since that time could have resulted in the chromosomal differentiation which becomes apparent when intraspecific hybridization is effected. Diploid (2n = 40) interspecific hybrids G. falcata × G. canescens, and G. falcata × G. tomentella grew poorly and did not reach flowering stage. Diploid (2n = 40) crosses between G. latifolia and G. tomentella produced inviable seedlings. Tetraploid (2n = 80) hybrids between G. tomentella and G. tabacina were vegetatively vigorous but sterile owing to low chromosome pairing at meiosis, indicating little pairing homology between the two species. Diploid hybrids between G. canescens and G. clandestina, however, showed almost complete chromosome pairing at diakinesis and partial fertility. Although morphologically distinct, these two species have not diverged sufficiently to prevent hybridization and possible gene exchange through recombination. Self compatibility, perennial growth habit, and geographic isolation have favored divergence among Glycine populations to the point that gene exchange appears no longer possible in many cases. Internal isolating mechanisms have been shown to operate at various levels of plant development from hybrid lethality at seedling stage, to failure of seed-set in sterile but vegetatively vigorous hybrids.     

Genomic relationships in the genus Glycine (Fabaceae: Phaseoleae): use of a monoclonal antibody to the soybean Bowman-Blrk inhibitor as a genome marker

We investigated the use of a monoclonal antibody (MAb 238) to the soybean Bowman-Birk inhibitor (BBI) to verify and understand the intergenomic relationships among the wild perennial Glycine species. Competitive enzyme linked immunosorbent assay and western blot screening studies revealed that the accessions of B-genome (G. latifolia, G. microphylla, and G. tabacina, 2n = 40) and C-genome (G. curvata and G. cyrtoloba) species did not contain the MAb 238 crossreactive proteins (BBI-nulls). By contrast, all the A-genome (G. argyrea, G. canescens, G. clandestina, and G. latrobeana), E-genome (G. tomentella, 2n = 38), and F-genome (G. falcata) species, G. arenaria (genome unknown), and the polyploid (2n = 78,80) G. tomentella accessions were BBI-positive. The D-genome G. tomentella (2n = 40) and tetraploid G. tabacina (2n = 80) contained both BBI-null and BBI-positive type accessions. Among the recently described species, G. hirticaulis (2n = 40), G. lactovirens, and G. pindanica contained the MAb 238 crossreactive proteins while G. albicans did not. Glycine hirticaulis, G. pindanica, and G. tomentella (2n = 38) displayed highly similar MAb 238 crossreactive isoelectric focusing banding patterns, indicating that they are genomically close to each other. Glycine hirticaulis was found to have both diploid (2n = 40) and tetraploid (2n = 80) cytotypes. We demonstrated that the MAb 238 was specific to the trypsin inhibitor domain of the BBI. The MAb 238 clearly reflected all the previously established relationships in the genus Glycine, validating its use as a genome marker.     

Broadening the Genetic Base of Soybean: A Multidisciplinary Approach

Soybean [Glycine max (L.) Merr.] is an economically important legume with 2n = 40 chromosomes, whose seeds contain an average of 40% protein and 20% oil, and its plants enrich the soil by fixing nitrogen in symbiosis with nitrogen-fixing bacteria. World soybean production has doubled in the past twenty years to over 220 million metric tons in 2006; the producing countries are U.S.A., Brazil, Argentina, China, and India. Soybean was domesticated in East Asia from its wild annual progenitor G. soja Sieb. & Zucc. (2n = 40). There are 26 wild perennial species, indigenous to Australia, of the subgenus Glycine but a common progenitor with 2n = 20 chromosomes has not been identified, and it may be extinct. It has been demonstrated that Glycine species are of either of allo-or auto-tetraploid origin. The cytogenetic knowledge of soybean lags far behind that of other model important crops (rice, maize, wheat, tomato), because it's somatic chromosomes are symmetrical, and only one pair of satellite chromosomes can be identified. Pachytene chromosome analysis created a chromosome map that has laid the foundation for producing primary trisomics. Several molecular linkage maps have been developed, but only 11 of the 20 molecular linkage groups (MLGs) have been associated with specific chromosomes. The genetic base of modern soybean cultivars is narrow and soybean breeders are confined to crossing within the primary gene pool (GP-1). Soybean does not have secondary gene pool (GP-2). Exploitation of the tertiary and quaternary gene pools (GP-3, GP-4) has been attempted but ended at the amphidiploid stage. A methodology for producing fertile lines derived from G. max and G. tomentella (2n = 78) cross has been developed, thereby making introgression of useful genes from GP-3. Genetic transformation has produced Roundup Ready® Soybeans, resistant to glyphosate herbicide.     

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     

FISH mapping of the 5S and 18S-28S rDNA loci in different species of Glycine.

Wild germplasms are often the only significant sources of useful traits for crops, such as soybean, that have limited genetic variability. Before these germplasms can be effectively manipulated they must be characterized at the cytological and molecular levels. Modern soybean probably arose through an ancient allotetraploid event and subsequent diploidization of the genome. However, wild Glycine species have not been intensively investigated for this ancient polyploidy. In this article we determined the number of both the 5S and 18S-28S rDNA sequences in various members of the genus Glycine using FISH. Our results distinctly establish the loss of a 5S rDNA locus from the "diploid" (2n = 40) species and the loss of two from the (2n = 80) polyploids of GLYCINE: A similar diploidization of the 18S-28S rDNA gene family has occurred in G. canescens, G. clandestina, G. soja, and G. max (L.) Merr. (2n = 40). Although of different genome types, G. tabacina and G. tomentella (2n = 80) both showed two major 18S-28S rDNA loci per haploid genome, in contrast to the four loci that would be expected in chromosomes that have undergone two doubling events in their evolutionary history. It is evident that the evolution of the subgenus Glycine is more complex than that represented in a simple diploid-doubled to tetraploid model.     

Chromosomal inheritance of parental rDNAs distribution pattern detected by FISH in diploid F1 hybrid progeny of Cobitis (Teleostei,Cobitidae) species has non-Mendelian character

This study was conducted to describe the major and the minor rDNA chromosome distribution in the spined loach Cobitis taenia (2n = 48) and the Danubian loach Cobitis elongatoides (2n = 50), and their laboratory-produced diploid reciprocal F₁ hybrid progeny. It was tested by fluorescence in situ hybridisation (FISH) whether the number of 28s and 5s rDNA sites in the karyotypes of diploid hybrids corresponds to the expectations resulting from Mendelian ratio and if nucleolar organiser regions (NOR)were inherited from both parents or nucleolar dominance can be observed in the induced F₁ hybrid progeny. Ten (females) or twelve (males) 28s rDNA loci were located in nine uniarm chromosomes of C. taenia. Two of such loci terminally bounded on one acrocentric chromosome were unique and indicated as specific for this species. Large 5s rDNA clusters were located on two acrocentric chromosomes. In C. elongatoides of both sexes, six NOR sites in terminal regions on six meta-submetacentric chromosomes and two 5s rDNA sites on large submetacentrics were detected. The F₁ hybrid progeny (2n = 49) was characterised by the intermediate karyotype with the sites of ribosome synthesis on chromosomes inherited from both parents without showing nucleolar dominance. 5s rDNA sites were detected on large submetacentric and two acrocentric chromosomes. The observed number of both 28s and 5s rDNAs signals in F₁ diploid Cobitis hybrids was disproportionally inherited from the two parental species, showing inconsistency with the Mendelian ratios. The presented rDNA patterns indicate some marker chromosomes that allow the species of the parental male and female to be recognised in hybrid progeny. The 5s rDNA was found to be a particularly effective diagnostic marker of C. elongatoides to partially discern genomic composition of diploid Cobitis hybrids and presumably allopolyploids resulting from their backcrossing with one of the parental species. Thus, the current study provides insight into the extent of rDNA heredity in Cobitis chromosomes and their cytotaxonomic character.     

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.     

Variation in the DNA Content of Glycine Species

Nuclei were isolated from cotyledons of a range of accessionsfrom 14 species of Glycine. These were stained with ethidiumbromide and the relative fluorescence for each genotype wasmeasured by flow cytometry. The DNA content was estimated bycomparison of relative fluorescence with that from nuclei fromseedling leaves of Allium cepa, whose DNA content has been calculatedpreviously by chemical assay. The 4C amounts for diploid Glycineranged from 3.80 to 6.59 pg. Two groups of diploid species appearedfrom the analysis. The first consisted of species with amountsranging from 3.80 to 5.16 pg and included G. canescens (AA),G. argyrea (A₁ A₁), G. clandestina (A²A²), G. microphylla(BB),G. latifolia (B₁B₁), G. tabacina 2n=40 (B²B²), G. tomentella2n=38 (EE) and 2n=40 (DD), G. max and G. soja (GG), G. arenariaand G. latrobeana. A second group had higher DNA contents rangingfrom 5.27 to 6.59 pg, and consisted of G. curvata, G. cyrtoloba(CC), and G. falcata (FF). The polyploid species, G. tabacina2n=80 (AABB, BBB¹B¹), G. tomentella 2n=78 and 2n=80 (AAEE andDDEE, respectively) contained amounts approximating to the sumsof the respective parental diploid species thought to have givenrise to these allotetraploids. Intraspecific variation was detectedin the DNA content of G. canescens. Within the overall distributionof DNA amounts found in A genome species, each genome containeda range of DNA contents specific to that species. This phenomenonwas also detected amongst B genome species.     

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.     

Chromosome phylogeny of <Emphasis Type="Italic">Zamia</Emphasis> and <Emphasis Type="Italic">Ceratozamia</Emphasis> by means of Robertsonian changes detected by fluorescence <Emphasis Type="Italic">in situ</Emphasis> hybridization (FISH) technique of rDNA

 Appearance and location of 45S rDNA and 5S rDNA signals were compared in chromosomes of nine species of the aneuploid Zamia and their taxonomically and phylogenetically closely related Ceratozamia mexicana. The 45S rDNA signal was detected in the proximal region of six chromosomes in Zamia angustifolia, Z. integrifolia, Z. pumila and Z. pygmaea (all 2n=16); in the proximal region of 6–14 chromosomes in Z. furfuracea, Z. loddigesii, Z. skinneri and Z. vazquezii (all 2n=18); and on the proximal region of 20 chromosomes in Z. muricata (2n=23). The 5S rDNA signals were commonly seen near the terminal region of the short arm of two metacentric chromosomes in the four species with 2n=16 and Z. furfuracea, Z. loddigesii and Z. vazquezii with 2n=18. Other 5S rDNA signals were seen near the terminal region of two terminal-centromeric chromosomes in Z. skinneri and near the terminal region of a metacentric and a telocentric chromosomes in Z. muricata. In contrast, those with 45S and 5S rDNA signals were exhibited in chromosomes of Ceratozamia mexicana in a different manner from those in the nine species of Zamia; the 45S rDNA signal in the terminal region of four metacentric and two submetacentric chromosomes and the 5S rDNA signal near the proximal region of two metacentric chromosomes. Received November 1, 1999 Accepted January 10, 2001     

Intersubgeneric hybridization of soybeans with a wild perennial species,Glycine clandestina Wendl

Summary The exploitation of wild perennial species of subgenus Glycine has been formidable in soybean breeding programs because of extremely poor crossability and an early pod abortion. The combination of gibberellic acid application to hybridized gynoecia and improved seed culture media formulations resulted in a new intersubgeneric hybrid between Glycine max (L.) Merr. (2n=40) and G. clandestina Wendt. (2n=40). Of the 31 immature seeds cultured, 1 regenerated 21 plants through organogenesis while the remaining 30 failed to germinate. All the regenerated plants were similar morphologically, carried expected 2n=40, possessed hybrid isozyme patterns and were completely sterile. Complete absence of chromosome pairing was observed in 40.9% sporocytes. The occurrence of 1 to 6 loosely paired rod bivalents suggests some possibilities of allosyndetic pairing. Hybrid plants set aborted pods after backcrossing to G. max.     

中国17种蔷薇属植物45S和5S的rDNA分布研究

为了探寻蔷薇属植物亲缘关系及系统发育研究的分子细胞遗传学证据,该研究采用双色FISH(荧光原位杂交)技术,对原产中国7个组的17种蔷薇属植物的45S和5S rDNA进行了定位分析。结果表明:(1)多数蔷薇属植物1组染色体对应1个45S rDNA位点和1个或2个5S rDNA位点,偶尔出现1~2个rDNA位点的丢失,但复伞房蔷薇(Rosa brunonii)的1组染色体对应了2个45S rDNA位点。(2)二倍体的蔷薇属植物至少有1对5S rDNA位点与45S rDNA位点共定位,而四倍体材料的5S rDNA位点与45S rDNA位点没有共定位,但所有四倍体材料均至少有1种rDNA信号纯合,表明它们应为二倍体直接加倍产生的同源四倍体。(3)绝大多数材料45S rDNA位于染色体短臂、5S rDNA位于染色体长臂,但缫丝花(R. roxburghii f. roxburghii)有1个5S rDNA信号位于染色体的短臂上,表明它与蔷薇属其他种的亲缘关系较远。(4)阿克苏地区和伊犁地区的疏花蔷薇的核型不同,且45S和5S rDNA的数量和位置不同,分子细胞遗传学证据也支持阿克苏地区的疏花蔷薇应为疏花蔷薇的新变种。(5)该研究中共有8个二倍体和6个四倍体蔷薇属植物的双色FISH为首次报道。研究认为,无论二倍体还是四倍体蔷薇属植物中出现的异形同源染色体、rDNA信号位置在同源染色体上的差异以及rDNA信号的增加和丢失,可能都与染色体结构变异和染色体重组有关,在分子细胞遗传学水平上证明染色体结构变异和染色体重组在蔷薇属植物演化过程中具有重要的作用。     

Gene mapping of 28S and 5S rDNA sites in the spined loach Cobitis taenia (Pisces, Cobitidae) from a diploid population and a diploid–tetraploid population

We compare the chromosomal 28S and 5S rDNA patterns of the spined loach C. taenia (2n = 48) from an exclusively diploid population and from a diploid–polyploid population using 28S and 5S rDNA probe preparation and labelling, and fluorescence in situ hybridization (FISH). The 5S rDNA was located in two to three chromosome pairs, and separated from the 28S loci for the males and one female (F1) from the diploid population. Loaches from a diploid–polyploid population, and one female (F2) from the diploid population were characterized by at least one chromosome pair with 5S and 28S overlapping signals. The fishes differed mainly in their number of 28S rDNA loci, located on 3–6 chromosomes. All individuals from both populations were characterized by one acrocentric chromosome bearing a 28S rDNA signal on the telomeres of its long arm. The number of major ribosomal DNA in the karyotype of C. taenia by FISH was always higher than the number of Ag-NORs. Our data confirm the extensive polymorphism of NORs in both populations, as already has been observed in closely related Cobitis species, and less polymorphic 5S rDNA pattern. However, this preliminary result highlights the need for a wider scale study.     

Dual-color FISH karyotype analyses using rDNAs in three Cucurbitaceae species

Dual-color fluorescence in situ hybridization (FISH) analysis of three Cucurbitaceae species from different genera was conducted using 5S and 45S rDNA probes. In Benincasa hispida (Thunb.) Cogn. (2n=24), the 45S rDNA probe hybridized on two chromosomes, one in the short arm of a medium-sized metacentric chromosome and another at the satellite of a chromosome. The 5S rDNA hybridized at a site proximal to the centromere of the same short arm of the 45S rRNA gene locus that occupied almost the entire short arm. For Citrullus lanatus (Thunb.) Matsum & Nakai (2n=22), the 45S rDNA probe hybridized at sites in the short arms of two chromosomes and the 5S rDNA probe was co-localized with the 45S rRNA locus at the region proximal to the centromere in one chromosome. The 45S rRNA loci occupied almost all of the short arms in both chromosomes. In Cucurbita moschata Duch. (2n=40), the 45S rDNA probe hybridized in five chromosomes in which the 45S rRNA genes occupied almost two-thirds of the chromosomes in two large chromosomes and the entire short arm of a medium-sized chromosome. Two other loci were present in two medium-sized chromosomes, one in the proximal region in the short arm of a chromosome and another at the tip of the long arm of a chromosome. Chromosomes of B. hispida were relatively larger than those of the other two species. The karyotype of B. hispida is composed of two metacentrics and 10 submetacentrics, while that of C. lanatus is composed of seven metacentrics and four submetacentrics and that of C. moschata is composed of 18 metacentrics and two submetacentrics. Comparative chromosome evolution among the three Cucurbitaceae species was attempted using the karyotypes and the chromosomal distribution patterns of the 5S and 45S rDNAs. The results presented herein will be useful in elucidating the phylogenetic relationships among Cucurbitaceae species, and will provide basic data for their breeding programs.     

Genomic in situ hybridization inArachis (Fabaceae) identifies the diploid wild progenitors of cultivated (A. hypogaea) and related wild (A. monticola) peanut species

Genomic in situ hybridization offers a powerful tool for investigating genome organisation and evolution of taxa known, or suspected, to be allopolyploids. The question of the diploid progenitors of cultivated peanut (Arachis hypogaea, 2n=4x=40) has been the subject of numerous studies at cytogenetical, cytochemical, biochemical and molecular levels, but no definitive conclusions have been reached. The biotinylated total genomic DNA from potential diploidArachis species were separately hybridized in situ to root tip chromosomes ofA. hypogaea and wild speciesA. monticola (2n=4x=40) without or mixed with an excess of unlabelled DNA from the species not used as a probe. Among the range of different species combinations used, the strong and uniform signals given by labelledA. ipaensis DNA when hybridized toA. hypogaea andA. monticola in combination with unlabelledA. villosa DNA indicates that overall molecular composition of twenty chromosomes ofA. hypogaea andA. monticola is very similar toA. ipaensis chromosomes. ProbingA. hypogaea andA. monticola chromosomes with labelled genomic DNA fromA. villosa mixed with unlabelled DNA fromA. ipaensis likewise labelled strongly and uniformly the other twenty chromosomes. BarringA. ipaensis, all the diploidArachis species presently investigated had characteristic centromeric bands in the twenty chromosomes within the complement indicating a clear division ofA. ipaensis from other species. InA. hypogaea andA. monticola only twenty chromosomes showed centromeric bands. These results (i) confirm the allopolyploid nature ofA. hypogaea andA. monticola, (ii) strongly support the view that wildA. monticola and cultivatedA. hypogaea are very closely related, and (iii) indicate thatA. villosa andA. ipaensis are the diploid wild progenitors of the tetraploid species studied. The present results also reveal that the nucleolus organizing region (NOR) originating fromA. villosa alone is expressed in the two tetraploid species.     

海岛棉原位杂交及核型比较

采用Ａ染色体组（Ａ genome)棉种亚洲基因组ＤＮＡ（gDNA)为探针,对海岛棉体细胞染色体进行荧光原位杂交（ＦＩＳＨ）,结果发现５２条染色体中有杂交信号与否的刚好各一半,从而直观地证实了海岛棉异源双二倍体起源的理论,但是,染色体的长度Ａ亚组的并非全部大于Ｄ亚组的。海岛棉基于ＦＩＳＨ图像的核型公式为：２n=4x=52=38m 14sm(sat)。３对随体染色体序号分别是Ａ亚组第１１、Ｄ亚组第２２和２５,均属于近中部着丝点（sm)类型,随体均在各自杂色体的短臂上,而且与所有染色体无关晨同一亚组起源。Ａ亚组第５、６和９对染色体长臂发生长了片段的易位,易位的片段较大,占所在染色体和蔗的百分率依次为１９．２１％、１７．６９％和１２．８８％,在Ｄ亚组１３对染色体中,最少５对的着丝点区域多或少地显示出与亚洲棉gDNA探针杂交的红色荧光信号,意味着有Ａ亚组染色体的交换。     

Assembly and annotation of a draft genome sequence for Glycine latifolia,a perennial wild relative of soybean

Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939‐Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked‐reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome‐scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91‐bp centromere‐specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92‐bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein‐coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine‐specific orthologous gene families. A total of 304 putative nucleotide‐binding site (NBS)‐leucine‐rich‐repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR‐NBS‐LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR‐receptor‐like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost‐effectiveness of the application of Chromium linked‐reads in diploid plant genome de novo assembly.     

Sex chromosomes and associated rDNA form a heterochromatic network in the polytene nuclei of Bactrocera oleae (Diptera: Tephritidae)

The olive fruit fly, Bactrocera oleae, has a diploid set of 2n?=?12 chromosomes including a pair of sex chromosomes, XX in females and XY in males, but polytene nuclei show only five polytene chromosomes, obviously formed by five autosome pairs. Here we examined the fate of the sex chromosomes in the polytene complements of this species using fluorescence in situ hybridization (FISH) with the X and Y chromosome-derived probes, prepared by laser microdissection of the respective chromosomes from mitotic metaphases. Specificity of the probes was verified by FISH in preparations of mitotic chromosomes. In polytene nuclei, both probes hybridized strongly to a granular heterochromatic network, indicating thus underreplication of the sex chromosomes. The X chromosome probe (in both female and male nuclei) highlighted most of the granular mass, whereas the Y chromosome probe (in male nuclei) identified a small compact body of this heterochromatic network. Additional hybridization signals of the X probe were observed in the centromeric region of polytene chromosome II and in the telomeres of six polytene arms. We also examined distribution of the major ribosomal DNA (rDNA) using FISH with an 18S rDNA probe in both mitotic and polytene chromosome complements of B. oleae. In mitotic metaphases, the probe hybridized exclusively to the sex chromosomes. The probe signals localized a discrete rDNA site at the end of the short arm of the X chromosome, whereas they appeared dispersed over the entire dot-like Y chromosome. In polytene nuclei, the rDNA was found associated with the heterochromatic network representing the sex chromosomes. Only in nuclei with preserved nucleolar structure, the probe signals were scattered in the restricted area of the nucleolus. Thus, our study clearly shows that the granular heterochromatic network of polytene nuclei in B. oleae is formed by the underreplicated sex chromosomes and associated rDNA.