Temporal variation of diversity in Italian durum wheat germplasm

The aim of this work is to analyse the temporal change of genetic diversity in Italian durum wheat germplasm. The germplasm deployed in this study (158 accessions), belonging to 5 different historical classes, was characterised for its microsatellite and gliadin markers. The level of genetic diversity (He), based on gliadin and SSR markers results – on average – greater in indigenous landraces present in Italy before 1915, with the exception of pure line material which had been selected from landraces (showing highest level of heterozigosity for gliadin markers). Genotypes obtained from crosses or mutagenesis (referring to the 1950–1960 period) along with those resulting from crosses between CIMMYT lines and old materials (1970s and beyond) were also genetically more diverse. Forty-nine percent of indigenous landraces were genetically heterogeneous. Nine out of 53 landrace accessions were able to capture 4 different SSR private alleles. It is speculated that the reduction of allele richness is an indicator of the genetic erosion of the pre-breeding germplasm and it is pointed out that the implementation of appropriate methods of genetic conservation of this germplasm is a priority for breeding and food safety.     

Sources of resistance to Hessian fly (Diptera: Cecidomyiidae) in Syria identified among Aegilops species and synthetic derived bread wheat lines

The Hessian fly, Mayetiola destructor (Say), is a major pest of wheat in North Africa, southern Europe, North America, and northern Kazakhstan. It is believed this pest (like wheat) originated in West Asia. The Syrian Hessian fly biotype has been found to be the most virulent worldwide, and has been used at the International Center for Agricultural Research in the Dry Areas (ICARDA) for screening wheat and its wild relatives to identify new sources of resistance. The screening was conducted in an insect rearing room set at 20°C and 70% RH using a Hessian fly population collected from Lattakia region, Syria. The experimental design was a randomized complete block with four replications. ‘Nasma’ (bread wheat) and ‘Cando’ (durum wheat) were used as susceptible and resistant checks, respectively. A total of 623 lines/accessions of wheat and its wild relatives (Aegilops and Triticum) were evaluated. Twenty-nine Aegilops accessions and four synthetic derived bread wheat lines were found resistant. The presence of dead first instars confirmed the resistance reaction and also showed that antibiosis is the major mechanism of resistance in these materials. These sources of resistance are used in ICARDA’s wheat breeding programs for the development of Hessian fly-resistant germplasm/varieties.     

Into the vault of the Vavilov wheats: old diversity for new alleles

Intensive selection in wheat (Triticum aestivum L.) breeding programs over the past 100 years has led to a genetic bottleneck in modern bread wheat. Novel allelic variation is needed to break the yield plateau, particularly in the face of climate change and rapidly evolving pests and pathogens. Landraces preserved in seed banks likely harbour valuable sources of untapped genetic diversity because they were cultivated for thousands of years under diverse eco-geographical conditions prior to modern breeding. We performed the first genetic characterisation of bread wheat accessions sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR) in St Petersburg, Russia. A panel comprising 295 accessions, including landraces, breeding lines and cultivars was subject to single seed descent (SSD) and genotyped using the genotyping-by-sequencing Diversity Arrays Technology platform (DArT-seq); returning a total of 34,311 polymorphic markers (14,228 mapped and 20,083 unmapped). Cluster analysis identified two distinct groups; one comprising mostly breeding lines and cultivars, and the other comprising landraces. Diversity was benchmarked in comparison to a set of standards, which revealed a high degree of genetic similarity among breeding material from Australia and the International Maize and Wheat Improvement Center (CIMMYT). Further, 11,025 markers (1888 mapped and 9137 unmapped) were polymorphic in the diversity panel only, thus representing allelic diversity potentially not present in Australian or CIMMYT germplasm. Open-access to DArT-seq markers and seed for SSD lines will empower researchers, pre-breeders and breeders to rediscover genetic diversity in the VIR collection and accelerate utilisation of novel alleles to improve wheat.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Genetic relationship among selected heat and drought tolerant bread wheat genotypes using SSR markers,agronomic traits and grain protein content

ABSTRACT

Assessing the genetic variation and relationships present in crop germplasm is a pre-requisite for parental selection and breeding. The objective of this study was to determine the genetic relationships present among selected heat and drought tolerant wheat genotypes using simple sequence repeat (SSR) markers, agronomic traits and grain quality parameters to select desirable parents for breeding. Twenty-four agronomically selected wheat genotypes sourced from the International Maize and Wheat Improvement Centre (CIMMYT)’s heat and drought tolerance nursery and four local check varieties were genotyped using 12 selected polymorphic SSR markers. The test genotypes were phenotyped using yield and yield-component traits, and grain protein content (GPC) under non-stressed (NS) and drought-stressed (DS) conditions. Expected heterozygosity mean value of 0.58 indicated moderate genetic diversity for breeding. The studied wheat genotypes were delineated into six genetic groups using cluster analysis. Significant genotypic differences were observed for agronomic traits and GPC under NS and DS conditions. Genetically unrelated breeding parents including LM02, LM13, LM23, LM41, LM44, LM71, LM73 and LM75 were selected for population development and breeding for enhanced grain yield and protein content under heat and drought-stressed environments.     

Multivariate Analysis of Diversity of Tetraploid Wheat Germplasm from Ethiopia

The variability of 2420 plants of tetraploid (2n = 4x = 28, AABB genome) wheat germplasm representing 121 accessions from Ethiopia were evaluated for 23 agro-morphological traits at Debre Zeit Agricultural Research Center area, Akaki substation, during the 2003 main season using multivariate methods. This enabled to assess the extent and pattern of variation of the germplasm with respect to regions, altitude classes and species and to identify the major traits contributing to the diversity. The first three and two principal components explained about 83 and 80% of the total variance among regions and altitudinal class, respectively. In the first principal component plant height, days to heading, the length and density of the spike, and kernel color were the most important traits contributing to variation that explained about 50% of regional variance. Cluster analysis grouped the accessions into 15 clusters, with 9 accessions remaining ungrouped. Based on the observed patterns of variation, it is concluded that there exists great variation in the germplasm, which provides opportunities to be utilized for genetic improvement.     

Centres of Crop Diversity and/or Origin, Genetically Modified Crops and Implications for Plant Genetic Resources Conservation

The concept of centres of crop diversity and/or origin of agriculture is briefly reviewed. The conservation status of crop genetic resources, either ex situ or in situ, cultivated or wild, has been assessed for species of the Central American and Mexican centre, demonstrating that that region is indeed one of the important centres of crop diversity for human kind. Furthermore, biotechnological developments with regard to the creation and spread of genetically modified crops have been analyzed. The likelihood of unintentional introgression of genetically modified traits into conventional seed lots, crops as well as into germplasm collections have been assessed. Related biosafety measures as well as the possible implications of intellectual property rights on transgenic crops and/or genes are being discussed vis-a-vis the possible implications they might have for germplasm management. The Central American crop genetic resources situation has been used as a “case study” to illustrate the potential impact of the spreading of GM varieties on the genetic diversity in genebanks and farmers’ fields and the need for effective and efficient conservation efforts. Conservation management strategies and practices are being proposed of mitigate the potential negative impact of GM crops on the conservation efforts.     

Pattern of genetic diversity of cultivated and non-cultivated mashua, <Emphasis Type="Italic">Tropaeolum tuberosum</Emphasis>, in the Cusco region of Perú

This paper analyzes the genetic diversity of mashua cultivars grown in six communities in the Cusco region of Perú, of non-cultivated forms collected in the same region, and a sample of cultivars from the germplasm collection at the International Potato Center (CIP). From the DNA fingerprinting generated by SRAP markers, it is clear that mashua is a genetically variable crop with a range of similarity ranging from 65 to 99%. The widest range of variation was found for the most isolated community, Sayllafaya. Another important finding was that most of the non-cultivated accessions are likely feral races resulting from escape to cultivation rather than wild relatives. In general the range of variation of the cultivars from the communities and their feral relatives are not represented in the cultivars sampled of the collection maintained at the International Potato Center, Perú.     

Realizing value of genetic resources of <Emphasis Type="Italic">Allium</Emphasis> in India

The genetic resources of Allium in India are potential source of genes for widening the crop genetic base. Despite their high economic value, limited number of germplasm accessions of wild species have been collected and conserved mainly due to difficult access to areas of occurrence. The present work mainly highlights information on species diversity distribution and utilization of wild Allium species to assess the value of Indian germplasm and prioritization for future collection and conservation programmes.     

Genetic Diversity of Glutenin Protein Subunits Composition in Durum Wheat Landraces [Triticum turgidum ssp. turgidum Convar. durum (Desf.) MacKey] from the Mediterranean Basin

The genetic diversity of high and low molecular weight glutenin subunits of 63 durum wheat landraces from different geographical regions in the Mediterranean Basin was studied using SDS-PAGE. Great variability in glutenin composition was found, with 42 high and low molecular weight glutenin haplotypes, 20 allele combinations at the HMW-GS loci, and 18 at the LMW-GS. All five possible LMW models were detected in all Mediterranean regions. Rare alleles were found at Glu-B1 locus in high frequencies and a priori related alleles to grain quality were also observed. Global genetic diversity index was relatively high (0.67); it ranged from 0.33 to 0.66. Cluster analysis on the frequency patterns of origins grouped genotypes following a geographical structure. Rogers’ distance coefficient on frequency pattern for each region of origin showed two germplasm pools with distinct quality profiles, where South West Asian landraces were very different from the landraces of other Mediterranean areas. The relationship between different regions of origin is discussed and two possible ways of introduction of wheat in the Iberian Peninsula (N Africa and SE Europe) are hypothesized. The use of Mediterranean durum wheat landraces as source of genetic variability for grain quality improvement is highly recommended.     

Genetic Diversity and Relationships of Wheat Landraces from Oman Investigated with SSR Markers

Little is known about genetic diversity and geographic origin of wheat landraces from Oman, an ancient area of wheat cultivation. The objectives of this study were to investigate the genetic relationships and levels of diversity of six wheat landraces collected in Oman with a set of 30 evenly distributed SSR markers. The total gene diversity, (H_T), conserved in the three durum wheat (Triticum durum desf.) landraces (H_T = 0.46) was higher than in the three bread wheat (Triticum aestivum L.) landraces (H_T = 0.37), which were similar to Turkish and Mexican bread wheat landraces calculated in previous studies. Genetic variation partitioning (G_ST) showed that variation was mainly distributed within rather than among the durum (G_ST = 0.30) and bread wheat (G_ST = 0.19) landraces. Based on modified Rogers’ distance (MRD), the durum and bread wheat landraces were distinct from each other except for a few individuals according to principal coordinate analysis (PCoA). One bread wheat landrace (Greda) was separated into two distinct sub-populations. A joint cluster analysis with other landraces of worldwide origin revealed that Omani bread wheat landraces were different from other landraces. However, two landraces from Pakistan were grouped somewhat closer to Omani landraces indicating a possible, previously unknown relationship. Implications of these results for future wheat landrace collection, evaluation and conservation are discussed.     

Grain Quality of Emmer Wheat Derived Synthetic Hexaploid Wheats

The wild diploid goat grass (Aegilops tauschii Cosson), and the cultivated tetraploid emmer wheat (Triticum turgidum L. subsp. dicoccon (Schrank) Thell.) may be important sources of genetic diversity for improving hexaploid bread wheat (Triticum aestivum L.). Through interspecific hybridization of emmer wheat and Ae. tauschii, followed by chromosome doubling, it is possible to produce homozygous synthetic hexaploid wheat. Fifty-eight such synthetic hexaploids were evaluated for grain quality parameters: grain weight, length, and plumpness, grain hardness, total protein content, and protein quality (SDS-Sedimentation volume, SDS-S). Most synthetics showed semi-hard to hard grain texture. Results showed significant genetic variation among the synthetic hexaploids for protein content, SDS-S values, and grain weight and plumpness. Quality measurement values of synthetic hexaploids were regressed on corresponding values of the emmer wheat parents. With this offspring-parent regression, protein content and SDS-S values explained 8.7 and 28.8%, respectively, of the variation among synthetics, indicating a significant contribution from the emmer wheat parents for these traits. The synthetic hexaploids, in general, had significantly higher protein content (15.5%, on average) and longer grains than ‘Seri M82’, the bread wheat control (13.1% protein content). Synthetics with SDS-S values and grain weights higher than those of ‘Seri M82’ were also identified. Protein content among synthetics showed significantly negative correlations with grain weight and plumpness, but no correlation with SDS-S values. Despite these negative correlations, 10 superior synthetic hexaploid wheats, derived from nine different emmer wheat parents and with above average levels of protein content, SDS-S values, and either grain weight or plumpness, were identified. This study shows that genetic variation for quality in tetraploid emmer wheat can be transferred to synthetic hexaploid wheats and combined with plump grains and high grain weight, to be used for bread wheat breeding.     

The Dynamics of on-farm Management of Sorghum in Ethiopia: Implication for the Conservation and Improvement of Plant Genetic Resources

On-farm conservation of plant genetic resources for food and agriculture has received strong support worldwide in recent years. It has been justified on appealing assumptions: it complements ex situ conservation, allows co-evolutionary interaction of host–pathogens and crop–weed complexes, and involves local knowledge systems. This article illustrates how on-farm conservation being set for its sake is extremely difficult under farmers’ dynamic management of plant genetic resources based on sorghum. The dynamics of their management could be explained by continued introduction, displacement, loss and maintenance of aboriginal landraces that have distinct functional attributes, patch-occupancy and relative abundance profiles. Such management and hence the dynamic landrace demography has largely been triggered by co-evolving biophysical stresses, spatial and seasonal variations. The best viable alternative to support farmers’ management of genetic resources is to link conservation to crop improvement both to enhance on-farm genetic diversity and make the biophysical environment a comfortable home for the plant genotypes.     

Testing of rye-specific markers located on 1RS chromosome and distribution of 1AL.RS and 1BL.RS translocations in Turkish wheat (Triticumaestivum L., T.durum Desf.) varieties and landraces

Rye (Secale cereale L.) is a valuable source for alien chromosome translocations in wheat breeding, due to its capability to grow and sustain under harsh environmental conditions. Wheat germplasm with 1AL.1RS and 1BL.1RS wheat-rye chromosome translocations have been used worldwide by breeders. Determining 1AL.1RS and 1BL.1RS translocations in wheat is therefore of important practical value for wheat improvement. In this study, nine rye-specific markers detecting the rye chromosome 1RS in wheat background were evaluated. The markers PAWS5/S6, SCM9 and O-SEC5′-A/O-SEC3′-R amplified specific bands associated with 1AL.1RS and 1BL.1RS translocations. These three markers therefore provide a quick and reliable tool to identify and to discriminate these two wheat-rye translocations in wheat background. Six out of nine rye specific markers were subsequently used to determine the frequency of these translocations in commonly grown bread and durum wheat cultivars from Turkey. One hundred seven wheat cultivars and landraces were molecularly screened. Among them, only 4% (‘Seri-82’, ‘Yıldız-98’, ‘Tahirova’, and ‘Osmaniyem’) harbor the 1BL.1RS translocation whereas the 1AL.1RS translocation was not found. The information provided here will contribute to the creation of new Turkish wheat populations with a larger genetic diversity necessary for future requirements.     

Development of Core Collection in Pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millspaugh] using Geographic and Qualitative Morphological Descriptors

Pigeonpea is an important pulse crop grown by smallholder farmers in the semi-arid tropics. Most of the pigeonpea cultivars grown to date are selections from the landraces, with a narrow genetic base. With the expansion of the crop to newer areas, problems of local importance are to be addressed. Hence, an economically feasible and faster germplasm evaluation mechanism, such as a core collection, is required. This article describes the development of core collection from 12,153 pigeonpea accessions collected from 56 countries and maintained at ICRISAT, Patancheru, India. The germplasm accessions from 56 countries were placed under 14 clusters based primarily on geographic origin. Data on 14 qualitative morphological traits were used for cluster formation by Ward’s method. From each cluster ≈10% accessions were randomly selected to constitute a core collection comprising 1290 accessions. Mean comparisons using Newman–Keuls test, variances’ comparisons by Levene’s test, and comparison of frequency distribution by χ²-test indicated that the core collection was similar to that of the entire collection for various traits and the genetic variability available in the entire collection is preserved in the core collection. The Shannon–Weaver diversity index for different traits was also similar for both entire and core collection. All the important phenotypic associations between different traits available in the entire collection were preserved in the core collection. The core collection constituted in the present study facilitates identification of useful traits economically and expeditiously for use in pigeonpea improvement.     

Who is sowing our seeds? A systematic review of the use of plant genetic resources in research

Collections of plant genetic resources managed by genebanks function to conserve the range of genetic diversity present in crop genepools. They can facilitate access to valuable allelic variation for both plant breeders and researchers who are able to request germplasm for use in crop improvement and both basic and applied scientific research. The direct impact of genebank collections is often unclear as downstream uses of germplasm samples may not be reported back to the genebank of origin. This study aims to systematically review scientific use of germplasm using the UK Vegetable Genebank (UKVGB) as a model. Between the years of 1980–2016, a total of 271 publications were identified as using UKVGB material. The frequency of publications and the international nature of use increased significantly over the time period studied. Accessions directly sourced from the UKVGB made up the majority of material used by researchers, but material from research-derived resources such as differential sets and core collections or diversity sets have also been used. Resistance to pests and diseases and genetic diversity were the main topics of study although germplasm was used to address a wide range of other research questions. Genebanks such as UKVGB provide an essential resource of allelic diversity in crop genepools which supports a diverse range of research projects. The utilisation of these plant genetic resources has increased over time, contributing to a substantial number of publications. Developments in sequencing technologies have no doubt played a part as larger numbers of accessions can be utilized in a single experiment, but the increase also no doubt reflects a greater interest in the use of allelic diversity to overcome challenges in crop improvement and research.     

Costing the ex situ conservation of plant genetic resources at AVRDC – The World Vegetable Center

AVRDC – The World Vegetable Center maintains the world’s largest international public collection of vegetable genetic resources at its headquarters in Taiwan. The ex situ conservation and dissemination of germplasm to researchers and breeders worldwide contributes to global food and nutrition security but also carries considerable costs. The objective of this study is to quantify these costs for the 12-month period from September 2011 to August 2012 using the Decision Support Tool developed by the International Food Policy Research Institute. The results show that the present value of capital assets is USD 1.99 million for the facilities and USD 0.48 million for the equipment. The total annual cost is USD 0.684 million, of which 74 % are labor costs. The average conservation and dissemination cost per accession is USD 10.08 per year. Seed regeneration, seed processing, characterization, and seed dissemination are the four most costly operations of the genebank. The storage itself only contributes 17 % of the cost. In comparison, the average cost per accession is USD 5.15 at ICARDA, USD 6.84 at CIMMYT, USD 8.62 at ICRISAT, USD 9.19 at IRRI, and USD 22.52 at CIAT (in 2012 US dollar values). High labor costs in Taiwan increase AVRDC’s average cost, but the fact that more vegetable species are self-pollinating and thus less labor intensive to regenerate than cross-pollinating species keeps the average costs in check. These results are important benchmarks for other genebanks.