Cocoa butterfat and cocoa powder are key economic products from the seeds of the cacao tree (Theobroma cacao L.). In this study, 323 accessions (comprised mainly of Upper Amazon Forasteros and Refractarios) from the International Cocoa Genebank, Trinidad were characterized for one biochemical and five morphological seed-derived traits. The data were analysed using non-parametric statistics including correlation analysis to identify promising parental candidates for future cacao breeding programmes. The Upper Amazon Forastero group had the greatest proportion of accessions with high butterfat content in cotyledons, whereas Refractario and Trinitario groups tended to contain more accessions with high butterfat content per fruit. The correlation of butterfat content of cotyledons with the dry mass of cotyledons was inconsistent in significance and direction. However, consistent significant positive correlations between butterfat content per fruit, cotyledon size and dry mass of cotyledons were found. The results suggested that butterfat content is a likely trait for independent selection but that selection for increased cotyledon size could lead to the selection of genotypes for high butterfat yield. Several promising accessions exhibited favourable levels of multiple traits and MATINA 1/7, CRU 51, AM 2/91 [POU], CRU 133, EET 58 [ECU] and POUND 18/A [POU] could be recommended as good choices for parental stock in breeding programmes for improving cacao butterfat content.

Ethiopia is believed to be the centre of origin and domestication for sorghum, where sorghum remains one of the main staple crops. Loss of biodiversity is occurring at an alarming rate in Ethiopia and crops, including sorghum, have long been recognized as vulnerable to genetic erosion. A major collection of sorghum germplasm was made in 1973 by Gebrekidan and Ejeta from north-eastern Ethiopia. A new collection of landraces was made in 2003, and these were field evaluated at Sirinka in 2004 along with representative samples from the 1973 collection. Farmer surveys and soil and climate surveys were also performed. Preliminary analysis demonstrated that some important landraces have disappeared either locally or regionally in the past 30 years and many other landraces have become marginalized. Landraces which are less preferred in terms of agronomic value and end use, and introductions, have become increasingly important. Late maturing landraces were found to be particularly vulnerable, with a number disappearing altogether. Farmers have become more risk averse, and factors such as declining soil fertility, more frequent drought and unreliable rainfall, and increased pest infestation have contributed to a change in farmer landrace selection. Data are presented on the variability and unique characters of some of the Ethiopian landraces, and implications for conservation are discussed.

Both stover and grain are important considerations in the adoption of the new pearl millet (Pennisetum glaucum) cultivars in crop–livestock farming system in north-west India. Local landrace germplasm contains many of the traits needed to breed new cultivars, which met such requirements. We evaluated 169 pearl millet landraces to assess their potential for breeding new open-pollinated varieties, and measured heterosis in landrace testcrosses to evaluate their potential for topcross hybrids breeding. There were significant differences among landraces in their total biomass, grain yield and stover yield. A high accumulation of biomass, followed by its efficient partitioning, was crucial in determining grain productivity under arid zone. There was also no trade-off between stover and grain productivity and several landraces outperformed check cultivars in both grain and stover yields. The manifestation of heterosis in the landrace-based topcross hybrids varied for different traits. Significant heterosis for biomass, grain yield and stover yield was observed in specific male-sterile seed parent × landrace-based pollinator combinations. Utilization of landraces in variety development and topcross hybrids breeding programmes targeting north-western India or similar regions are discussed.

Karnal bunt (KB) of wheat, caused by Tilletia indica (Mitra) Mundkur, adversely affects international wheat trading and the movement of germplasm between countries due to quarantine restrictions. Breeding for host plant resistance requires the identification of KB resistance sources. Accessions of the D genome progenitor of bread wheat, Aegilops tauschii, were screened in a specially designed screen-house, where the optimum environmental conditions conducive for KB development were simulated by controlling temperature, humidity, fogging and shading. The 183 accessions were subjected to artificial inoculation with a mixture of nine KB isolates, and seven proved highly resistant and four moderately resistant over three rounds of screening over 3 years.

The potential yield levels of sorghum, an important crop in the semi-arid regions of the world, are stagnating due to the narrow genetic base of the genotypes utilized in the sorghum improvement programmes worldwide. For utilization of genetic diversity in any crop, adequate genetic characterization of relevant germplasm is a prerequisite. Therefore, we attempted to identify the potential germplasm lines for improvement of yield in a set of 135 germplasm lines belonging to different races. The experiment was carried out in an augmented design during 2002, and in Randomized complete block design (RCBD) for selected lines during 2003. The correlation studies indicated that besides panicle weight, the number of grains/unit length of primary branch and the number of secondary branches/primary branch had significant positive relation with grain yield. IS nos 1259, 5447, 5725 and 2036 were promising for more than one yield component. The study indicated that besides caudatum race, the lines belonging to guinea, kafir and inter-races with them are good sources for different yield components. Genetic diversity and cluster analysis grouped 40 germplasm lines into eight clusters, with maximum inter-cluster distance between clusters II and III. Utilization of the germplasm lines belonging to different clusters in improving yield components is discussed.

Information on genetic diversity and genetic relationships among taxa of Brassica rapa (n = 10, AA genome) is currently limited. Grown for oil, vegetable and fodder use in Europe and Asia, previous studies have indicated western and eastern groups corresponding to independent centres of origin. This study evaluated patterns and levels of genetic diversity in 93 accessions [includes 25 Agriculture and Agri-Food Canada (AAFC) breeding lines (BL)] of B. rapa based on 307 amplified fragment length polymorphisms (AFLP), testing subspecific separateness and the affiliation of four previously unassigned AA genome species (B. perviridis, B. purpuraria, B. ruvo and B. septiceps). AFLP data revealed three main clusters (I, II, III) corresponding to European (I), Indian (III), and a mixed Asian/European/Indian (II) purported origins of the taxa, with several subclusters observed in I and II. Mean AFLP polymorphism levels for Asian, European, Indian and AAFC-BL accessions were 79, 74, 66 and 62%, respectively. Few of the subspecies formed unique clusters and some, particularly subspecies chinensis and pekinensis, were assigned to several clusters. AFLP-based genetic distance information can be used by breeders to select diverse genotypes for cultivar development and fingerprinting of genotypes/cultivars. For example, a single AFLP primer pair was sufficient to uniquely identify all breeding lines in the AAFC B. rapa breeding programme.

Australia's native grass species contain a diverse array of wild cereal relatives which are adapted to a broader range of environmental conditions than current commercial cereals and may contain novel alleles which have utility in commercial production systems. Characterizing the available variation in endosperm morphology is one of the first steps towards in planta manipulation of endosperm by either the introgression of novel alleles or bioengineering cereal starch and protein. The endosperm of 19 crop wild relatives (CWR) was examined using scanning electron microscopy (SEM). Mature caryopses were fixed, dehydrated, critical-point dried and then snap fractured transversely through the grain. Wild relatives exhibited similar types of starch granules to that of their respective cultivated species, though in general the wild species retained a greater proportion of the endosperm cell wall at maturity. The two species examined with no closely related cultivated species exhibited a rice-like endosperm. Wild sorghum relatives exhibited an abundance of endosperm variations described as variations in starch granule size, shape and surface morphology, and the distribution of protein bodies. This is particularly important because the grain of Sorghum bicolor has inherently low starch and protein digestibility. These variations within the wild relatives of commercial cereals may provide novel sources of genetic diversity for future grain improvement programmes.

Germplasm of 153 flax (Linum usitatissimum) accessions from 24 countries held at Plant Gene Resources of Canada (PGRC) was evaluated for resistance to fusarium wilt (Fusarium oxysporum), anthracnose (Colletotrichum lini) and pasmo (Septoria linicola). The screening was conducted at the All-Russian Flax Research Institute (VNIIL) at Torzhok, Russia, over 3 years for fusarium wilt and anthracnose, and over 2 years for pasmo. A disease severity index ranging from 0% (no infection) to 100% (heavy infection) was calculated based on observations after artificial inoculation with the pathogens in the greenhouse (fusarium wilt) or in field nurseries (anthracnose and pasmo). The average disease severity index for fusarium wilt was 56.6 ± 34.4% (range 0–100.0%), for anthracnose 59.8 ± 8.1% (range 43.8–83.9%) and for pasmo 74.2 ± 11.8% (range 27.3–100.0%). The variation of disease severity indices among the years and within each accession was highest for fusarium wilt. Higher than average resistance for all three diseases was found in accessions from East Asia, while germplasm from the Indian subcontinent showed considerably lower than average resistance. Germplasm from North America and South America (mostly linseed) displayed above average resistance to fusarium wilt, while European accessions (mostly fibre flax) showed lower than average resistance to this disease. The different resistance levels reflected the improvements made by plant breeding and differences in the environments under which the germplasm accessions evolved. Accessions with potential use in linseed and fibre flax breeding were identified.

The aim of this research was to use variance components to calculate total phenotypic variation for 12 vegetative and reproductive maize traits. A set of 59 accessions, belonging to nine Peruvian highland maize races, were grown at two consecutive planting seasons in 2 years at one inter-Andean site in northern Peru. The trial data provided a means for calculating the variance components using the restricted maximum-likelihood method. The variance components were assumed to be stable while the number of environments and replications varied to simulate phenotypic variation for each trait. The least number of environments and replications, which does not affect the precision of phenotyping, was selected for assessing each trait. Tabulated data provide the number of environments and replications that can be used as a reference for Peruvian highland trials to assess quantitative variation in plant and reproductive traits. The results suggest that fewer environments and replications are needed for reproductive than for plant traits because the former show higher heritability than vegetative traits.

The potential for the phylogeographical analysis of cereal landraces to determine the initial patterns of agricultural spread through Europe is discussed in relation to two of the first cereals to be domesticated, emmer wheat (Triticum turgidum subsp. dicoccum) and barley (Hordeum vulgare). Extant landraces available from germplasm collections have a patchy distribution, largely being confined to regions of rugged upland topography, and the phylogeographical patterns observed may be due to ‘overstamping’ by more recent crop movements. Phylogeographical studies of non-viable historical landrace material held in herbarium and old seed collections and found in historical buildings have the potential to fill in the gaps in time and space. We explore the importance of precise geographical provenance and the limitations of this in extant and historical material. Additionally, we consider the effect of various chemicals and the preservation of DNA in the historical material.

A total of 1968 accessions of cultivated eggplants, belonging to Solanum melongena and Solanum aethiopicum and procured from the IVC/JAAS (Nanjing) and IVC/ZAAS (Hangzhou), China, were examined for 23 morphological traits, such as characteristics of plant, stems, leaves, flowers, fruits and original geographic information. A comprehensive numerical classification methodology, including two types of genetic distance, viz. Mahalanobis (Ma) distance and Euclidean (Eu) distance; four clustering methods, viz. unweighted pair group average (UPGA), Ward's (W), complete linkage (CL) and single linkage (SL) methods; three sampling strategies, viz. random (R), preferred (P) and deviation (D); and four sampling sizes (10, 15, 20 and 30% of initial collection), was used to divide all accessions into main groups and subgroups for the establishment of candidate collections. The evaluation of these candidate collections showed that a combination of Eu distance, UPGA clustering method, and R or P sampling strategy with sampling size at 15–20% was suitable for establishing the core collection, providing an adequate and representative genetic diversity of the initial collection of the cultivated eggplants.

The genetic structure of marram grass populations at coastal and inland locations, 200 m apart, was investigated at three sites by means of amplified fragment length polymorphism (AFLP) DNA markers. We expected a genetic differentiation between coastal and inland populations and more genetic variation in the coastal areas as a result of different events of colonization by different plant materials. An assignment test showed that the sampled Ammophila arenaria could be assigned to two groups based on AFLP data. The spatial distribution of the two AFLP types of A. arenaria varied with sampling location. In two of the three locations, mainly one type (1) was found in the newly formed dunes. This type did also occur further landward, but the second type (2) was preferentially found in inland populations. Genetic diversity was very low and of similar value in both coastal and inland populations. For each site, outlier loci with respect to FST value were identified, which may be indicative of different selection pressures in coastal compared with inland clusters. However, no identical outlier loci were found at all three sites. Possible explanations for the observed difference in distribution of type 1 and 2 populations between coastal and inland sites are discussed.

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.

The sequence-specific amplified polymorphism (S-SAP) method was used to genotype 198 Nordic bread wheat landraces and cultivars from the 19th to the 21st centuries. It was shown that the Sukkula-9900-LARD retrotransposon primer was highly suitable for resolving closely related wheat materials. Cluster analysis was generally consistent with pedigree information and revealed a clear separation for growth habit but not for countries. A principal coordinates analysis (PCoA) showed a separation into different time periods (before 1910, 1910–1969 and 1970–2003). These results are consistent with the breeding history and pedigree information, indicating that little hybridization has occurred between winter and spring wheat, in contrast to frequent exchange of germplasm between the Nordic countries. Estimates of gene diversity, the PCoA results, and changes in band frequencies across time indicate that plant breeding has led to substantial genetic shifts in Nordic wheat. Diversity was reduced through selections from landraces during the early 20th century, followed by a period of relatively lower genetic diversity, and a subsequent increase and net gains in diversity from the late 1960s onwards through the use of exotic germplasm. Thus, an anticipated loss of overall genetic diversity was found to be negligible, although allele losses have occurred at specific loci.

Seventeen populations of niger (Guizotia abyssinica), representing all regions in Ethiopia where this crop is grown, were investigated using the amplified fragment length polymorphism (AFLP) technique, in order to determine the extent and distribution of its genetic diversity. A total of 539 AFLP loci were scored using seven primer combinations applied to 170 individual plants. Of these, 90% were polymorphic and all the individuals investigated were genetically unique. Despite the fact that most of the variation was within populations, populations were differentiated at a significant level (analysis of molecular variance; P < 0.001). There were no significant differences between populations in relation to the extent and altitude of cultivation. A significant positive correlation was revealed between Nei's standard genetic distance and geographic distance. Cluster analysis and principal coordinate analysis revealed that populations from the same regions were clustered together in most cases. Further collection of niger germplasm from areas underrepresented in gene bank collections is recommended.

Aegilops species provide an invaluable source of genes for the improvement of cultivated wheats. This paper illustrates how the existing geo-referenced passport data associated with Aegilops species can be used to identify gaps in current conservation and also to develop a more systematic conservation strategy for the genus. Taxonomic, ecological, geographic and conservation information for the 22 Aegilops species were collated from ICARDA, EURISCO, GRIN and SINGER datasets, synthesized and analysed. The combined database contained 9866 unique geo-referenced observations collected between 1932 and 2004. Patterns of specific distribution based on the germplasm accession data and the predicted distribution using climatic models were compared in conservation gap analysis using GIS tools. The ex situ conservation status of each taxon was assessed and used to provide a priority ranking. Future ex situ collection is recommended in Cyprus, Egypt, Greece, Iran, Israel, Libya, Spain, Syria, Tajikistan, Tunisia, Turkey, Turkmenistan and Uzbekistan. The species identified with the highest ex situ conservation priority are as follows: Aegilops bicornis, Aegilops comosa, Aegilops juvenalis, Aegilops kotschyi, Aegilops peregrina, Aegilops sharonensis, Aegilops speltoides, Aegilops uniaristata and Aegilops vavilovii. Patterns of species richness based on the germplasm accession passport data are presented and five complementary regions of Aegilops diversity were identified in west Syria and north Lebanon, central Israel, north-west Turkey, Turkmenistan and south France. Within these areas, 16 IUCN-recognized protected areas are found and these are identified as potential sites to establish genetic reserves. However, the premier Aegilops hotspots on the Syrian/Lebanese border are not coincident with any existing internationally recognized protected areas, and here there is a need to establish a novel protected area.

‘Broccolo fiolaro’ (Brassica oleracea L. convar. Italica) is a typical vegetable produced in a restricted hill country area around Creazzo (Vicenza) in north-eastern Italy. The cultivation of this vegetable dates back several centuries ago, but a very few farms are still involved in the production. ‘Broccolo fiolaro’ is a variety of broccoli highly valued for its agronomic and organoleptic features.

Four ‘Broccolo fiolaro’ selections were characterized by simple sequence repeats (SSRs) molecular markers and compared with other five cultivated varieties of broccoli of the Italica group in order to reconstruct their genetic structure and evaluate the degree of similarity among and within populations. The analysis of 12 SSR polymorphic loci pointed out a low genetic variability among the four ‘Broccolo fiolaro’ selections. Moreover, the whole ‘Fiolaro’ group showed significant differentiation from the other broccoli cultivars and could be easily distinguished by cluster analysis. An assignment test on ~30 genotyped plants randomly chosen from each broccoli population correctly recognized the proper accession 88% of the time, proving this method to be useful for cultivar identification.

An assessment of morphological variation among 70 accessions of greater yam (Dioscorea alata L.) collected throughout Malaysia was made. Data of 47 morphological variables measured from the accessions were subjected to multivariate analysis using principal component (PCA) and cluster analysis (CA). The PCA results indicated that the characters contributing largely to the species variability were those related to the shape, size and flesh colour of underground tubers; shape and colour of aerial tubers; position, shape, size and vein colour of the leaves; petiole colour; shoot growth rate; and number of days for shoots to germinate. The two-dimensional plot of the first two PCs showed a separation between accessions of purple tuber groups and those of white tuber groups, but was unable to distinguish accessions according to tuber shape groups, i.e. irregular, oblong and round, as revealed by visual observation. The dendrogram of CA revealed four major groups of D. alata in Malaysia, which supported the PCA grouping. This study demonstrated that D. alata in Malaysia consists of numerous genotypes revealing wide inter- and intra-group variability.

Flavonoid content was quantified by high performance liquid chromatography (HPLC) and seed-coat colour was recorded from different legume seeds. Soybean seeds generally contained significantly higher amounts of daidzein (315–354 μg/g), genistein (438–458 μg/g), kaempferol (38–68 μg/g) and total measured flavonoids (892–917 μg/g), while cowpea and peanut seeds contained a significantly higher amount of quercetin (214–280 μg/g and 133–289 μg/g, respectively) than the other legumes tested. Significant variation for flavonoid content existed among and within legume species. Daidzein was significantly correlated with genistein and kaempferol (r = 0.92, P < 0.0001; r = 0.68, P < 0.0001), respectively. Genistein was also significantly correlated with kaempferol (r = 0.84, P < 0.0001). Due to differences in genetic background, no consistent relationship was observed between seed-coat colour and flavonoid content. Variation observed in flavonoid content and seed-coat colour would be useful for legume breeding programmes and consumer use.

Kernel texture (grain hardness) in common wheat (Triticum aestivum L.) is of primary technological importance and is largely determined by puroindoline gene sequence and expression. We investigated the puroindoline haplotypes of 246 Asian common wheat varieties. All but three were conclusively characterized for puroindoline a and b haplotypes. Of the total, 174 possessed the soft Pina-D1a/Pinb-D1a ‘wild-type’ gene sequences with SKCS hardness indexes (HI) ranging from 13.5 to 61.8. Among the remaining 72 varieties with HIs of 56.1–97.8, nearly half (30) were Pina-D1a/Pinb-D1b, 4 were Pina-D1a/Pinb-D1c, 19 were Pina-D1a/Pinb-D1p, 10 were Pina-D1b/Pinb-D1a (‘a-null’), 3 were Pina-D1l/Pinb-D1a, 2 possessed a new C-to-T SNP mutation at position 382, which is tentatively designated Pinb-D1ab, 1 was a ‘double null’ with neither puroindoline a nor b expressed and no PCR-detectable gene sequence, and 3 had undetermined/ambiguous puroindoline a sequence but possessed Pinb-D1a. The double null was the hardest of all varieties tested with an HI of 97.8. The frequency of soft and hard varieties and puroindoline hardness haplotype varied depending on the origin of the varieties. The lowest frequency of hard varieties occurred in Korea and south-western Japan. Tibet and Pakistan also had low frequencies of hard varieties. The highest frequency of hard varieties appeared in north-east China followed by north-west China and Nepal. Within Asia, the Pinb-D1p allele appears in a region extending from north-eastern China through Inner Mongolia, north-western China, Xinjiang and Tibet, with the greatest frequency in north-western China. This allele was also present in Pakistan and Afghanistan, but not found in Japan, and may have been dispersed along the ‘Silk Road’. All three Pina-D1l varieties came from China. The newly discovered SNP originated in Afghanistan and the ‘double null’ in Xinjiang.