A low-copy-number Sorghum DNA sequence that detects hypervariable EcoRV fragments

A sorghum genomic DNA clone that hybridized on Southern blots in simple but different patterns to fragments produced by digestion of DNA from the parents of an F₂ mapping population was hybridized to EcoRV-digested DNA from 53 accessions. Forty-six different fragment patterns were observed, each comprised of from one to ten bands. Much less variability was detected in EcoRI than EcoRV digests of a selected subset of the accessions. Base-sequence analysis of the clone did not reveal a functional identity for the sequence and the clone does not contain repeated sequences often associated with hypervariable loci. Clones such as this will be especially useful in evaluating germplasm diversity and in identifying the potential parentage of hybrids.     

Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers

 The level of genetic diversity and the population genetic structure of sorghum landraces from North-western Morocco have been investigated based on direct field-sampling using both allozyme and microsatellite markers. As expected, microsatellite markers showed a much higher degree of polymorphism than allozymes, but relative measures of genetic structure such as Wright’s inbreeding coefficient F _IS and Nei’s coefficient of genetic differentiation G _ST were similar for the two sets of markers. Substantial inbreeding was found to occur within fields, which confirms that sorghum is predominantly selfing under cultivation. Most of the genetic diversity in Moroccan landraces occurs within fields (more than 85%), as opposed to among fields or among regions, a result which contrasts to those of studies based on accessions from germplasm collections. It is suggested that individual fields of sorghum constitute valuable units of conservation in the context of in situ conservation practices. Received: 8 December 1998 / Accepted: 28 December 1998     

Genetic diversity assessment in Somali sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) accessions using microsatellite markers

In the north-western region of Somalia, bordering Ethiopia, sorghum represents an important resources for human and animal nutrition. The critical situation of Somalia is threatening the preservation of this valuable resource and it becomes urgent to develop a strategy of correct evaluation of the sorghum germplasm in order to promote conservation and preservation programs. Microsatellites, also known as Simple Sequence Repeats (SSRs), are reproducible molecular markers useful in assessing the level of genetic diversity of plants. A total of 5 sorghum SSR-specific primer pairs were used to assess the genetic diversity of Somali sorghum landraces. Extensive variation was found at the microsatellite loci analysed, except for a locus that resulted in a monomorphic for some accessions. Considerable differences were found between total and effective number of alleles indicating non uniform allele frequency. Moreover allele frequency at a single locus significantly changed among accessions. Total gene diversity calculated for each locus ranged from 0.44 to 0.79. Most of the genetic diversity occurred within accessions demonstrating that accessions are not under selection processes and/or there is a continuous exchange of genes between sorghum populations. In any case, the patterns of clustering were significantly affected by the presence/absence of some alleles with high discriminant weight. Accessions Carabi, Abaadiro, Masego Cas and Masego Cad represent distinct genotypes confirming finding observed in previous phenotypic studies. The results highlight the central role of local farmers in maintaining and shaping local germplasm.     

Improved Culture Media for Embryogenic Callus Generation in Sorghum [<i>Sorghum bicolor</i> (L.) Moench]

Many attempts on optimization of sorghum [Sorghum bicolor (L.) Moench] tissue culture induction media have been made, but the culture system remains with some bottlenecks compared to that of other crops. This study aimed at assessing the suitability of various induction media to produce embryogenic callus (yellow and friable) with high induction rates and reduced phenolic exudation. The six culture medium modifications: 3 based on Murashige and Skoog (MS) medium and one each based on Chu N6, Gamborg B5 and 190-2 media respectively were applied in the culture of mature embryos from 10 sorghum genotypes. Although there was a genotype influence on the attainment of a yellow callus, friability of the callus was determined to be dependent on the culture medium and not the genotype. Half strength MS medium with 0.2 mg/l 2,4-D with 2.8 g/l Gelrite® as the gelling agent modified with 1.0 g/l KH₂PO₄, 1.0 g/l L-proline, 1.0 g/l L-asparagine and 0.16 mg/l CuSO₄·5H₂O (type E) was found to be the most effective resulting in about 60% yellow coloured callus induction with 25% friability. Addition of CuSO₄·5H₂O, KH₂PO₄, L-proline and L-asparagine significantly reduced the phenolic production. Half strength MS medium was observed to contribute to quality callus production when compared to full strength MS media modified with the compounds. The half strength MS medium was also observed to suppress phenolic production. Medium 190-2 produced the highest regeneration frequency (40%) among the 3-regeneration media tested. The results provide information on a suitable sorghum callus induction medium necessary for embryogenesis.     

Population genetic diversity of <Emphasis Type="Italic">Curcuma zedoaria</Emphasis> (Christm.) Roscoe – a conservation prioritised medicinal plant in Bangladesh

Curcuma zedoaria (Christm.) Roscoe, a member of the family Zingiberaceae, is one of the most widely distributed Curcuma species in Bangladesh. It is a well-known and important species because of its medicinal and horticultural values. However, some plant populations are predicted to be depleted due to habitat destruction and due to extensive collection by local inhabitants. In order to estimate the level of genetic diversity within and between natural populations, RAPD analyses were performed using individual plants from different populations. We used Shannon’s index to partition genetic diversity which clearly demonstrated that hilly populations of Srimangal, Chittagong and Sitakundu maintain rather higher genetic diversity than that of plain land and plateau land populations of Savar and Birganj, respectively. We found a high intrapopulational (H′_pop/H′_sp) genetic diversity of 0.717 that was higher than the interpopulation diversity G _ST[(H′_sp−H′_pop)/H′_sp] value of 0.283. Principal Coordinates Analysis (PCoA) showed that individuals of the hilly populations were combined in one group, separated from the plain land and plateau land populations. From a conservation point of view, our results suggest that special attention should be kept on the small populations of plain and plateau lands that are critically threatened due to high anthropogenic activities.     

Cloning and characterization of a centromere-specific repetitive DNA element from Sorghum bicolor

 A 823-bp Sau3AI fragment (pSau3A10) was subcloned from a sorghum bacterial artificial chromosome (BAC) clone, 13I16, that contains DNA sequences specific to the centromeres of grass species. Sequence analysis showed that pSau3A10 consists of six copies of an approximately 137-bp monomer. The six monomers were organized into three dimers. The monomers within the dimers shared 62–72% homology and the dimers were 79–82% homologous with each other. Fluorescence in situ hybridization (FISH) analysis indicated that the Sau3A10 family is present only in the centromeres of sorghum chromosomes. Sequencing, Southern hybridization, and Fiber-FISH analyses indicated that the Sau3A10 family is tandemly arranged and is present in uninterrupted stretches of up to at least 81 kb of DNA. Slot-blot analysis estimated that the Sau3A10 family constitutes 1.6–1.9% of the sorghum genome. The long stretches of Sau3A10 sequences were interrupted by other centromeric DNA elements. Southern analysis indicated that the Sau3A10 sequence is one of the most abundant DNA families located in sorghum centromeres and is conserved only in closely related sorghum species. Methylation experiments indicated that the cytosine of the CG sites in sorghum centromeric regions is generally methylated. The structure and organization of the Sau3A10 family shared similarities with centromeric DNA repeats in other eukaryotic species. It is suggested that the Sau3A10 family is probably an important part of sorghum centromeres. Received: 11 November 1997 / Accepted: 17 November 1997     

Genetic differentiation between populations of swimming crab <Emphasis Type="Italic">Portunus trituberculatus</Emphasis> along the coastal waters of the East China Sea

Portunus trituberculatus is a commercially important species widely spread in the East China Sea. Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 213 individuals from six localities (Changjiang Estuary, Shengsi Islands, Zhoushan Islands, Dongtou Islands, Dinghai Bay, and Quanzhou Bay) ranging from north (31°21′N) to south (24°55′N) coastal waters of the East China Sea. Overall, a total of 27 mtDNA haplotypes and 21 variable sites were detected in the 787 bp segment of COI gene. Analysis of mtDNA COI sequence data revealed that crabs from the six localities were characterized by moderately high haplotypic diversity (h = 0.787 ± 0.026), while sequence divergence values between haplotypes were relatively low (π = 0.00241 ± 0.00098). Each population was characterized by a single most frequent haplotype, shared among all six localities, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population. However, neither the neighbor-joining tree nor the minimum spanning network (MSN) based on the haplotype data exhibited geographical patterns of the six populations. Mismatch distribution analysis of P. trituberculatus individuals sampled from the six localities suggested that sudden population expansion might have occurred in CJ and SS population that might be consistent with over-exploitation of the swimming crab. Analysis of molecular variance (AMOVA) and F _ST statistics showed that significant genetic differentiation existed among the SS, ZS, DT, DH, and QZ populations, suggesting that gene flow might be reduced, even between the geographically close sites, despite the high potential of dispersal. The possible causes of the observed genetic heterogeneity among the P. trituberculatus populations and the potential applications of the mtDNA COI marker in the artificial breeding and fisheries management are discussed. Handling editor: C. Sturmbauer     

Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor

Summary Fifty-six accessions of cultivated and wild sorghum were surveyed for genetic diversity using 50 low-copy-number nuclear DNA sequence probes to detect restriction fragment length polymorphisms (RFLPs). These probes revealed greater genetic diversity in wild sorghum than in cultivated sorghum, including a larger number of alleles per locus and a greater portion of polymorphic loci in wild sorghum. In comparison to previously published isozyme analyses of the same accessions, RFLP analysis reveals a greater number of alleles per locus. Furthermore, many RFLP alleles have frequencies between 0.25–0.75, while the vast majority of isozyme alleles are either rare (< 0.25) or near fixation (> 0.75). Correlations between genetic and geographic distances among the accessions were stronger when calculated with RFLP than with isozyme data. Systematic relationships revealed by nuclear and chloroplast restriction site analysis indicate that cultivated sorghum is derived from the wild ssp. arundinaceum. The portion of the wild gene pool most genetically similar to the cultivars is from central-northeastern Africa. Previous published data also suggested that this is most likely the principal area of domestication of sorghum. Introgression between wild and cultivated sorghum was inferred from disconcordant relationships shown by nuclear and chloroplast DNA markers. Introgression apparently occurs infrequently enough that the crop and its wild relatives maintain distinct genetic constitutions.     

Screening for drought tolerance in Sorghum using cell culture

Summary Callus growth from 10 cultivars ofSorghum bicolor (L.) Moench was measured with increasing levels of polyethylene glycol (PEG) as an osmoticum in the medium to determine whether differences among these cultivars at the cellular level in response to osmotic stress existed. These cellular ratings were compared to field ratings from the 10 tolerant-to-susceptible cultivars when grown under drought conditions to determine whether cellular ratings corresponded to differences in drought tolerance at the plant level. Callus cultures were grown on Murashige and Skoog inorganic salt formulation plus vitamins, 2,4-dichlorophenoxyacetic acid (2,4-D), kinetin and sucrose, supplemented with 0 to 25% (wt/vol) PEG corresponding to −0.2 to −1.62 MPa osmotic potential. Results suggest that PEG-induced osmotic stress on callus cultures can be used to screen sorghum cultivars for potential early field (preflowering) drought tolerance. This implies that at least a component of the early field drought tolerance in sorghum may have a cellular basis. This study was supported by U.S. Agency for International Development Grant AID/DSAN/XII/G-0149, and USDA Competitive Grants Program.     

Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p <0.001). However, morphological and AFLP data showed non-significant correlation (p >0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.     

High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum)

Theobroma grandiflorum (cupuassu) is an important fruit tree native to the Brazilian Amazon. Establishing the genetic diversity and structure of populations is critical to define long-term strategies for cupuassu conservation presently threatened by rapid deforestation. Three natural populations collected at the putative center of diversity, three groups of accessions established at a germplasm collection, and one derived from commercial plantings were analyzed. The genetic diversity was assessed using 21 polymorphic microsatellite loci originally developed for Theobroma cacao, disclosing a total of 113 alleles. The estimated genetic diversity parameters averaged over cupuassu populations (A = 3.53 alleles per locus; H _e = 0.426; H _o = 0.346) were lower than the values reported for other Neotropical tree species. The three natural populations presented a positive and significant fixation index (f), ranging from 0.133 to 0.234. Cupuassu apparently adhered to a general pattern of genetic diversity structure of some Neotropical tree species occurring at low densities, with a low intrapopulation genetic diversity and important levels of endogamy, possibly due to biparental inbreeding derived from the presence of spatial genetic structure in the populations. A high level of genetic divergence was detected among the natural populations (θ _p = 0.301), a strong differentiation caused by limited gene flow, and suggesting that human interference in spreading and/or stimulating plantings might have had a smaller effect than expected. The approximate location of the T. grandiflorum center of diversity could not be confirmed by analyzing natural populations from the putative region.     

Sorghum root length density and the potential for avoiding striga parasitism

Striga hermonthica is a serious root parasite of sorghum in the semiarid tropics. Successful parasitism is dependent on interactions of Striga seeds and host roots. Several sorghum cultivars have been found which resist parasitism. The basis of resistance is not well known. One possible method for reducing the chances of parasitism is by restricted host root development. This research was conducted to evaluate this hypothesis in sorghum known to possess resistance to parasitism by Striga.Root length density of 21-day-old pot-grown resistant cultivars, Framida, N-13, IS-9830, Tetron and P-967083, were compared to that of the susceptible check, Dabar, using the line intercept method of measuring root length. There was no significant difference between resistant cultivars and the susceptible cultivar Dabar. The RLD of resistant P-967083 however was significantly less than Framida, another resistant cultivar.The RLD of Dabar was compared to that of Framida and P-967083 in USA and Niger field trials. Root length density was determined on soil cores taken at flowering with a Giddings Soil Sampler. Each core was divided into 10-cm fractions for estimating RLD by the line intercept method. In the USA Dabar had significantly greater RLD than the two resistant cultivars in the upper 10-cm portion of the soil profile, but only significantly greater than P-967083 in the 10–20-cm portion. Significant differences in RLD between susceptible and resistant cultivars were not found at depths between 20–60 cm. In field trials in Niger, RLD of Dabar was significantly greater than either resistant cultivar in the (0 to 30 cm) portion of the soil core. These results suggest that part of the Striga resistance of P-967083 and perhaps Framida may be a result of avoiding interactions between parasitic seeds and host roots.     

A RFLP linkage map of Sorghum bicolor (L.) Moench

A RFLP linkage map of sorghum composed principally of markers detected with sorghum low-copy-number nuclear DNA clones has been constructed. The map spans 1789 cMs and consists of 190 loci grouped into 14 linkage groups. The 10 largest linkage groups consist of from 10 to 24 markers and from 103 to 237 cMs, and the other 4 linkage groups consist of from 2 to 5 markers and from 7 to 62 cMs. The map was derived in Sorghum bicolor ssp. bicolor by analysis of a F₂ population composed of 50 plants derived from a cross of IS 3620C, a guinea line, and BTx 623, an agronomically important inbred line derived from a cross between a zera zera (a caudatum-like sorghum) and an established kafir line. The restriction fragment length polymorphism (RFLP) frequency detected in this population using polymerase chain reaction (PCR)-amplifiable low-copy-number sorghum clones and five restriction enzymes was 51%. A minimal estimate of the number of clones that detect duplicate sequences is 11 %. Null alleles occurred at 13% of the mapped RFLP loci.     

Chloroplast DNA polymorphism in fertile and male-sterile cytoplasms of sorghum (Sorghum bicolor (L.) Moench)

Summary Restriction endonuclease patterns of chloroplast DNA (cpDNA) were consistently distinguishable between fertile and male-sterile cytoplasms of sorghum [Sorghum bicolor (L.) Moench], whereas no differences in restriction patterns of cpDNA among male-sterile (A₁) lines, including six isocytoplasmic strains, were revealed in this study. It is suggested that chloroplast DNA may contribute to the male sterility of A₁ lines used currently in hybrid sorghum production.This research was supported by a research grant from Kansas Grain Sorghum Commission, Kansas Board of Agriculture. Contribution 90-293-J from the Kansas Agricultural Experiment Station     

Scaling patterns of plankton diversity: a study of ciliates in a tropical coastal lagoon

Although spatial and temporal variation in plankton diversity is regularly investigated in surveys, experiments, and models, there is a lack of methods for predicting spatial patchiness of plankton diversity. We develop and apply a suite of geostatistical and multiple-regression analysis tools to assess ciliate diversity in a tropical coastal lagoon; these methods can predict spatial and temporal patterns of diversity, provide error estimates associated with these predictions, and assess which environmental factors may drive diversity patchiness. Geostatistical analysis was applied to H′ (Shannon diversity index) from 25 to 35 data collected from a sampling grid (40 × 40 m), and 10 dispersed lagoonal sites, in the dry and rainy seasons, on numerous occasions. Conditional simulation and kriging were used to predict diversity at the lagoonal and small scales, respectively. The relationship between diversity (H′) and the environment was examined by multiple-regression analysis. Thirty-six ciliate morphospecies occurred; H′ ranged from 0 to 1.9 and was patchy. Multiple regression indicated ciliate diversity changed seasonally, increasing when the sand bar was open and the lagoon was connected with the sea. Geostatistical analysis extended the recognition that seasonal changes alter diversity: when the rainy season produced a variable environment, relatively small scale patches and diversity gradients occurred; in the dry season, when the lagoon was physically uniform, larger and fewer diversity patches occurred; at the sublagoonal scale, diversity patches were similarly structured in the two seasons. Results indicate environmental variability and immigration can be the main drivers behind ciliate diversity in the lagoon. We recommend the patterns these data reveal and methods we employ be considered when further studies are continued to examine diversity on local and larger scales. Handling editor: S. Declerck     

Allelic variation of the β-, γ- and δ-kafirin genes in diverse Sorghum genotypes

The β-, γ- and δ-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic diversity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally diverse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic α-kafirins. Significant diversity was found for each locus, with the cysteine-rich β-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce β-kafirin. An analysis of flour viscosity reveals that these β-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less diversity at the protein level within the cysteine-rich γ-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the δ-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the δ-kafirin locus displayed comparatively low genetic variation. This study has identified genetic diversity in all single copy seed storage protein genes, including a null mutant for β-kafirin in Sorghum.     

Causal analysis of the diversity of medusae in East China Sea

Based on the maritime data collected from 23°30′–33°00′ N and 118°30′–128°00′ E of the East China Sea (ECS) in four seasons during 1997–2000, the dynamics of medusae diversity and their causes were analyzed. A total of 103 medusae species were identified, and these species mainly distributed in the southern and northern offshore areas of the ECS. Species diversity index (H′) of medusae was higher in the south than those in the north, higher in summer and winter than in spring and autumn, and higher in offshore than in the nearshore areas. The species number was closely correlated with H′ value, whereas the abundance of species had no significant relationship with the diversity index. The lower H′ value of the nearshore in spring and autumn resulted from the aggregation of Muggiaea atlantica in the south nearshore and Diphyes chamissonis in the north nearshore. In addition, water temperature, followed by salinity, is the main environmental factor influencing the distribution of species diversity. The H′ value was related to the water temperature at the 10 m layer in winter and spring, and it was associated with the surface water temperature in summer and with the 10 m-salinity-layer in autumn. In spring and summer, the isoline distribution of H′ value reflected the direction of the Taiwan Warm Current and the variation of the water masses in the ECS. In winter, the isoline of the H′ value indicated the incursion of Kuroshio current. In conclusion, the H′ isoline is an good indicator for water masses in ECS. __________ Translated from Biodiversity Science, 2006, 14(6): 508–516 [译自:生物多样性]     

Genetic variations in the hybrids of rice (Oryza sativa) and sorghum (Sorghum vulgare)

Summary Some of results from morphological and cytological observations and esterase-isozyme studies of a rice-sorghum hybrid are presented in this paper. There is a great diversity of morphological characters and some special characteristics in the progenies of the hybrids of rice with sorghum. The meiosis of pollen mother cells in the early generations of the hybrid was found to be abnormal. One main band coinciding with one found in sorghum but lacking in rice appeared in the majority of the hybrid lines. This band is characteristic of a are the specificities of the distant hybridization of rice and sorghum, and is rarely observed in the intervariety hybrids or hybrids between subspecies of Oryza sativa, indica and japonica. On the basis of these facts we concluded that the hybrids obtained are true hybrids of rice and sorghum.     

Identification of a New Race of Sporisorium reilianum and Characterization of the Reaction of Sorghum Lines to Four Races of the Head Smut Pathogen

Sporisorium reilianum is the causal agent of head smut on sorghum and maize. In order to effectively utilize host resistance to control this important disease in crops, it is necessary to monitor changes in disease dynamics and virulence of the pathogen. An outbreak of head smut was recently observed in a sorghum field, near Gaoping, Shanxi, China, and research was undertaken to characterize a putative new race of S. reilianum. A set of differential sorghum lines with resistance to several conventional races was used to characterize the newly collected isolate of S. reilianum. The reactions of differential cultivars/germplasm lines to the new isolate indicate that it is a new physiological race of S. reilianum. The new race is highly virulent on sorghum line A₂V4 and its hybrid, Jinza 12, that are known as resistant to all existing Chinese races of S. reilianum, including races 1, 2, and 3. The new isolate of S. reilianum is different from all of the described races of the pathogen; thus, it is designated as race 4 of S. reilianum. Furthermore, a collection of 34 sorghum genotypes including commercial cultivars and germplasm lines was evaluated for disease reaction to the newly described race and the three known races of the pathogen.