Using high-throughput amplified fragment length polymorphism to distinguish sorghum greenbug (Homoptera: Aphididae) biotypes

Abstract 1 The greenbug Schizaphis graminum (Rondani) is a serious pest of Sorghum bicolor L. and small grains in the Southern Plains of the U.S.A. Use of resistant cultivars, the major greenbug management strategy, has been challenged by the rapid development of new greenbug biotypes that overcome plant resistance. 2 We used a high‐throughput amplified fragment length polymorphism (AFLP) fingerprinting method to examine genetic divergence among eight greenbug biotypes (B, C, E, G, I and K, New York and South Carolina). Clustering analysis based on 1775 scored AFLP markers clearly showed that biotypes (C, E, I and K), which are able to infest sorghum fields, share more common polymorphisms among themselves than with other biotypes. 3 This result suggests that common genetic factors exist among these biotypes, enabling them to predominate and thrive in monoculture crops. Our study demonstrated the sensitivity of AFLP in obtaining large quantities of biotype‐associated polymorphic information across the entire greenbug genome.     

Molecular mapping of QTLs for resistance to the greenbug <Emphasis Type="Italic">Schizaphis graminum</Emphasis> (Rondani) in <Emphasis Type="Italic">Sorghum bicolor</Emphasis> (Moench)

Sorghum is a worldwide important cereal crop and widely cultivated for grain and forage production. Greenbug, Schizaphis graminum (Rondani) is one of the major insect pests of sorghum and can cause serious damage to sorghum plants, particularly in the US Great Plains. Identification of chromosomal regions responsible for greenbug resistance will facilitate both map-based cloning and marker-assisted breeding. Thus, a mapping experiment was conducted to dissect sorghum genetic resistance to greenbug biotype I into genomic regions. Two hundred and seventy-seven (277) F(2) progeny and their F(2:3) families from a cross between Westland A line (susceptible parent) and PI550610 (resistant parent) combined with 118 polymorphic simple sequence repeat (SSR) markers were used to map the greenbug resistance QTLs. Composite interval mapping (CIM) and multiple interval mapping (MIM) revealed two QTLs on sorghum chromosome nine (SBI-09) consistently conditioned the resistance of host plant to the greenbug. The two QTLs were designated as QSsgr-09-01 (major QTL) and QSsgr-09-02 (minor QTL), accounting for approximately 55-80%, and 1-6% of the phenotypic variation for the resistance to greenbug feeding, respectively. These resistance QTLs appeared to have additive and partially dominant effects. The markers Xtxp358, Xtxp289, Xtxp67 and Xtxp230 closely flanked the respective QTLs, and can be used in high-throughput marker-assisted selections (MAS) for breeding new resistant parents and producing commercial hybrids.     

Identification of a major quantitative trait locus conditioning resistance to greenbug biotype E in sorghum PI 550610 using simple sequence repeat markers

Greenbug, Schizaphis graminum (Rondani), represents the most important pest insect of sorghum, Sorghum bicolor (L.) Moench, in the Great Plains of the United States. Biotype E is the most widespread and dominant type not only in sorghum and wheat, Triticum aestivum L., fields, but also on many noncultivated grass species. This study was designed to determine sorghum accession PI 550610 resistance to greenbug biotype E, to map the resistance quantitative trait loci (QTLs) by using an established simple sequence repeat (SSR) linkage map and to identify SSR markers closely linked to the major resistance QTLs. In greenhouse screening tests, seedlings of PI 550610 showed strong resistance to the greenbug at a level similar to resistant accession PI550607. For QTL mapping, one F2 population containing 277 progeny and one population containing 233 F2:3 families derived from Westland A line x PI 550610 were used to genotype 132 polymorphic SSR markers and to phenotype seedling resistance to greenbug feeding. Phenotypic evaluation of sorghum seedling damage at 7, 12, 17, and 21 d postinfestation in the F2:3 families revealed that resistance variation was normally distributed. Single marker analysis indicated 16 SSRs spread over five chromosomes were significant for greenbug resistance. Composite interval and multiple interval mapping procedures indicated that a major QTL resided in the interval of 6.8 cM between SSR markers Xtxp358 and Xtxp289 on SBI-09. The results will be valuable in the development of new greenbug biotype E resistant sorghum cultivars and for the further characterization of major genes by map-based cloning.     

Biotypic diversity in greenbug (Hemiptera: Aphididae): characterizing new virulence and host associations

Biotypic diversity of the greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae), was assessed among populations collected from cultivated wheat, Triticum aestivum L., and sorghum, Sorghum bicolor (L.) Moench, and their associated noncultivated grass hosts. Greenbugs were collected during May through August 2002 from 30 counties of Kansas, Nebraska, Oklahoma, and Texas. Discounting the presumptive biotype A, five of the remaining nine letter-designated greenbug biotypes were collected; however, biotypes C, F, J, and K were not detected. Biotypes E and I exhibited the greatest host range and were the only biotypes collected in all four states. Sixteen greenbug clones, collected from eight plant species, exhibited unique biotype profiles. Eleven were collected from noncultivated grasses, three from wheat, and two from sorghum. The most virulent biotypes were collected from noncultivated hosts. The great degree of biotypic diversity among noncultivated grasses supports the contention that the greenbug species complex is composed of host-adapted races that diverged on grass species independently of, and well before, the advent of modern agriculture.     

Genetic mapping of QTLs associated with greenbug resistance and tolerance in Sorghum bicolor

Ninety three recombinant inbreds of Sorghum bicolor (L. Moench) were derived from a cross between two sorghum lines GBIK and Redlan. This population was used to identify quantitative trait loci (QTLs) for resistance and tolerance to greenbug (Schizaphids graminum Rondani) Biotypes I and K. One hundred and thirteen loci (38 SSRs and 75 RAPDs) were mapped in 12 linkage groups covering 1,530 cM. In general, nine QTLs were detected affecting both resistance and tolerance to greenbug (GB) Biotypes I and K. The phenotypic variance explained by each QTL ranged from 5.6% to 38.4%. Four SSRs and one RAPD marker were associated with the expression of all resistance and tolerance traits. These markers appear to be linked to biotype non-specific resistance and tolerance genes. Four additional markers were associated with biotype-specific resistance or tolerance traits. The detection of more than one locus for each biotype supports the hypothesis that several regions, which represent different genes, control the expression of resistance and tolerance to greenbug in sorghum. The results can be used for marker-assisted selection and the breeding of greenbug-tolerant sorghum cultivars.     

感病与抗病圭亚那柱花草遗传多样性的AFLP分析

圭亚那柱花草(Stylosanthes guianensts Swartz)原产中南美洲及非洲,是一种重要的热带豆科牧草,已在我国华南热带、南亚热带地区种植并利用.由胶孢炭疽菌(Colletotrichum gloeosporioides(Penz.)Sacc.)引起的炭疽病是柱花草的主要病害.采用扩增片段长度多态性(AFLP)技术分析了42个圭亚那柱花草品系的遗传多样性,同时对其抗病性进行了接种鉴定.从96个选择性引物对中筛选出较好的4个,分别对42个圭亚耶柱花草品系进行扩增,共获得出225条带,其中多态性带215条,平均多态性水平为95.5%,表现出高度的多态性.采用NTSYS-pc软件计算了品系间的遗传相似系数,其变化范围为0.31～0.95.根据非加权成对平均数法(uPGMA)进行聚类分析,建立了42个品系的聚类树系图,以所有品系的平均遗传相似系数0.48为阈值,共分为5类.主成分分析表明:第一主成分和第二主成分对全部品系间遗传变异的贡献率分别为56.04%和6.40%,并建立了品系间相互关系的二维图,各品系在二维图中的分布与UPGMA分类相吻合.抗病性鉴定结果表明:各品系对两种典型的病原菌的抗性有差异,其中抗病品系对两种病原菌的抗病相关系数达到0.904,表明抗病品系对两种病原菌有共同抗性.此外,抗病品系在UPGMA聚类中呈随机分布.这些结果表明,AFLP技术是分析圭亚那柱花草遗传多样性的有效方法.     

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.     

Genetic diversity in colonial bentgrass (Agrostis capillaris L.) revealed by EcoRI-MseI and PstI-MseI AFLP markers.

Colonial bentgrass (Agrostis capillaris L.) is a potential source for genetic improvement of resistance to environmental stress and disease for other bentgrass species (Agrostis spp.). To conserve and study the existing genetic resources of colonial bentgrass for use in breeding, genetic diversity was investigated using amplified fragment length polymorphism (AFLP) markers. Included in this study were 22 accessions from US Department of Agriculture germplasm collected from 11 countries, in conjunction with 14 accessions from northern Spain and 3 commercial cultivars. Ten EcoRI-MseI and 6 PstI-MseI AFLP primer combinations produced 181 and 128 informative polymorphic bands, respectively. Cluster analysis of genetic similarity estimates revealed a high level of diversity in colonial bentgrass species with averages of 0.51 (EcoRI-MseI) and 0.63 (PstI-MseI). Greater genetic diversity was detected by the EcoRI-MseI AFLP primer combinations. A low but significant positive correlation (r = 0.44, p = 0.0099) between the 2 Jaccard similarity matrices was obtained by the Mantel test. Commercial cultivars of bentgrass showed a narrow genetic background. The assessment of genetic diversity among colonial bentgrass accessions suggested the potential value of the colonial bentgrass germplasm in turfgrass cultivar improvement.     

高粱抗蚜研究进展

高粱(Sorghum bicolour)是世界上最重要的粮食、饲料、酿造和能源作物之一, 也是C₄植物研究的模式植物。蚜虫是农业生产上的重要害虫, 几乎危害所有的栽培作物。危害高粱的蚜虫主要包括高粱蚜(Melanaphis sacchari)、麦二叉蚜(Schizaphis graminum)和玉米蚜(Rhopalosiphum maidis)。高粱的抗蚜资源尚不丰富且缺乏深入系统的研究。目前研究较多的是麦二叉蚜的抗性遗传方面, 已定位20个抗性QTLs, 单一QTL对抗性差异贡献率最高可达80.3%, 对高粱蚜和玉米蚜的研究尚需进一步加强。高粱的理化特性与其抗蚜性能相关, 故可与育种实践相结合。高粱和蚜虫(Acyrthosiphon pisum)的全基因组测序工作已经完成, 这将有助于蚜虫-植物间的相互作用关系及植物对蚜虫的抗性机制研究。目前已克隆到2个抗蚜基因, 且多个抗蚜基因(位点)已被定位在染色体上。该文重点综述了上述研究成果并对高粱抗蚜的研究前景进行了展望。     

Molecular analysis of sorghum resistance to the greenbug (Homoptera: Aphididae)

Chromosomal regions of sorghum, Sorghum bicolor (L.) Moench, conferring resistance to greenbug, Schizaphis graminum (Rondani), biotypes C, E, I, and K from four resistance sources were evaluated by restriction fragment-length polymorphism (RFLP) analysis. At least nine loci, dispersed on eight linkage groups, were implicated in affecting sorghum resistance to greenbug. The nine loci were named according to the genus of the host plant (Sorghum) and greenbug (Schizaphis graminum). Most resistance loci were additive or incompletely dominant. Several digenic interactions were identified, and in each case, these nonadditive interactions accounted for a greater portion of the resistance phenotype than did independently acting loci. One locus in three of the four sorghum crosses appeared responsible for a large portion of resistance to greenbug biotypes C and E. None of the loci identified were effective against all biotypes studied. Correspondingly, the RFLP results indicated resistance from disparate sorghums may be a consequence of allelic variation at particular loci. To prove this, it will be necessary to fine map and clone genes for resistance to greenbug from various sorghum sources.     

Tritrophic interaction of parasitoid Lysiphlebus testaceipes (Hymenoptera: Aphidiidae), greenbug, Schizaphis graminum (Homoptera: Aphididae), and greenbug-resistant sorghum hybrids

Interactions of the parasitoid Lysiphlebus testaceipes (Cresson) and the greenbug, Schizaphis graminum (Rondani), on greenbug-resistant 'Cargill 607E' (antibiosis), 'Cargill 797' (primarily tolerance), and -susceptible 'Golden Harvest 510B' sorghum, Sorghum bicolor (L.) Moench, were tested using three levels of biotype I greenbug infestation. The parasitoid infestation rate was 0.5 female and 1.0 male L. testaceipes per plant. For all three greenbug infestation levels, the parasitoid brought the greenbug under control (i.e., prevented the greenbugs from killing the plants) on both resistant hybrids, but it did not prevent heavy leaf damage at the higher greenbug infestation rates. At the low greenbug infestation rate (50 greenbugs per resistant plant when parasitoids were introduced), greenbugs damaged 5 and 18% of the total leaf area on 'Cargill 797' and 'Cargill 607E', respectively, before greenbugs were eliminated. Leaf damage was higher for the intermediate infestation study (120 greenbugs per plant), 21% and 30% leaf area were damaged on the resistant sorghum hybrids 'Cargill 797' and 'Cargill 607E', respectively. At the high greenbug infestation rate (300 greenbugs per plant), heavy damage occurred: 61% on 'Cargill 607E' and 75% on 'Cargill 797'. The parasitoids did not control greenbugs on the susceptible sorghum hybrid 'Golden Harvest 510B'. L. testaceipes provided comparable control on both greenbug-resistant hybrids. This study supports previous studies indicating that L. testaceipes is effective in controlling greenbugs on sorghum with antibiosis resistance to greenbugs. Furthermore, new information is provided indicating that L. testaceipes is also effective in controlling greenbugs on a greenbug-tolerant hybrid.     

Molecular mapping of sorghum genes expressing tolerance to damage by greenbug (Homoptera: Aphididae)

Genetic linkage maps are fundamental for the localization of genes conferring tolerance to greenbug, Schizaphis graminum (Rondani), feeding damage in sorghum, Sorghum bicolor (L.) Moench. Thirteen linkage groups (LGs) containing 60 simple sequence repeat (SSR) loci were mapped by using a set of sorghum recombinant inbred lines (RILs) obtained from the cross '96-4121' (greenbug-tolerant parent) x Redlan (greenbug-susceptible parent). The LG spanned a distance of 603.5 cM, with the number of loci per LG varying from 2 to 14. Seventeen additional SSR loci were unlinked at a log of odds value of 3.0. Based on chlorophyll loss occurring after greenbug feeding, visual damage ratings, and soil plant analysis development (SPAD), chlorophyll-loss indices were recorded for each RIL and for the parents used in the cross. Composite-interval mapping identified three quantitative trait loci (QTLs) associated with biotype I and five QTLs associated with biotype K. The amount of phenotypic variation explained by these QTLs ranged from 9 to 19.6%. The identification of QTLs that influence greenbug tolerance will not only facilitate the use of marker-assisted selection in sorghum breeding programs but also will provide a solid foundation for detailed characterization of individual loci implicated in greenbug tolerance in sorghum.     

Complementarity of genes for resistance to greenbug [Schizaphis graminum (Rondani)], biotype E,in sorghum [Sorghum bicolor (L.) Moench]

Summary Gene complementarity among various sources of resistance to greenbug biotype E was assessed. Analysis of the F₂ generation of crosses between susceptible and resistant parents (mating 1) and among sources of resistance (mating 2) suggested that resistance in sorghum to greenbug biotype E was complexly inherited and, to some extent, dependent on the nature of both the resistant and susceptible parents. Positive transgressive segregation in the F₂ generations of both matings was found to be due to effective plus factors, contributed by both parents in a cross, which complemented each other. The number of plus factors ranged from one to two in the susceptible parents and from two to five in the resistant parents of mating 1, and from one to five in the parents of mating 2. The consistently significant reciprocal effects shown by Sarvasi and PI264453 indicated that these sources had major factors for resistance in their cytoplasms, which were expressed in all their crosses. The results from this study indicated that the sources of resistance complemented each other to give increased number of F₂ segregates with increased resistance. Thus, it should be possible to increase and diversify resistance of sorghum to greenbug biotype E by accumulating different, effective plus factors from various sources through recurrent selection.Contribution No. 90-106-J from the Kansas Agricultural Experiment Station, Kansas State University, Manhattan, KS 66506, USA     

Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat.

Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a PCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.     

Diversity and Species Relationship in Pearl Millet (Pennisetum typhoides) and Related Species

Thirteen accessions of pearl millet (Pennisetum typhoides (L) Leeke) collected from different states of India and eight wild species of the genus Pennisetum across the world were analyzed for genetic diversity using AFLP markers. A combined analysis of eight primer combinations showed 35% polymorphism among P. typhoides accessions while analysis with five primer combinations showed 99% polymorphism among the wild species. The dendrogram constructed for the P. typhoides accessions based on the UPGMA method revealed two major clusters with samples from Gujarat forming a separate cluster from the rest of the samples. Principal component analysis of the same data set revealed similar results with the first principal component accounting for 65% of the total variation. The percentage of rare and common alleles contributing to the diversity in the sample was analyzed using the Shannon Weiner diversity index. The SW index revealed that the samples from Gujarat contributed significantly to the overall diversity among the accessions. Among accessions of each geographical region, considerable variation was revealed by SW index with samples from Tamil Nadu being most polymorphic. The genetic diversity in the accessions could be utilized for future breeding work. The dendrogram constructed for the wild species revealed the extent of genetic diversity among them. Analysis with one primer combination showed P. typhoides being closer to P. mollissimum than to the other analyzed species.     

Genomic diversity among sorghum genotypes with resistance to sorghum shoot fly, Atherigona soccata

Host plant resistance is one of the important components for management of sorghum shoot fly, Atherigona soccata. The levels of resistance in cultivated germplasm are low to moderate, and therefore, it is important to identify sorghum genotypes with diverse mechanisms of resistance based on physico-chemical and or molecular markers. We assessed the genetic diversity of 15 sorghum genotypes with different levels of resistance/susceptibility to shoot fly, A. soccata using 93 sorghum simple sequence repeat (SSR) primer pairs and simultaneously characterized for 15 morpho-biochemical traits associated with shoot fly resistance. Of these 93 SSR primer pairs, amplification products from 79, thought to correspond to single-copy loci distributed across all ten sorghum chromosome pairs, showed good polymorphism across the 15 sorghum genotypes. The polymorphic information content (PIC) values of these 79 SSR markers ranged from 0.06 to 0.86. The Principal Coordinate Analyses (PCoA) and cluster analyses based on dissimilarity matrices derived from SSR based allelic variation (Neighbor-Joining distance) and variation in 15 morpho-biochemical traits (based on Gower??s distance), revealed grouping of most susceptible genotypes in single cluster. The improved breeding lines grouped with resistant or susceptible genotypes, based on shared pedigree. Based on these results, three resistant accessions viz., IS 1054, IS 1057 and IS 4664 were found diverse to IS 18551, which is widely used as shoot fly resistance donor. These diverse sources, after further characterization for resistance mechanisms, can be used in breeding programs for improving shoot fly resistance.     

用SSR和AFLP技术分析花生抗青枯病种质遗传多样性的比较

由Ralstonia solanacearum E.F.Smith引起的青枯病是若干亚洲和非洲国家花生生产的重要限制因子,利用抗病品种是防治这一病害最好的措施。虽然一大批抗青枯病花生种质资源材料已被鉴定出来,但对其遗传多样性没有足够的研究,限制了在育种中的有效利用。本研究以31份对青枯病具有不同抗性的栽培种花生种质为材料,通过简单序列重复(SSR)和扩增片段长度多态性(AFLP)技术分析了它们的遗传多样性。通过78对SSR引物和126对AFLP引物的鉴定,筛选出能显示抗青枯病种质多态性的SSR引物29对和AFLP引物32对。所选用的29对多态性SSR引物共扩增91条多态性带,平均每对引物扩增3.14条多态性带;32对多态性AFLP引物共扩增72条多态性带,平均扩增2.25条多态性带。在所筛选引物中,4对SSR引物(14H06,7G02,3A8,16C6)和1对AFLP引物(P1M62)检测花生多态性的效果优于其他引物。SSR分析获得的31个花生种质的遗传距离为0.12-0.94,平均为0.53,而AFLP分析获得的遗传距离为0.06～0.57,平均为0.25,基于SSR分析的遗传距离大于基于AFLP分析的遗传距离,疏枝亚种组的遗传分化相对大于密枝亚种组。基于两种分析方法所获得的聚类结果基本一致,但SSR数据聚类结果与栽培种花生的形态分类系统更为吻合。根据分析结果,对构建青枯病抗性遗传图谱群体的核心亲本和抗性育种策略提出了建议。     

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.     

Genetic diversity of Dioscorea dumetorum (Kunth) Pax using Amplified Fragment Length Polymorphisms (AFLP) and cpDNA

We have utilized Amplified Fragment Length Polymorphisms (AFLP) in conjunction with chloroplast DNA (cpDNA) sequence data to study the genetic diversity in 53 accessions of Dioscorea dumetorum from six countries in West and Central Africa. Our results provide a comparison of the two marker systems with regards to their applicability to differentiate intraspecific genotypes and the grouping of the accessions based on localities of collection. A total of 1052 AFLP fragments (of which 94.1% were polymorphic) produced from twelve primer combinations indicate a relatively high level of polymorphism among the accessions. Three major genetic groups that do not strictly follow a geographic distribution pattern were identified using Neighbour-joining and the principal coordinate (PCo) analyses. Accessions from Togo showed higher numbers of private fragments and the highest percentage polymorphism (59.4%). The detection of highest genetic diversity in accessions from Nigeria and Togo and their relationship to other accessions suggest that these countries are the centre of origin and diversity of D. dumetorum. The moderately high genetic diversity (average of 61%) is suggesting great influence on the D. dumetorum germplasms through exchange and transfer of cultivars among local farmers in the sub-region. In contrast, DNA sequence data from the psbA-trnH and the rpoB-trnC chloroplast regions revealed no variation among accessions from the different localities and clearly differentiated by AFLP patterns. The results demonstrate the usefulness of the AFLP marker in generating high polymorphism in the D. dumetorum accessions from West and Central Africa and hence may be used for agronomic purposes.     

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs,AFLPs and SSRs

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.