A useful biological interpretation of diploid heterozygotes is in terms of the dose of the common allele (0, 1 or 2 copies). We have developed a PERL script that converts FASTA files into coded spreadsheets suitable for principal component analysis. In combination with R and R Commander, two- and three-dimensional plots can be generated for visualizing genetic relationships. Such plots are useful for characterizing plant genetic resources. This method nicely illustrated the spectrum of genetic diversity in tomato landraces and the varieties categorized according to human-mediated dispersal.

In this study, the targetting-induced local lesions in genomes approach was used to identify mutants for genes related to starch metabolism in barley. Starch is the major reserve of plants and serves as primary carbohydrate component in human and livestock diets and has also numerous industrial applications. Mutants for biosynthetic or regulatory genes of starch metabolism often produce starch granules with abnormal morphological and molecular features that could be of interest for technological applications. We report the identification of 29 mutations in five starch-related barley genes (Bmy1, GBSSI, LDA1, SSI and SSII) through the molecular screening of TILLMore, a sodium azide-mutagenized population. Almost all the mutations detected were CG–TA transitions and several (c. 60%) implied a change in amino-acid sequence and therefore possible phenotypic effects. Four mutants showed non-sense or splice-junction alterations, which could drastically affect the protein function.

This study reviews the various conservation strategies applied to the four redwood species, namely coast redwood (Sequoia sempervirens), Sierra redwood or giant sequoia (Sequoiadendron giganteum), dawn redwood (Metasequoia glyptostroboides) and South American redwood or alerce (Fitzroya cupressoides), which are endemic in the USA, China and South America, respectively. All four redwood genera belong to the family Cupressaceae; they are monospecific, share a number of common phenotypic traits, including red wood, and are threatened in their native ranges due to human activity and a changing climate. Therefore, the management objective should be to conserve representative populations of the native species with as much genetic diversity as possible for their future survival. Those representative populations exhibiting relatively high levels of genetic diversity should be selected for germplasm preservation and monitored during the conservation phase by using molecular markers. In situ and ex situ strategies for the preservation of germplasm of the redwoods are discussed in this study. A holistic in situ gene conservation strategy calls for the regeneration of a large number of diverse redwood genotypes that exhibit adequate levels of neutral and adaptive genetic variability, by generative and vegetative methods for their preservation and maintenance in their endemic locations. At the same time, it would be desirable to conserve the redwoods in new ex situ reserves, away from their endemic locations with similar as well as different environmental conditions for testing their growth and survival capacities. In addition, other ex situ strategies involving biotechnological approaches for preservation of seeds, tissues, pollen and DNA in genebanks should also be fully exploited in the face of global climate change.

Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), diversity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Advent of the next generation sequencing technologies coupled with advances in bioinformatics offers the possibility of undertaking large-scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.

Chickpea is the third most important pulse crop worldwide. Changes in cropping system that necessitate late planting, scope for expansion in rice fallows and the global warming are pushing chickpeas to relatively warmer growing environment. Such changes demand identification of varieties resilient to warmer temperature. Therefore, the reference collection of chickpea germplasm, defined based on molecular characterization of global composite collection, was screened for high temperature tolerance at two locations in India (Patancheru and Kanpur) by delayed sowing and synchronizing the reproductive phase of the crop with the occurrence of higher temperatures ( ≥ 35°C). A heat tolerance index (HTI) was calculated using a multiple regression approach where grain yield under heat stress is considered as a function of yield potential and time to 50% flowering. There were large and significant variations for HTI, phenology, yield and yield components at both the locations. There were highly significant genotypic effects and equally significant G × E interactions for all the traits studied. A cluster analysis of the HTI of the two locations yielded five cluster groups as stable tolerant (n = 18), tolerant only at Patancheru (n = 34), tolerant only at Kanpur (n = 23), moderately tolerant (n = 120) and stable sensitive (n = 82). The pod number per plant and the harvest index explained ≥ 60% of the variation in seed yield and ≥ 49% of HTI at Kanpur and ≥ 80% of the seed yield and ≥ 35% of HTI at Patancheru, indicating that partitioning as a consequence of poor pod set is the most affected trait under heat stress. A large number of heat-tolerant genotypes also happened to be drought tolerant.

Zingiber barbatum Wall. (family Zingiberaceae), is an underutilized medicinal plant and commonly known as ‘Meik tha-lin’ in Myanmar where it is used in the indigenous system of medicine. In the present study, 19 accessions of Z. barbatum from five provinces in Myanmar have been utilized to characterize and assess genetic diversity. Twenty-nine morphological characters were noted, including growth habit, leaf, pseudo-stem and rhizome characters. Fifteen primer sets of P450-based analogue (PBA) markers were used to reveal molecular characteristics. Of the 29 morphological characters, 22 showed a high degree of variation within wild ginger accessions, whereas 20 of these characters contributed significantly to morphological variation. Eleven amplified primer sets gave a total of 175 bands and exhibited 92.15% polymorphism across Z. barbatum accessions. Based on morphological characters and PBA markers, 19 accessions can be divided into two morphotype groups with comparatively higher genetic diversity. This information can be applied in future crop improvement, proper conservation and better use of this underutilized medicinal species.

We have established mutant collections of the model species Medicago truncatula according to current protocols. In particular, we used a transposon (Tnt1) tagging method and an ethyl methanesulfonate (EMS) mutagenesis approach (TILLING). The collections were subjected to both forward and reverse genetics screenings, and several mutants were isolated that affect plant traits (e.g. shoot, root developments, flower morphology, etc.) and also biosynthetic pathways of secondary compounds (saponins and tannins). Genes responsible for some of the mutations were cloned and further characterized.

Dwarfing genes play an important role in improving yield and adaptability of wheat cultivars in most production environments. Understanding the allelic distribution at dwarfing loci is very important for any wheat-breeding programmes. In this study, we reported the allelic constitution at microsatellite locus Xgwm261 and the two major height-reducing genes Rht-B1 and Rht-D1 among a set of 56 bread wheat cultivars and nine landraces, based on diagnostic polymerase chain reaction assays. With respect to Rht-B1, 37% of the accessions carried the dwarfing allele Rht-B1b, while at Rht-D1, only one accession carried the dwarfing allele Rht-D1b. The allelic state at Rht8 was assayed indirectly by genotyping for the linked microsatellite locus Xgwm261. About 26% of the accessions carried the 192 bp allele (linked with Rht8 gene in some cases), whereas 35 and 12% genotypes carried 165 and 174 bp allele at the microsatellite locus Xgwm261. Cultivars released from 1980 onwards increasingly carried either Rht-B1b or Rht8. This information should allow for a more rational use of this collection for the purpose of wheat improvement in Turkey.

The Onobrychis genus comprises a few agronomically important forage legume species, with sainfoin (Onobrychis viciifolia) being the most widespread. O. viciifolia has a long history of traditional culture worldwide, but its use has declined in western countries over the last decades. It suffers from low productivity and is more difficult to maintain than other legumes but is known to have valuable characteristics such as palatability and drought tolerance. Recent studies suggest that it has several other highly beneficial properties due to its unique tannin and polyphenol composition. Condensed tannins present in Onobrychis species have been shown to confer anthelmintic properties, increase protein utilization and prevent bloating; they may also have the potential to reduce greenhouse gas emissions. Positive effects on wildlife and honey production could also be advantageous in the context of sustainable farming. Modern breeding programmes have not been a priority, leading to a lack of genetic knowledge in comparison to extensively used forage legumes. It is expected that potential for O. viciifolia improvements could be achieved by rigorous characterization of the available germplasm and utilization of characters derived from close relatives of the genus. Breeding priorities for the future would include enhanced germination and improved early establishment, allied to the best anthelmintic properties observed in some varieties.

The International Cocoa Genebank, Trinidad, is the largest field genebank collection of cacao (Theobroma cacao L.) in the public domain and the correct identity of each tree is crucial for germplasm movement, evaluation and phenotypic characterization. Nine microsatellite loci were used to assess the identity of 1477 trees from 486 cacao accessions representing approximately 16.9% of the trees and 29.2% of the accessions within the genebank. Heterogeneous plots (plots containing more than one genotype group) averaged 25.1% in The International Cocoa Genebank, Trinidad, with maximal admixture (32.6%) being recorded in Field 5B. The error rate did not differ significantly among different fields. Mislabeling error could be affected by accession grouping with an average error rate of 27.4% for accession groups in the genebank. Synonymous accessions were estimated to account for 14.4% of the field genebank. The results of the present study provide essential information for the management and utilization of the germplasm collection. Single-tree genotyping of every tree in this collection is strongly recommended.

Alternative oxidase (AOX) has been proposed as a promising functional marker candidate for multiple plant stress behaviour. The present paper describes natural polymorphism in AOX2b of Daucus carota L. (DcAOX2b). Exon-primed intron crossing-PCR (EPIC-PCR) revealed length variation (intron length polymorphisms, ILPs) in intron 1. Six fragment patterns were identified in 40 genotypes. However, no more than two fragments were found per genotype, suggesting the presence of two alleles. The ILPs were able to discriminate between single plant genotypes in cv. Rotin and to distinguish individual wild carrot plants. The repetitive pattern of intron 1 length variation allows the grouping of genotypes for functional analysis in future studies. Sequence analysis in intron 1 of polymorphic but also of obviously identical PCR-fragments revealed underlying high levels of sequence polymorphisms between alleles and genotypes. Variation was due to repetitive insertion/deletion (InDel) events and single-nucleotide polymorphisms (SNPs). The results suggest that high AOX2b gene diversity in D. carota may be a source of functional markers for agronomic traits related to environmental stress responses.

Faba bean (Vicia faba L.) was used as the rootstock for lentil scions to test the feasibility of using in vivo inter-generic grafting techniques as a substitute for root induction and as a tool in lentil genetic improvement. An accession of each of the six wild Lens species was used as the scion in grafts to faba bean breeding line FB50-9 rootstock. Successful grafts were obtained for all species with survival of grafts to seed maturity between 70.7 and 87.7% except for Lens orientalis PI 72735 with 55.3% survival. Days to flower remained the same after grafting, except for scions of L. nigricans PI 72560 and L. orientalis PI 72735 which had a lag phase of 9 and 7 d, respectively. For all six wild species, seed diameter and seed weight were not significantly different between non-grafted controls and scions grafted onto faba bean rootstocks. This simple approach opens the possibility of using in vivo grafting techniques to rescue inter-specific hybrids of lentil. The technique has potential as a useful tool in lentil breeding, as a means of improving seed multiplication rate of rare genetic resources of wild lentil and as a way to reduce the costs of germplasm multiplication of wild lentil species.

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

Based on the distribution, molecular similarity and use of Morinda citrifolia L., and occurrence of a wild Morinda species, Southeast Asia and Micronesia have been suggested to be the places where noni originated. The present article discusses the indices used by Vavilov and subsequent authorities on the origin of crop plants to argue that South Asia (Southeast India) has a greater probability of being the centre of domestication/origin for noni than Southeast Asia or Micronesia. The basic reasoning is that economically important plant cannot originate without richness in biodiversity and ingenuity of local people. India with rich floristic diversity, one of the centres of origin of crop plants with a natural distribution of Morinda species, including M. citrifolia L. and its immediate ancestors, has the oldest reference of occurrence, use and cultivation (Vedic literature); therefore, it appears to be the more probable centre of noni's origin. The ancient history of the expansion of Indian culture, religion and trade to Southeast Asian countries corroborate the possible role of Indians in the introduction of noni or knowledge regarding its value to Southeast Asia, from which it was carried to Micronesia and Polynesia, which provided a more favourable environmental niche for perpetuation and use.

Triticale possesses favourable agronomic attributes originating from both its wheat and rye progenitors, including high grain and biomass yields. Triticale, primarily used as animal feed in North America, is an excellent candidate for production of industrial bio-products. Little is known about the coordination of gene expression of rye and wheat genomes in this intergeneric hybrid, but significant DNA losses from the parental genomes have been reported. To clarify the regulation of gene expression in triticale, we carried out 454 sequencing of cDNAs obtained from root, leaf, stem and floral tissues in different lines of triticale and rye exhibiting different phenotypes and assembled reads into contigs. Related to the data assembly were the absence of reference genomes and the paucity of rye sequences in GenBank or other public databases. Consequently, we have sequenced cDNA libraries from roots, seedlings, leaves, floral tissues and immature seeds to facilitate the identification of triticale sequences originating from rye. To further characterize the wheat-derived cDNAs, we also developed a database close to 25,000 non-redundant full-length wheat coding sequence genes, based on existing databases and contigs that were verified against protein sequences from the grass genomes of Brachypodium distachyon, rice, sorghum and maize.

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgaris L.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescent versus non-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

Mineral concentration levels in cultivated vegetables have received very little concern in the context of biodiversity despite the fact that most vegetables have a rich micronutrient composition. Swiss chard is an important salad crop which is high yielding and rich in minerals, vitamins and phenolic compounds. It is also extremely easy to grow. However, there is a lack of information on the genetic variability of mineral concentration of Swiss chard. Mineral composition diversity of 54 genetically diverse Swiss chard accessions, representative of all Turkish Swiss chard genetic resources, was investigated using multivariate analysis. These traits are useful in evaluating germplasm diversity in the nutritional concentration context and for use in further breeding programmes which will focus on improving mineral concentrations in Swiss chard cultivars. The results displayed significant differences among accessions and remarkably high nutrient contents. The data gathered were analyzed using principal components (PCs) and cluster analysis and revealed five major groupings. The data also observed 74.39% of total variation. The first three PCs accounted for 49.86% of the total variation in the population. Present values provided great variability among accessions and the results demonstrate that it is possible to identify genetic differentiation among Swiss chard accession for some nutritional elements. The genetic resources that exist indicate that potentially important accessions could be used as a gene source due to their high levels of K, Ca, Cu and Zn in breeding programmes.

In Arabidopsis, a variety of mapping populations have been used for the detection of quantitative trait loci (QTLs) responsible for natural variation. In this study, we present an overview of the advantages and disadvantages of the different types of populations used. To do this, we compare the results of both experimental and natural populations for the commonly analysed trait flowering time. It is expected that genome wide association (GWA) mapping will be an increasingly important tool for QTL mapping because of the high allelic richness and mapping resolution in natural populations. In Arabidopsis, GWA mapping becomes ever more facilitated by the increasing availability of re-sequenced genomes of many accessions. However, specifically designed mapping populations such as recombinant inbred lines and near isogenic lines will remain important. The high QTL detection power of such experimental populations can identify spurious GWA associations, and their unique genomic structure is superior for investigating the role of low-frequency alleles. Future QTL studies will therefore benefit from a combined approach of GWA and classical linkage analysis.

Amplified fragment length polymorphism analysis was employed to investigate the population structure of 32 Iranian Silybum marianum populations along with two commercial varieties. A total of 415 polymorphic marker loci were produced by 27 primer combinations with an average of 15.37 markers per combination. Polymorphic information content ranged from 0.24 to 0.44 with an average of 0.35 per primer combination, and marker index was in the range of 2.56–9.50 with an average of 5.37. The average Nei's genetic diversity (HE) and Shannon's diversity index (I) were 0.201 and 0.296, respectively. The coefficient of differentiation among populations (GST) was 0.44, indicating that 44% of the total molecular diversity resulted from differences between populations. We identified three major groups based on cluster analysis and principal coordinate analysis, which were mostly in concordance with the geographical grouping of the populations. The molecular diversity estimate could be useful for selecting appropriate populations to improve S. marianum through conventional and molecular breeding.

Pigeonpea (Cajanus cajan (L.) Millsp. is one of the most important legume crops as major source for proteins, minerals and vitamins, in addition to its multiple uses as food, feed, fuel, soil enricher, or soil binder, and in fencing, roofing and basket making. ICRISAT's genebank conserves 13,632 accessions of pigeonpea. The extensive use of few parents in crop improvement is contrary to the purpose of collecting a large number of germplasm accessions and has resulted in a narrow base of cultivars. ICRISAT, in collaboration with the Generation Challenge Program, has developed a composite collection of pigeonpea consisting of 1000 accessions representing the diversity of the entire germplasm collection. This included 146 accessions of mini core collection and other materials. Genotyping of the composite collection using 20 microsatellite or simple sequence repeat (SSR) markers separated wild and cultivated types in two broad groups. A reference set comprising 300 most diverse accessions has been selected based on SSR genotyping data. Phenotyping of the composite collection for 16 quantitative and 16 qualitative traits resulted in the identification of promising diverse accessions for the four important agronomic traits: early flowering (96 accessions), high number of pods (28), high 100-seed weight (88) and high seed yield/plant (49). These accessions hold potential for their utilization in pigeonpea breeding programmes to develop improved cultivars with a broad genetic base. Pigeonpea germplasm has provided sources of resistance to abiotic and biotic stresses and cytoplasmic-male sterility for utilization in breeding programmes.