Factors modulating the levels of the allelochemical sorgoleone in Sorghum bicolor

Sorgoleone is the major component of the hydrophobic root exudate of sorghum [Sorghum bicolor (L.) Moench]. The presence of this allelochemical is intrinsically linked to root growth and the development of mature root hairs. However, factors modulating root formation and the biosynthesis of sorgoleone are not well known. Sorgoleone production was independent of early stages of plant development. The optimum temperature for root growth and sorgoleone production was 30°C. Seedling development and sorgoleone levels were greatly reduced at temperatures below 25°C and above 35°C. The level of sorgoleone was also sensitive to light, being reduced by nearly 50% upon exposure to blue light (470 nm) and by 23% with red light (670 nm). Applying mechanical pressure over developing seedlings stimulated root formation but did not affect the biosynthesis of this lipid benzoquinone. Sorgoleone production did not change in seedlings exposed to plant defense elicitors. On the other hand, sorgoleone levels increased in plants treated with a crude extract of velvetleaf (Abutilon theophrasti Medik.) root. This stimulation was not associated with increased osmotic stress, since decreases in water potential (Ψ_w) by increasing solute concentrations with sorbitol reduces sorgoleone production. Sorgoleone production appears to be constitutively expressed in young developing sorghum plants. Other than with temperature, changes in the environmental factors had either no effect or caused a reduction in sorgoleone levels. However, the stimulation observed with velvetleaf root crude extract suggests that sorghum seedlings may respond to the presence of other plants by releasing more of this allelochemical.     

Population differences in levels of linkage disequilibrium in the wild

Information about the levels of linkage disequilibrium (LD) in wild animal populations is still limited, and this is true particularly with respect to possible interpopulation variation in the levels of LD. We compared the levels and extent of LD at the genome‐wide scale in three Siberian jay (Perisoreus infaustus) populations, two of which (Kuusamo and Ylläs) represented outbred populations within the main distribution area of the species, whereas the third (Suupohja) was a semi‐isolated, partially inbred population at the margin of the species’ distribution area. Although extensive long‐range LD (>20 cM) was observed in all three populations, LD generally decayed to background levels at a distance of 1–5 cM or c. 200–600 kb. The degree and extent of LD differed markedly between populations but aligned closely with both observed levels of within‐population genetic variation and expectations based on population history. The levels of LD were highest in the most inbred population with strong population substructure (Suupohja), compared with the two outbred populations. Furthermore, the decay of LD with increasing distance was slower in Suupohja, compared with the other two populations. By demonstrating that levels of LD can vary greatly over relatively short geographical distances within a species, these results suggest that prospects for association mapping differ from population to population. In this example, the prospects are best in the Suupohja population, given that minimized marker genotyping and a minimum marker spacing of 1–5 cM (c. 200–600 kb) would be sufficient for a whole genome scan for detecting QTL.     

An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench.

We report the development, testing, and use (for genetic mapping) of a large number of polymerase chain reaction (PCR) primer sets that amplify DNA simple sequence repeat (SSR) loci of Sorghum bicolor (L.) Moench. Most of the primer sets were developed from clones isolated from two sorghum bacterial artificial chromosome (BAC) libraries and three enriched sorghum genomic-DNA (gDNA) libraries. A few were developed from sorghum DNA sequences present in public databases. The libraries were probed with radiolabeled di- and trinucleotide oligomers, the BAC libraries with four and six oligomers, respectively, and the enriched gDNA libraries with four and three oligomers, respectively. Both types of libraries were markedly enriched for SSRs relative to a size-fractionated gDNA library studied earlier. However, only 2% of the sequenced clones obtained from the size-fractionated gDNA library lacked a SSR, whereas 13% and 17% of the sequenced clones obtained from the BAC and enriched gDNA libraries, respectively, lacked a SSR. Primer sets were produced for 313 SSR loci. Two-hundred sixty-six (85%) of the loci were amplified and 165 (53%) of the loci were found to be polymorphic in a population composed of 18 diverse sorghum lines. (AG/TC)n and (AC/TG)n repeats comprised 91% of the dinucleotide SSRs and 52% of all of the SSRs at the polymorphic loci, whereas four types of repeats comprised 66% of the trinucleotide SSRs at the loci. Primer sequences are reported for the 165 polymorphic loci and for eight monomorphic loci that have a high degree of homology to genes. Also reported are the genetic map locations of 113 novel SSR loci (including four SSR-containing gene loci) and a linkage map composed of 147 SSR loci and 323 RFLP (restriction fragment length polymorphism) loci. The number of SSR loci per linkage group ranges from 8 to 30. The SSR loci are distributed relatively evenly throughout approximately 75% of the 1406-cM linkage map, but segments of five linkage groups comprising about 25% of the map either lack or contain few SSR loci. Mapping of SSR loci isolated from BAC clones located to these segments is likely to be the most efficient method for placing SSR loci in the segments.     

高粱遗传转化研究进展

高粱（Sorghum bicolor）是一种重要的多用途作物, 其遗传转化研究对于高粱的分子育种和分子遗传学基础研究都具有重要意义。该文对高粱遗传转化的方法、标记基因、遗传转化的启动子和受体系统进行了综述, 并提出了今后高粱遗传转化应当集中研究的问题。     

Non-cellulosic mixed linkage beta-D-glucan in sorghum, Sorghum bicolor (L.) Moench--localization and biological activity studies

Fluorescence of Calcofluor and Congo Red was observed in stained sections of sorghum grain (Sorghum bicolor (L.) Moench), especially in the sub-aleurone cells indicating the presence of mixed linkage beta-D-glucan. Relatively less fluorescence intensity was observed in the single layered (approximately 20 microns thick) aleurone. Alkali extracted beta-D-glucan (fraction 2) of sorghum showed 30% activation of rat peritoneal macrophages (in vitro) at 100 micrograms ml-1 concentration in 10 min. This activation was found mediated mainly through PLA2 pathway. A phagocytic index k of 0.102 +/- 0.008 was observed in vivo carbon clearance test in mice in the group treated with fraction 2. Accumulation of colloidal carbon particles in spleen and liver of mice was moderate in this group, compared to control.     

Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.     

Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor

Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.     

Sorghum bicolor - an important species for comparative grass genomics and a source of beneficial genes for agriculture

A high-resolution genetic, physical, and cytological map of the sorghum genome is being assembled using AFLP DNA marker technology, six-dimensional pooling of BAC libraries, cDNA mapping technology, and cytogenetic analysis. Recent advances in sorghum comparative genomics and gene-transfer technology are accelerating the discovery and utilization of valuable sorghum genes and alleles.     

基于MSAP和SSR标记的高粱甲基化连锁群LGC、LGD的构建

以高粱(Sorghum bicolor(L.)Moench)品种‘B_2V_4’和‘1383-2’杂交获得的F_2群体为材料,通过SSR和MSAP标记检测高粱基因组差异,构建其甲基化遗传连锁群。结果显示,高粱甲基化连锁群LGC含有3个SSR标记和23个甲基化标记,覆盖高粱基因组44.3 cM;甲基化连锁群LGD含有4个SSR标记和8个甲基化标记,覆盖高粱基因组46.2 cM。LGC上甲基化位点仅来源于EcoRⅠ/MspⅠ酶切组合,而LGD上有来源于EcoRⅠ/MspⅠ和EcoRⅠ/HpaⅡ两种酶切组合的甲基化位点。在LGC连锁群Xtxp 69附近检测到一个密集的甲基化位点区域。研究结果表明MSAP标记可以快速检测植物基因组甲基化差异,适用于构建甲基化连锁群。     

Patterns of linkage disequilibrium in the human genome

Particular alleles at neighbouring loci tend to be co-inherited. For tightly linked loci, this might lead to associations between alleles in the population a property known as linkage disequilibrium (LD). LD has recently become the focus of intense study in the hope that it might facilitate the mapping of complex disease loci through whole-genome association studies. This approach depends crucially on the patterns of LD in the human genome. In this review, we draw on empirical studies in humans and Drosophila, as well as simulation studies, to assess the current state of knowledge about patterns of LD, and consider the implications for the use of LD as a mapping tool.     

Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

Current genome-wide linkage-mapping single-nucleotide polymorphism (SNP) panels with densities of 0.3 cM are likely to have increased intermarker linkage disequilibrium (LD) compared to 5-cM microsatellite panels. The resulting difference in haplotype frequencies versus that predicted may affect multipoint linkage analysis with ungenotyped founders; a common haplotype may be assumed to be rare, leading to inflation of identical-by-descent (IBD) allele-sharing estimates and evidence for linkage. Using data simulated for the Genetic Analysis Workshop 14, we assessed bias in allele-sharing measures and nonparametric linkage (NPL all) and Kong and Cox LOD (KC-LOD) scores in a targeted analysis of regions with and without LD and with and without genes. Using over 100 replicates, we found that if founders were not genotyped, multipoint IBD estimates and delta parameters were modestly inflated and NPL all and KC-LOD scores were biased upwards in the region with LD and no gene; rather than centering on the null, the mean NPL all and KC-LOD scores were 0.51 +/- 0.91 and 0.19 +/- 0.38, respectively. Reduction of LD by dropping markers reduced this upward bias. These trends were not seen in the non-LD region with no gene. In regions with genes (with and without LD), a slight loss in power with dropping markers was suggested. These results indicate that LD should be considered in dense scans; removal of markers in LD may reduce false-positive results although information may also be lost. Methods to address LD in a high-throughput manner are needed for efficient, robust genomic scans with dense SNPs.     

Degradation of crude oil in the rhizosphere of Sorghum bicolor

Dissipation of petroleum contaminants in the rhizosphere is likely the result of enhanced microbial degradation. Plant roots may encourage rhizosphere microbial activity through exudation of nutrients and by providing channels for increased water flow and gas diffusion. Phytoremediation of crude oil in soil was examined in this study using carefully selected plant species monitored over specific plant growth stages. Four sorghum (Sorghum bicolor L.) genotypes with differing root characteristics and levels of exudation were established in a sandy loam soil contaminated with 2700 mg crude oil/kg soil. Soils were sampled at three stages of plant growth: five leaf, flowering, and maturity. All vegetated treatments were associated with higher remediation efficiency, resulting in significantly lower total petroleum hydrocarbon concentrations than unvegetated controls. A relationship between root exudation and bioremediation efficiency was not apparent for these genotypes, although the presence of all sorghum genotypes resulted in significant removal of crude oil from the impacted soil.     

Haplotype blocks and linkage disequilibrium in the human genome

There is great interest in the patterns and extent of linkage disequilibrium (LD) in humans and other species. Characterizing LD is of central importance for gene-mapping studies and can provide insights into the biology of recombination and human demographic history. Here, we review recent developments in this field, including the recently proposed 'haplotype-block' model of LD. We describe some of the recent data in detail and compare the observed patterns to those seen in simulations.     

DNA polymorphisms and linkage disequilibrium in the angiotensinogen gene

A number of recent studies have implicated the angiotensinogen gene in the aetiology of essential hypertension in Caucasian, Japanese and African Caribbean subjects. We have genotyped 153 healthy white Caucasian subjects at a dinucleotide repeat polymorphism and seven diallelic sites in the coding or flanking regions of the angiotensinogen gene, including one polymorphism not previously studied. We have also documented patterns of linkage disequilibrium between polymorphisms. There is evidence of variation in the frequency of several mutations when compared with published results from other Caucasian control populations, possibly due to cryptic ethnic differences between these groups. This should be considered in the design and interpretation of studies of the angiotensinogen gene. Received: 10 November 1995 / Revised: 25 March 1996     

Induced variability during the process of adaptation in Sorghum bicolor

The coefficient of variation of some anatomical and physiologicalparameters has been measured in plants of Sorghum bicolor (L.)Moench exposed to conditions inducing adaptation to salt. Thekinetic analysis of the variability of shoot DW and shoot Na⁺concentration revealed a specific phase of increase in variabilitybetween days 6 and 16 following exposure to salinity. The increasein variability observed in a population of adapted plants, ascompared to a population of control plants, appeared as a wholeplant process since variability for most of the parameters werepositively correlated. Variability within plant populationsof 11 Sorghum genotypes, each presenting a different capacityfor adaptation, was determined during the middle of the adaptationprocess. A strong linkage between the level of adaptation andthe increase in variability was observed. The relatively lowlevel of variability observed in populations of Sorghum varietieswhich did not adapt to salinity suggested that the increasein variability was not a direct consequence of exposure to stressconditions, but that it was specifically related to the adaptationprocess. The data presented suggest the occurrence of modificationsat the, level of genome expression during the adaptation process. Key words: Adaptation, resistance, variability, salinity, Sorghum     

Light induced changes in the polypeptide composition of Sorghum bicolor

Two dimensional gel electrophoresis resolved total protein extracted from Sorgum bicolor (L.) Moench shoots into 430 polypeptides detectable by silver staining. The relative amunts of 82 polypeptides increased and 192 decreased upon exposure of etiolated shoots to light. Total protein extracted from etiolated mesocotyls was resolved into 360 polypeptides. The relative amounts of 23 mesocotyl polypeptides increased and 5 decreased after light exposure. Of 274 polypeptides whose relative amounts was altered in shoots exposed to light, 189 were found in mesocotyls. The relative amounts of only 6 polypeptides showed the same response to light in mesocotyls as in shoots. Immunoblotting identified 2 subunits of phosphoenolpyruvate carboxylase (PEPCase) differing in isoelectric point and molecular weight. The 81 000 dalton subunit was the major subunit found in mesocotyls while the 95 000 dalton subunit was the major subunit found in green shoots suggesting that these subunits are derived from a non-photosynthetic and photosynthetic isozyme of PEPCase. In etiolated shoots but not in mesocotyls, light induced the 81 000 and 95 000 apparent molecular weight (MW) subunits of PEPCase, the subunit of pyruvate orthophosphate dikinase (PPDK) as well as the large and small subunits of ribulose-1,5-bisphosphate carboxylase (RuBPCase). Specific activity measurements indicated that light induced the accumulation of the peroxisomal enzyme hydroxypyruvate reductase and inhibited the accumulation of the mitochondrial enzyme serine hydroxymethyltransferase in both mesocotyls andshoots. NADP-glyceraldehyde-3-phosphate dehydrogenase activity was light induced in shoots but undetectable in mesocotyls. In shoots and meocotyls, light had little effect on the mitochondrial enzyme fumarase or the cytoplasmic enzyme NAD-glyceraldehyde-3-P-dehydrogenase.     

Phytochrome Control of Chlorophyll and Carotenoid Accumulation in Sorghum bicolor

Etiolated Sorghum bicolor seedlings manifested a significantmorphological response to short term irradiations by red andfar-red light and to a continuous far-red light. Accumulationof chlorophylls in white light and carotenoids in darkness isunder red/far-red reversible control as well as along with theeffectiveness of ‘High Irradiance Reaction’. Phytochromeis also found to eliminate the lag phase during the accumulationof chlorophylls and carotenoids in white light. (Received March 11, 1981; Accepted May 2, 1981)