Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Microsatellite markers are increasingly being used in crop plants to discriminate among genotypes and as tools in marker-assisted selection. Here we evaluated the use of microsatellite markers to quantify the genetic diversity within as well as among accessions sampled from the world germplasm collection of sorghum. Considerable variation was found at the five microsatellite loci analysed, with an average number of alleles per locus equal to 2.4 within accessions and 19.2 in the overall sample of 25 accessions. The collection of sorghum appeared highly structured genetically with about 70% of the total genetic diversity occurring among accessions. However, differentiation among morphologically defined races of sorghum, or among geographic origins, accounted for less than 15% of the total genetic diversity. Our results are in global agreement with those obtained previously with allozyme markers. We were also able to show that microsatellite data are useful in identifying individual accessions with a high relative contribution to the overall allelic diversity of the collection. Received: 10 August 1999 / Accepted: 27 August 1999     

Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR)

Twenty seven accessions of sorghum conserved in the national gene bank of Zambia, representing two of the three agroecological regions of the country, were investigated using simple sequence repeats (SSR) markers in order to determine the extent and distribution of its genetic diversity. We used 10 microsatellite primer-pairs, which generated 2-9 alleles per locus and a total of 44 alleles across the 27 accessions. The observed heterozygosity (Ho(P) ) among the accessions ranged from 0 to 0.19 with an average of 0.04 whereas the average expected heterozygosity (He(P) ) among accessions was 0.07 in line with the fact that sorghum is predominately inbreeder. The analysis of molecular variance (AMOVA) revealed that 82% of the total genetic variation was attributable to the genetic variation among accessions (F(ST) = 0.824; p < 0.001) whereas the genetic variation within accessions accounted for 18% of the total genetic variation. AMOVA on sorghum accessions grouped based on four ethnic groups (Soli, Chikunda, Lozi and Tonga) associated with collection sites revealed a highly significant variation among groups (23%; p < 0.001). Although cluster analysis grouped most accessions according to their sites of collection, some accessions that originated from the same site were placed under different clusters. In addition to the extent and pattern of genetic diversity, consideration should also be given to other factors such as ecogeographic and ethnic differences when sampling sorghum genetic resources for rational and efficient conservation and utilization in the breeding program.     

基于农艺性状指标的山西高粱地方品种核心种质构建

利用1285份山西省高粱地方品种18个农艺性状的历史数据,通过比较不同取样方法、取样比例和聚类方法组合的构建方法,确定了"多次聚类偏离度取样法+15％取样比例+欧氏距离+最长距离法"为山西省高粱地方核心种质构建的方法.192份初选核心种质和所有样本的均值差异百分率、方差差异百分率、极差符合率和变异系数变化率分别为0、8...     

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.     

Microsatellite markers reveal high genetic diversity in date palm (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) germplasm from Sudan

Genetic diversity in date palm germplasm from Sudan representing 37 female and 23 male accessions was investigated using 16 loci of microsatellite (SSR) primers. Eight female accessions from Morocco were included as reference material. The tested SSR markers showed a high level of polymorphism. A total of 343 alleles were detected at the 16 loci. The number of alleles per marker ranged from 14 to 44 with an average of 21.4 per locus. A high level of expected heterozygosity was observed among Sudan cultivars (0.841), Morocco cultivars (0.820) and male accessions (0.799). The results indicate that the genetic groups of the Sudan cultivars and/or males do not follow a clear geographic pattern. However, the morocco group showed significant differentiation in relation to the Sudan groups, as measured by F (ST) values and genetic distances. The effect of the methods of pollination and cultivar selection on the genetic structure was clearly detected by the weak clustering association that was observed for the majority of accessions originating from Sudan and Morocco as well. This suggests the need for further investigation on the genetic diversity of Sudanese date palm germplasm. A deeper insight will be revealed by a detailed analysis of populations originating from different geographic locations.     

Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm

Many core collections have been developed from large collections of crop germplasm, but most of these have not been characterized, particularly using molecular techniques, for germplasm management and utilization. We have attempted to characterize a structured sample representing a world collection of 11,622 cultivated hexaploid oat accessions in the hope of understanding the genetic structure of the world collection. The amplified fragment length polymorphism (AFLP) technique was applied to screen 670 accessions representing 79 countries and one group of uncertain origin. For each accession, 170 AFLP polymorphic bands detected by five AFLP primer pairs were scored. Analyses of the AFLP data showed the effectiveness of the stratified sampling applied in capturing country-wise AFLP variation. The frequencies of polymorphic bands ranged from 0.11 to 0.99, with an average of 0.72. The majority (89.9%) of the AFLP variation resided within accessions of each country, and only 6.2% of the AFLP differences existed among accessions of major geographic regions. Accessions from the Mediterranean region were the most distinct, while those from Russia and the USA were the most diverse. The two distinct groups that were observed were separated largely on the basis of common oat and red oat. Red oat was genetically more diverse than its common and hull-less counterparts, and hull-less oat was more related to common oat than red oat. Landrace and non-landrace accessions displayed similar AFLP variation patterns. These patterns are significant for understanding the domestication of cultivated oat and are useful in classifying the intraspecific diversity of oat germplasm, developing specific core subsets of the oat collection, and exploring new sources of genes for oat improvement.     

高粱种质资源主要品质性状鉴定与评价

对“十五”期间存入国家种质库的532份高粱种质资源的粗蛋白、粗淀粉、赖氨酸、单宁等四个主要品质性状进行了鉴定评价和相互关系分析。结果表明,四个主要品质的含量呈现近似正态分布。不同品质性状变异程度不同,其中单宁含量变异最大。性状间存在着不同的相关性。不同来源的种质品质性状比较结果表明,选育品种的赖氨酸、单宁含量明优于地方品种。通过鉴定,筛选出一批多项、双项或单项品质优良的高粱种质资源。     

Qualitative Traits Variation in Sorghum (<Emphasis Type="Italic">Sorghum Bicolor</Emphasis> (L.) Moench) Germplasm from,Eastern Highlands of Ethiopia

Forty-five sorghum germplasm growing in the Eastern Highlands of Ethiopia were evaluated for 10 qualitative traits. Phenotypic frequencies between the accessions from each of the nine Aanaas and Alemaya University, grouped in 10 localities were tabulated. Phenotypic diversity index, H′, was analysed and the result indicated the between localities component of diversity to be relatively smaller than the variation in H′ among characters within localities. The value of H′ for all sample germplasm ranged from 0.36 to 0.95 with a mean of 0.71. The results showed that there is a wide morpho-agronomical diversity among the sample germplasm studied. This information can be used for the conservation of these germplasm resources and future improvement work of the sorghum crop.     

Methods of developing a core collection of annual Medicago species

A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection.     

Patterns of allozyme variation in cultivated and wild Sorghum bicolor

Summary Patterns of allozyme variation were surveyed in collections of cultivated and wild sorghum from Africa, the Middle East, and Asia. Data for 30 isozyme loci from a total of 2067 plants representing 429 accessions were analyzed. Regional levels of genetic diversity in the cultivars are greater in northern and central Africa compared to southern Africa, the Middle East, or Asia. The spatial distribution of individual alleles at the most variable loci was studied by plotting allele frequencies on geographic maps covering the distribution of sorghum. Generally, many of the alleles with frequencies below 0.25 are localized in specific portions of the range and are commonly present in more than one race in that region. Several alleles occur in both wild and cultivated sorghum of one region and are absent from sorghum elsewhere, suggesting local introgression between the wild and cultivated forms. Although the same most common allele was found in the wild and cultivated gene pools at 29 of the 30 loci, phenetic analyses separated the majority of wild collections from the cultivars, indicating that the two gene pools are distinct. Wild sorghum from northeast and central Africa exhibits greater genetic similarities to the cultivars compared to wild sorghum of northwest or southern Africa. This is consistent with the theory that wild sorghum of northeast-central Africa is ancestral to domesticated sorghum. Wild sorghums of race arundinaceum of northwest Africa and race virgatum from Egypt are shown to be genetically distinct from both other forms of wild sorghum and from the cultivars. Suggestions for genetic conservation are presented in light of these data.     

Random-amplified-polymorphic DNA markers in sorghum

Conditions have been identified that allow reproducible amplification of RAPD markers in sorghum. High resolution of RAPD markers was accomplished by radiolabeling PCR-amplified DNAs followed by separation on denaturing 5% polyacrylamide gels. Reaction parameters including MgCl₂ concentration and temperature significantly influenced yield and the type of amplification products synthesized. Unexplained amplified DNAs increased when more than 35 cycles of PCR amplification were used. Under standard conditions, approximately 80% of the primers tested amplified DNA, and most revealed 1–5 polymorphisms between BTx 623 and IS 3620C. Primers were used to amplify RAPDs in 32 genotypes of sorghum. In addition, 8 primers detected RAPDs in a population previously used to create an RFLP map for sorghum. These RAPDs were mapped successfully using a population of 50 F₂ plants.     

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.     

Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

Simple sequence repeats (SSRs) were used to assess genetic diversity and study genetic relatedness in a large collection of Malus germplasm. A total of 164 accessions from the Malus core collection, maintained at the University of Illinois, were genotyped using apple SSR markers. Each of the accessions was genotyped using a single robust SSR marker from each of the 17 different linkage groups in Malus. Data were subjected to principal component analysis, and a dendrogram was constructed to establish genetic relatedness. As expected, this diverse core collection showed high allelic diversity; moreover, this allelic diversity was higher than that previously reported. Cluster analysis revealed the presence of four distinct clusters of accessions in this collection.     

Allozyme variation among the spontaneous species of Sorghum section Sorghum (Poaceae)

Summary A survey of allozyme variation among the spontaneous taxa of Sorghum section Sorghum was undertaken. Eight plants each of 90 accessions representing the diploid S. bicolor (ssp. arundinaceum and drummondii) and the tetraploids S. almum and S. halepense were analyzed for 17 enzyme systems encoded by 30 loci. Low levels of variation were found within and among accessions, although there was more variation than is typical of inbreeding species. We found an average of 3.2 alleles per locus in ssp. arundinaceum, with a mean expected heterozygosity for the accessions of 0.034 and total panmictic heterozygosity of 0.154. An analysis of the apportionment of genetic variation among accessions of ssp. arundinaceum indicated that 26% of the variation occurs within accessions and 74% among accessions. Cultivated sorghum contains far less allozymic variation than ssp. arundinaceum, its presumed progenitor. This is consistent with the prediction that cultivated sorghum experienced a loss of genetic variation during domestication. For the most part, cultivated sorghum contains a subset of the allozymes found in ssp. arundinaceum. Principal component analysis revealed continuous variation among the accessions and geographic regions, with accessions failing to segregate into discrete clusters. However, accessions of race virgatum of ssp. arundinaceum occupied one end of the continuum and were, in that sense, distinguished from the other accessions. Similarly, most accessions of S. halepense and S. almum occupied the central portion of the continuum. The allozymic data presented here are consistent with the hypothesized origin of S. halepense via autopolyploidy or segmental allopolyploidy.     

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.     

Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs non-random sampling procedures A. Using morpho-agronomical and passport data

A large collection, such as the sorghum [Sorghum bicolor (L.) Moench] landrace collection held at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), represents a challenge for the maintenance of both the accessions of and the information documented for the germplasm collection. The accessibility and knowledge of the landrace collection are the essential factors for an efficient utilization of the genetic resources by both breeders and farmers. Different sampling strategies, either random or non-random, were proposed to obtain subsets of reduced size (core collection). Three subsets were established; a random sampling within a stratified collection (logarithmic strategy: L); a sample based upon morpho-agronomic diversity (principal component score strategy: PCS); and a sample based upon an empirical knowledge of sorghum (taxonomic strategy: T). Comparisons of these three samples for morpho-agronomic characterization and passport information were assessed to determine their impact on phenotypic diversity. For their overall diversity, the three subsets did not differ, as shown with the two-dimensional representation of the morpho-agronomic diversity and the Shannon-Weaver diversity indices. When comparisons for morpho-agronomic and passport data were considered, the PCS subset looked similar to the entire landrace collection. The L subset showed differences for characters associated with the photoperiod reaction that was considered in the stratification of the collection. The T subset was the most distinct from the entire landrace collection as it over-represented the landraces selected by farmers for specific uses and covered the widest range of geographical adaptation and morpho-agronomic characteristics. Received: 5 October 1999 / Accepted: 3 November 1999     

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid

 A sorghum composite linkage map was constructed with two recombinant inbred line populations using heterologous probes already mapped on maize and sugarcane. This map includes 199 loci revealed by 188 probes and distributed on 13 linkage groups. A comparison based on 84 common probes was performed between the sorghum composite map and a map of a sugarcane (Saccharum spp.) cultivar being developed and presently comprising 10 tentative linkage groups. A straight synteny was observed for 2 pairs of linkage groups; in two cases, 1 sorghum linkage group corresponded to 2 or 3 sugarcane linkage groups, respectively; in two cases 1 sugarcane link- age group corresponded to 2 separate sorghum linkage groups; for 2 sorghum linkage groups, no complete correspondance was found in the sugarcane genome. In most cases loci appeared to be colinear between homoeologous chromosomal segments in sorghum and sugarcane. These results are discussed in relation to published data on sorghum genomic maps, with specific reference to the genetic organization of sugarcane cultivars, and they, illustrate how investigations on relatively simple diploid genomes as sorghum will facilitate the mapping of related polyploid species such as sugarcane. Received: 12 August 1996 / Accepted: 30 August 1996     

Adaptation of sorghum: characterisation of genotypic flowering responses to temperature and photoperiod

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop grown in a wide range of tropical and temperate environments. This study was conducted to characterise the photothermal flowering responses of sorghum genotypes and to examine relationships between photothermal characteristics and environment of origin in order to better understand the phenological basis of adaptation to environment in sorghum. Twenty-four germplasm accessions and one hybrid from 24 major sorghum-growing areas were grown in a wide range of environments varying in temperature and photoperiod in India, Kenya and Mali between 1992 and 1995. Times from sowing to flowering (f) were recorded, and the responsiveness of 1/f to temperature and photoperiod was quantified using photothermal models. Times from sowing to flowering were accurately predicted in a wide range of environments using a multiplicative rate photothermal model. Significant variation in the minimum time to flower (F_m) and photoperiod sensitivity (critical photoperiod, P_c, and photoperiod-sensitivity slope, P_s) was observed among the genotypes; in contrast there was little variation in base temperature (T_b). Adaptation of sorghum to the diverse environments in which it is grown was largely determined by photoperiod sensitivity and minimum time to flower; photoperiod sensitivity determines broad adaptation to latitude (daylength), while variation in the minimum time to flower determines specific adaptation within smaller ranges of latitude, e.g. within the humid and sub-humid tropics. Received: 16 January 1999 / Accepted: 11 March 1999