Multivariate analysis of diversity of tef (Eragrostis tef (Zucc.) Trotter) germplasm from western and southern Ethiopia

Sixty tef germplasm populations consisting of 3,000 panicle-derived lines from six western and southern regions of Ethiopia were evaluated for 17 pheno-morphic and agronomic traits on pellic Vertisols at Debre Zeit Agricultural Research Center during the 1999 main season. The objectives were to study the extent and pattern of variation of the germplasm with respect to regions and altitude zones, to classify the populations into relatively homogenous groups and to identify the major traits contributing to the overall diversity of the populations. At 75 % similarity level, the 60 populations aggregated into nine complexes of two to 10, with 12 populations remaining un-grouped. Five principal components (PC) extracted about 81 % of the gross variance among the populations. About 40 % of the variance accounted for by the first PC alone resulted largely from variations in diameters of the two basal culm internodes, grain yield and number of spikelets/panicle, shoot phytomass and grain yield/plant, and number of culm internodes. The entire regional as well as the clinal (altitude zone) variation was explained by five and two PCs, respectively. The discriminant analyses depicted about 77 % correct grouping of the 47 populations into nine clusters and about 62 % and 68 % correct origin-based classification of the germplasm in terms of altitude zones and regions, respectively. In general, the study demonstrated the existence of regional and clinal (altitude zone) variation patterns in the tef germplasm populations. The broad trait variation in the germplasm implies ample opportunities for genetic improvement of tef through selection and hybridization.     

Trait diversity, heritability and genetic advance in selected germplasm lines of tef

The genetic improvement of the Ethiopian cereal, tef, Eragrostis tef (Zucc.) Trotter, depends upon the variability in the indigenous germplasm. A bi-replicated randomized complete block field experiment was, therefore, carried out at Debre Zeit and Alem Tena in Ethiopia during the 1996 main season to study the pheno-morphic and agronomic trait diversity in 320 tef germplasm lines. All of the 17 traits assessed showed substantial (p < or = 0.001) variation among the lines. Genotypes and locations interacted significantly (p < or = 0.05) on 11 of the traits. At about 50% similarity level, the tef lines grouped into six major clusters of nine to 243 lines. Five principal components (PCs) extracted about 71% of the entire variation of the lines. About 28% of the total variance explained by the first PC was due chiefly to variation in main shoot culm length, diameters of the two basal culm internodes, panicle length and grain yield/panicle. About 16% of the whole variance explained by the second PC originated mainly from variation in the length of the first and second basal culm internodes, grain yield/plant, and peduncle length. The third PC accounting for about 12% of the entire variance resulted largely from variation in harvest index and shoot phytomass yield/plant. Across traits, the phenotypic and genotypic coefficients of variation varied in that order from about 2% for grain yield/panicle to 58% for number of fertile tillers/plant, and from less than 1% for diameters of the two basal culm internodes and grain yield/panicle to 35% for panicle length. Estimates of broad sense heritability and genetic advance (as ratio of the mean) were highest for panicle length (71%) and number of fertile tillers/plant (21%), respectively. But both of these were lowest for the second basal culm internode diameter (< 1%). Overall, the study confirmed that tef is a highly versatile crop with broad trait diversity in the germplasm, and this offers ample opportunities for improvement through breeding.     

Inter simple sequence repeat (ISSR) analysis of genetic diversity in tef [Eragrostis tef (Zucc.) Trotter

The DNA polymorphism among 92 selected tef genotypes belonging to eight origin groups was assessed using eight inter simple sequence repeat (ISSR) primers. The objectives were to examine the possibility of using ISSR markers for unravelling genetic diversity in tef, and to assess the extent and pattern of genetic diversity in the test germplasm with respect to origin groups. The eight primers were able to separate or distinguish all of the 92 tef genotypes based on a total of 110 polymorphic bands among the test lines. The Jaccard similarity coefficient among the test genotypes ranged from 0.26 to 0.86, and at about 60 % similarity level the clustering of this matrix using the unweighted pair-group method based on arithmetic average (UPGMA) resulted in the formation of six major clusters of 2 to 37 lines with further eight lines remaining ungrouped. The standardized Nei genetic distance among the eight groups of origin ranged between 0.03 and 0.32. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of three clusters of the eight groups of origin with bootstrap values ranging from 56 to 97. The overall mean Shannon Weaver diversity index of the test lines was 0.73, indicating better resolution of genetic diversity in tef with ISSR markers than with phenotypic (morphological) traits used in previous studies. This can be attributed mainly to the larger number of loci generated for evaluation with ISSR analysis as compared to the few number of phenotypic traits amenable for assessment and which are further greatly affected by environment and genotype x environment interaction. Analysis of variance of mean Shannon Weaver diversity indices revealed substantial (P < or = 0.05) variation in the level of diversity among the eight groups of origin. In conclusion, our results indicate that ISSR can be useful as DNA-based molecular markers for studying genetic diversity and phylogenetic relationships, DNA fingerprinting for the identification of varieties or cultivars, and also for genome mapping in tef.     

Clinal differentiation during invasion: <Emphasis Type="Italic">Senecio inaequidens</Emphasis> (Asteraceae) along altitudinal gradients in Europe

The dynamics of plant population differentiation may be integral in predicting aspects of introduced species invasion. In the present study, we tested the hypothesis that European populations of Senecio inaequidens (Asteraceae), an invasive species with South African origins, differentiated during migration from two independent introduction sites into divergent altitudinal and climatic zones. We carried out 2 years of common garden experiments with eight populations sampled from Belgian and ten populations from French altitudinal transects. The Belgian transect followed a temperature and precipitation gradient. A temperature and summer drought gradient characterized the French transect. We evaluated differentiation and clinal variation in plants germinated from field-collected seed using the following traits: days to germination, days to flowering, height at maturity, final plant height and aboveground biomass. Results showed that S. inaequidens populations differentiated in growth traits during invasion. During the 1st year of sampling, the results indicated clinal variation for growth traits along both the Belgium and French altitudinal transects. Data from the 2nd year of study demonstrated that with increasing altitude, a reduction in three growth traits, including plant height at maturity, final plant height and aboveground biomass, was detected along the French transect, but no longer along the Belgian one. Phenological traits did not exhibit a clear clinal variation along altitudinal transects. The possible evolutionary causes for the observed differentiation are discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Morphological, genetic, and chromosomal variation at a small spatial scale within a mosaic hybrid zone of the grasshopper Dichroplus pratensis Bruner (Acrididae)

Hybrid zones are regions where genetically different populations meet and mate, resulting in offspring of mixed characteristics. In organisms with limited dispersal, such as melanopline grasshoppers, hybrid zones can occur at small spatial scales (i.e., <500 m). We assessed levels of morphological, chromosomal, and molecular variability in adult males of the grasshopper Dichroplus pratensis Bruner (N = 137 males, 188 females) collected at 12 sites within a mosaic hybrid zone in a heterogeneous environment in Sierra de la Ventana, Argentina. In this hybrid zone, 2 Robertsonian chromosomal races, polymorphic for different centric fusions, meet (the "Northern race" at low altitudes and the "Southern race" at higher altitudes), forming hybrids that show monobrachial homologies during meiosis. High morphometric variation in 6 traits was revealed among grasshoppers of both sexes, with male body size positively and significantly correlated with increasing altitude. Frequency of Robertsonian fusions characteristic of the Southern race increased significantly with altitude. Moreover, fusion frequencies covaried between samples. Considerable genetic variation was revealed by random amplification of polymorphic DNA markers, with heterozygosity ranging from 0.3477 to 0.3745. Insects from low-altitude and high-altitude populations showed significant genetic differentiation, as indicated by F(ST) values. The proposed model for D. pratensis, involving the generation and maintenance by chromosomal fusions, of gene complexes adaptive in different environments, could explain the observed clinal patterns within the contact zone.     

RFLP linkage map of the Ethiopian cereal tef [Eragrostis tef (Zucc) Trotter]

Tef [Eragrostis tef (Zucc)Trotter] is one of the most important cereal crops in Ethiopia. It is an allotetraploid species with a genome size of 720 Mbp. In this paper we report results of genetic linkage-map construction for E. tef using tef and heterologous cDNA probes for the first time. One hundred and sixteen F₈ recombinant inbred lines (RILs) from the cross E. tef cv Kaye Murri×Eragrostis pilosa (accession30–5) were used for mapping. Parental lines were digested with nine restriction enzymes and screened using 159 tef cDNA and 162 heterologous probes including the grass genome anchor probes. The polymorphism level between parental lines was 66.9%. One hundred and thirty nine polymorphic probes were hybridized against 116 RILs. Both the tef and the heterologous probes hybridized well against tef genomic DNA. The linkage map defined 1,489 cM of the tef genome comprising 149 marker loci distributed among 20 linkage groups. The average interval between markers was 9.99 cM. A fraction (14.8%) of the markers deviated significantly from the expected segregation. Such a genetic linkage map is useful for tagging economically useful genes in tef because a wide range of agronomically important traits is segregating within this population. This would enable the use of a marker assisted breeding strategy which, in turn, will enhance breeding efficiency. Alignment of the tef RFLP map with the rice RFLP map indicates that a number of syntenic chromosomal fragments exist between tef and rice in which the gene order was for the most part collinear. The comparative mapping information should enable tef scientists to take advantage of whatever genetic progress is made on the cereal model species rice. Received: 9 June 2000 / Accepted: 31 August 2000     

Morphological diversity of Ethiopian barley (Hordeum vulgare L.) in relation to geographic regions and altitudes

A total of 199 germplasm accessions collected from 10 administrative regions of Ethiopia and four released cultivars, which were used for estimating of error variance, of barley in Ethiopia were field evaluated for nine agronomic traits at Holetta and Bekoji Agricultural Research Centers of Ethiopia during the 2006 main cropping season using non-replicated augmented design plots consisting of four incomplete blocks. The objectives were to assess the extent and pattern of morphological variation in the barley accessions with respect to regions and altitude of collection, to classify the genotypes tested into relatively homogenous groups and to identify the major traits contributing to the overall observed diversity in the germplasm. Genotype variance estimate of regions and altitudes indicated wide variation among accessions depending on the traits involved. The presence of high morphological variation within regions and altitudes particularly above 2000 m a.s.l. indicated the potential of each region and high altitude zones for barley improvement and conservation in the country. The clustering of accessions did not show grouping on the basis of regions of origin. Traits like thousand kernel weight, plant height, days to head and days to maturity accounted for most of the gross variance among the barley accessions and played role in differentiating accessions collected from different regions and altitude classes into principal components. In general because of environmental factors on the observed morphological variation future germplasm collection should consider to explore wide geographical and climatic differences within the country.     

Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench)

 Quantitative trait loci (QTLs) for grain quality, yield components and other traits were investigated in two Sorghum caudatum×guinea recombinant inbred line (RIL) populations. A total of 16 traits were evaluated (plant height, panicle length, panicle compactness, number of kernels/panicle, thousand-kernel weight, kernel weight/panicle, threshing percentage, dehulling yield, kernel flouriness, kernel friability, kernel hardness, amylose content, protein content, lipid content, germination rate and molds during germination and after harvest) and related to two 113- and 100-point base genetic maps using simple (SIM) and composite (CIM) interval mapping. The number, effects and relative position of QTLs detected in both populations were generally in agreement with the distributions, heritabilities and correlations among traits. Several chromosomal segments markedly affected multiple traits and were suspected of harbouring major genes. The positions of these QTLs are discussed in relation to previously reported studies on sorghum and other grasses. Many QTLs, depending on their relative effects and position, could be used as targets for marker-assisted selection and provide an opportunity for accelerating breeding programmes. Received: 14 February 1998 / Accepted: 4 March 1998     

Studies on some genetic parameters of rice (Oryza sativa L.)

Summary In order to utilize the available useful variation in breeding rice to improve yield and quality of grain, the performance of a wide range of rice germ plasm comprising 30 varieties was evaluated in northern India, a major rice growing belt. Plant performance revealed high genetic divergence and phenotypic variability in the crop, with the maximum range of variation being for grain number per panicle and the minimum for grain dimensions. There were also significant differences among varietal means for ten phenotypic traits. Genotypic and phenotypic variance contributed profoundly to the variance of the phenotypic traits studied, but, since genetic variability in the traits related to yield was considerable, there is scope for further improvement in yielding ability. Grain number per panicle, number of effective tillers per plant and culm length exhibit high heritability, and genotypic coefficient of variation and therefore a high genetic advance. Thus, selection for these traits would be effective in crop improvement. Moreover, grain number per panicle shows a significant positive correlation with yield, and this trait could profitably form a reliable index for the yielding capacity of this crop.     

Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude

? Understanding the adaptive basis of life history variation is a central goal in evolutionary ecology. The use of model species enables the combination of molecular mechanistic knowledge with ecological and evolutionary questions, but the study of life history variation in natural environments is required to merge these disciplines. ? Here, we tested for clinal variation in life history and associated traits along an environmental and altitudinal gradient in the model species Arabidopsis thaliana. Seventeen natural populations of A. thaliana were geo-referenced in north-eastern Spain on a gradient in which precipitation increases but maximum spring temperature and minimum winter temperature decrease with altitude. ? One hundred and eighty-nine genotypes from the 17 populations were grown under uniform controlled conditions. Variations in traits related to biomass allocation, fecundity, phenology and vegetative growth were tested for relationships with the altitude and climatic variables associated with the home sites. Above-ground mass, number of rosette leaves at bolting, developmental time and seed weight increased with the home site's altitude. Root allocation, vegetative growth during winter and number of seeds decreased with altitude. ? We suggest that the differences among home sites provide clues to the variation in adaptive strategies associated with the climatic gradient. We compared these results with adaptations and clinal relationships reported for other species and with molecular mechanisms described in Arabidopsis.     

Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter.

Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11-42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.     

Geographical Clines for Quantitative Traits in Natural Populations of a Tropical Drosophilid: Zaprionus Indianus

We analyzed natural populations of Zaprionus indianusin 10 Indian localities along a south-north transect (latitude: 10–31°3 N). Size traits (body weight, wing length and thorax length) as well as a reproductive trait (ovariole number) followed a pattern of clinal variation, that is, trait value increased with latitude. Wing/thorax ratio, which is inversely related to wing loading, also had a positive, but non-significant correlation with latitude. By contrast, bristle numbers (sternopleural and abdominal) exhibited a non-significant but negative correlation with latitude. Sex dimorphism, estimated as the female/male ratio, was very low in Z. indianus, contrasting with results already published in other species. Genetic variations among populations were also analyzed according to other geographic parameters (altitude and longitude) and to climatic conditions from each locality. A significant effect of altitude was found for size traits. For abdominal bristles, a multiple regression technique evidenced a significant effect of both latitude and altitude, but in opposite directions. Genetic variations were also correlated to climate, and mainly with average year temperature. Taking seasonal variations into account failed however to improve the predictability of morphometrical variations. The geographic differentiation of Z.indianusfor quantitative traits suggests adaptive response to local conditions, especially to temperature, but also reveals a complex situation according to traits investigated and to environmental parameters, which does not match results on other drosophilid species.     

Local adaptation of stress related traits in Drosophila buzzatii and Drosophila simulans in spite of high gene flow

We addressed the question if local adaptation to a thermal gradient is possible in spite of a high gene flow among closely spaced populations of two species of Drosophila from the island of La Gomera (Canary Islands). Variation in multiple traits related to stress resistance in different life stages was measured in both species in flies collected from five localities at different altitudes and thereby with different climatic conditions. Based on microsatellite loci, the populations were not genetically differentiated. However, 18 of the 24 independent traits measured showed significant differentiation among populations of Drosophila buzzatii, but only nine of 25 for Drosophila simulans. This difference in the number of traits might reflect higher habitat specificity and thus higher potential for local adaptation of D. buzzatii than D. simulans. We found clinal variation, as some traits showed significant linear regressions on altitude, but more on altitude cubed.     

Flow cytometric analysis of nuclear genome of the Ethiopian cereal tef [Eragrostis tef (Zucc.) Trotter]

Flow cytometric analysis of nuclear DNA content was performed by using nuclei isolated from young leaf tissue of tef (Eragrostis tef). The method was very useful for rapid screening of ploidy levels in cultivars and lines of tef representing the phenotypic variability of this species in Ethiopia. The results of the analysis showed that all cultivars were tetraploid. Flow cytometry was also used to determine nuclear DNA content in absolute units (genome size) in four tef cultivars. Nuclei isolated from tomato (Lycopersicon esculentum, 2C=1.96 pg) were used as an internal reference standard. The 2C DNA content of individual tef cultivars ranged from 1.48 to 1.52 pg (1C genome size: 714 Mbp-733 Mbp), the differences among them being statistically nonsignificant. The fact that the nuclear genome of tef is only about 50% larger than that of rice should make it amenable for analysis and mapping at the molecular level.     

A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism

A genetic linkage map of tef was constructed with amplified fragment length polymorphism (AFLP) markers using F₅ recombinant inbred lines (RILs) derived by single seed descent from the intraspecific cross of ’Kaye Murri’×’Fesho’. A total of 192 EcoRI/MseI primer combinations were screened for parental polymorphism. Around three polymorphic fragments per primer combination were detected, indicating a low polymorphism level in tef. Fifty primer combinations were selected to assay the mapping population, and 226 loci segregated among 85 F₅ RILs. Most AFLP loci behaved as dominant markers (presence or absence of a band), but about 15% of the loci were codominant. Significant deviations from the expected Mendelian segregation ratio were observed for 26 loci. The genetic linkage map comprised 211 markers assembled into 25 linkage groups and covered 2,149 cM of genome. AFLP is an efficient marker system for mapping plant species with low polymorphism such as tef. This is the first genetic linkage map constructed for tef. It will facilitate the mapping of genes controlling agronomically important traits and cultivar improvement in tef. Received: 27 April 1998 / Accepted: 4 January 1999     

Phenotypic Diversity of Acer ginnala (Aceraceae) Populations at Different Altitude

In this study, we analyzed the phenotypic variation of Acer ginnala natural populations at different altitude in Qiliyu, investigated the level of phenotypic diversity by using ANOVA analysis, correlation analysis and cluster analysis. The results showed that there were significant differences in phenotypic variation among and within populations. Coefficient of variation (CV) varied from 705% to 3812%. High phonotypic diversity (1.9253) occurred within A.ginnala populations, the mean phenotypic diversity index of populations ranged from 1.9022 to 1.9837. Phenotypic differentiation coefficient (VST) among populations (13.79%) was less than that of within populations (86.21%). The variation within populations comprised a majority of total phenotypic variation. A significant relation had occurred between phenotypic traits and soil factors. Phenotypic diversity index had a very significant correlation with soil total nitrogen (P<0.05), no significant relation with altitude. Five populations gathered into two groups by cluster analysis, which consistent with the geographic distribution of Aginnala in Qiliyu. The traits variations of natural populations at different altitude were affected mainly by micro-environmental heterogeneity of different Aginnala populations. Utilizing of variation within and among populations is important significance for genetic improvement of A.ginnala.     

水稻轮回选择群体XTBG-HP1表型遗传多样性分析

该研究基于4个陆稻群体及172个水稻品种或杂交组合,构建了水稻多亲本隐性核不育轮回选择群体XTBG-HP1,并经过4次轮回重组,采用16个表型性状对其进行了遗传多样性分析。结果表明:(1)该群体14个数量性状符合正态分布,各表型均存在极端性状个体。(2)数量性状变异系数范围为0.08～0.41,均值为0.20; Shannon-Wiener多样性指数范围为0.72～1.92,均值为1.50。(3)群体在株型与产量构成因子性状方面有显著的相关性,对株型的选择可以实现产量性状的改良。(4)剑叶长、每穗粒总数、千粒重、穗长、粒长、一次枝梗数、有效穗数、剑叶宽、二次枝梗数、抽穗期10个性状可作为群体综合评价指标。(5)剑叶长、二次枝梗数、每穗粒总数3个表型性状具有较高的遗传变异、丰富的遗传多样性及与综合得分F值相关系数较高。综合以上结果发现,后期群体进行基因挖掘、品种改良以及优良育种材料的选育可以基于剑叶长、二次枝梗数及每穗粒总数3个表型性状,同时要充分利用群体株型与产量构成因子性状间的显著相关性。此外,该研究群体中极端单性状或综合得分F值较高的个体,可进一步用于品种选育。     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter).

Tef (Eragrostis tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA libraries: seedling leaf, seedling root, and inflorescence of E. tef and seedling leaf of Eragrostis pilosa, a wild relative of E. tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 tef unigenes. Approximately 3/4 of tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68% of the putative tef genes with gene ontology categories. Identification of the translated unigenes for conserved protein domains revealed 389 protein family domains (Pfam), the most frequent of which was protein kinase. A total of 170 ESTs containing simple sequence repeats (EST-SSRs) were identified and 80 EST-SSR markers were developed. In addition, 19 single-nucleotide polymorphism (SNP) and (or) insertion-deletion (indel) and 34 intron fragment length polymorphism (IFLP) markers were developed. The EST database and molecular markers generated in this study will be valuable resources for further tef genetic research.