The complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.

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.

Genetic diversity and relationships among 112 mango (Mangifera indica) plants native to 16 states of Mexico and four controls [three mango cultivars (Ataulfo, Manila and Tommy Atkins) and one accession of Mangifera odorata] were evaluated based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Mango germplasm shows broad dispersion through Mexico and genetically similar germplasm from different agroecological regions has previously been found by our group. Both AFLP and SSR analyses indicated high genetic similarity among mango populations that were clustered in two major groups: mangos from Gulf of Mexico coastline and mangos from Pacific Ocean coastline and locations far away from the sea. The highest genetic diversity was found within plants from each state, and significant genetic differentiation (FST = 0.1921, AFLPs and 0.1911, SSRs) was also observed among mango populations based on geographical origin and genetic status (cultivars versus landraces). Heterozygosity values ranged from low (0.38) to moderate (0.68), and no heterozygote deficits were found. The highest genetic variability was found in mango populations from Tabasco, Michoacán and Oaxaca. Data suggested that mangoes are subjected to natural or induced pollination, so segregation as well as genetic recombination plays major roles on genetic diversification of Mexican mangos. AFLP analysis was more robust than SSR for determining the genetic relationships among mango landraces from Mexico.

Brinjal (Solanum melongena L.) is an important solanaceous vegetable in many countries of Asia and Africa. It is a good source of minerals and vitamins in the tropical diets. Assessment of genetic resources is the starting point of any crop improvement programme. In India, the National Bureau of Plant Genetic Resources is the nodal institute for management of germplasm resources of crop plants and holds more than 2500 accessions of brinjal in its genebank. In the present study, morphological diversity in a set of 622 accessions, comprising 543 accessions from indigenous sources and 79 accessions of exotic origin, was assessed. Wide range of variations for 31 descriptors, 13 quantitative and 18 qualitative, were recorded. The wide regional variations for plant, flower and fruit descriptors revealed enough scope for improvement of yield characters by selection. The genetic differences among the landraces are potentially relevant to breeding programmes in that the variability created through hybridization of the contrasting forms could be exploited.

Sugar and acidity levels are the main criteria of general fruit quality and for citrus juices pulp, in particular. The constituents of the acidity (organic acids) and the sweetness (glucose, fructose and sucrose) and the genes involved in their regulation have seldom been used to explore Citrus genetic diversity. We evaluated the juice composition of primary metabolic components for 87 varieties belonging to the eight major Citrus species grown under the same environmental and cultivation conditions by HPLC. We investigated the sequence polymorphism of nine candidate genes encoding for key enzymes of sugars and organic acids metabolic pathways by single strand conformation polymorphism (SSCP). Whatever the biochemical or molecular analyses, the observed structure of Citrus diversity was organized around three groups corresponding to the ancestral species (mandarin, pummelo and citron). As expected, the secondary species were closely related to their putative ancestors except for Citrus aurantium. Biochemical diversity was strongly correlated to molecular SSCP diversity at the genus level but not at the intraspecific level. Compared with other molecular marker types, higher diversity has been observed with SSCP technology, which makes it suitable for future quantitative trait loci mapping approach on gene polymorphism in citrus pulp acidity and sweetness regulation.

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.

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

The ICRISAT genebank, Patancheru, India holds 22,211 pearl millet germplasm accessions from 50 countries, including 19,063 landraces. Among these, 15,904 landraces that were geo-referenced are either thermo-sensitive (52.5%), or photoperiod-sensitive (45.6%), or insensitive to both temperature and photoperiod (2%). Latitude ranges of 10–15°N with 39.6% and 15–20°S with 13.1% of total accessions are the important regions for pearl millet germplasm. A study on climate data of the germplasm collection sites revealed that most accessions from latitudes ranging from 10 to 20° on both sides of the equator were highly sensitive to longer photoperiod (>12.5 h) and/or lower temperature ( < 12°C). Accessions that originated in locations at higher latitudes (>20–35°) on both the hemispheres exhibited low sensitivity to both photoperiod and low temperature, as they were exposed to such climates during their evolution. The accessions that are insensitive to both photoperiod and temperature were few but they originated from locations spread across all latitudes, although the highest numbers were from mid-latitudes (15–20°) in both hemispheres. As germplasm accessions are sensitive to climatic variables such as temperature and photoperiod, recording of location-specific geo-reference data while collecting the germplasm, which can help to elucidate the sensitivity of accessions to temperature and photoperiod, is emphasized. Critical evaluation of photoperiod-sensitive accessions that are late flowering for forage production and the photoperiod-insensitive early-maturing accessions for grain production, multiple cropping and development of parental lines with synchronized flowering for the development of hybrids is suggested.

The International Center for Agricultural Research in the Dry Areas (ICARDA) is participating in a large-scale programme, Subprogram 1 of the Consultative Group on International Agricultural Research (CGIAR) Generation Challenge Program, that aims to explore the genetic diversity of the global germplasm collections held by the CGIAR research centres. This project will identify a ‘composite collection’ of germplasm for individual crops, representing the range of diversity of each crop species and its wild relatives, and characterize each composite set using anonymous molecular markers, mainly simple sequence repeats (SSRs). The overall goal of this project is to study diversity across given genera and identify genes for resistance to biotic and abiotic stresses that can be used in crop improvement programmes. ICARDA was responsible for creating the composite collection for lentil. ICARDA has the global mandate for lentil and houses the largest global collection of this crop with 10,509 accessions. From this collection, a global composite collection of 1000 lentil accessions was established with the aim to represent genetic diversity and the agro-climatological range of lentil. Accessions for the composite collection were compiled from landraces, wild relatives, and elite germplasm and cultivars. The methodology presented here combined classical hierarchical cluster analyses using agronomic traits and two-step cluster analyses using agro-climatological data linked to the geographical coordinates of the accessions' collection sites. Genotyping for 30 SSR loci will be carried out for all 1000 accessions. Plants grown for DNA analysis will be harvested and progeny will be evaluated under field conditions at ICARDA.

Chilli (Capsicum spp.) is an economically important vegetable and spice. The Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus has collected more than 2500 chilli germplasm accessions since 1989. Investment to maintain and evaluate such a large germplasm collection is high. For efficient germplasm management and to reduce the cost of germplasm maintenance, a core collection needs to be established. Therefore, this study aimed to investigate the genetic diversity of chilli germplasm using microsatellites. A total of 230 chilli germplasm accessions were evaluated using ten anchored Capsicum microsatellite loci. These loci generated 42 alleles with a size ranging from 87 to 323 bp. The average polymorphic information content was 0.57, ranging from 0.414 to 0.681, and the probability of identity (PI) ranged from 0.17 to 0.49. The combined PI of the ten microsatellite loci was 2.30 × 10− 6. The similarity index ranged from 0.29 to 1.00. The 230 chilli accessions were divided into two major groups. Group I comprised mainly C. annuum, and group II comprised all four Capsicum species with the majority being C. frutescens, C. chinense and C. baccatum. The matrix comparison showed that a cophenetic correlation of 0.798 indicated the best fit of the obtained dendrogram. The PowerCore program selected 28 representative chilli accessions to form a core collection, which maintained a similar level of diversity to that of the overall 230 chilli accessions. The representative alleles in those 28 core accessions equalled all the alleles present in the entire collection.

Clovers (Trifolium species) are a large and widespread genus of legumes. Recent work supports the Mediterranean origin of the genus in the Early Miocene period, and centres of diversity for clovers occur in the Eastern Mediterranean, East Africa and South America. A number of clovers are of agricultural importance as forage species in grassland agriculture around the world, particularly in temperate areas. White clover (Trifolium repens L.) is the most important legume of grazed pastures, and red clover (T. pratense) is widely cut and conserved as a winter feed. We consider the current state of collected resources in clovers, which have been collated in the most important databases. These are European Internet Search Catalogue (EURISCO), germplasm resources information network and system-wide information network for genetic resources together with the collection held at AgResearch, New Zealand. In total, collections have been made of 204 species with 48 species having more than 100 accessions in these databases. As expected, the majority of accessions are of the agriculturally important species. The geographical origin of collected material is outlined and, for the major species, accessions are broken down according to their status, e.g. wild population, breeders' lines. We then describe some of the ways in which genetic resources of white and red clovers and their relatives have been used in the breeding of these species. These include introgression of stress tolerance traits, targetting improvements in resource use efficiency and increasing seed yield.

In this study, genetic diversity in 340 finger millet accessions from Kenya, Tanzania and Uganda and 15 minicore accessions was assessed using 23 single-sequence repeat markers and five qualitative traits. Nineteen markers were polymorphic with a mean polymorphic information content value of 0.606 and a range of 0.035–0.889, with allele size ranging from 148 to 478. A total of 195 alleles were detected (range of 3–23 and average of 10.3 alleles per locus), with 57.7% being rare and 17.4% being private. Differentiation between the accessions of the three countries was weak, with most of the genetic diversity being explained by variability within the countries and subregions than by that among the countries and subregions. The highest genetic diversity was observed in the Kenyan accessions (0.638 ± 0.283) and the least in the Ugandan accessions (0.583 ± 0.264). The highest differentiation based on Wright's fixation index was observed between the Ugandan and Tanzanian accessions (FST= 0.117; P< 0.001). There was no association between the morphological traits assessed and the genetic classes observed. The low variability between the countries could be attributed to a shared gene pool, as the crop originated from the East African region. Farmers' selection for adaptation and end use could have contributed to the high diversity within the countries. Concerted efforts need to be made to characterize the large germplasm stocks in East Africa for their effective conservation and utilization. The lack of representation of accessions from the three countries in all global minicore diversity clusters points to the need to explore the East African germplasm to identify the diversity not captured earlier to be included in the global repository.

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.

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

A five-point drought stress screening methodology for muskmelon based on visual observation has been standardized by modifying an earlier field screening method. The scale (1 to 5), were categorized into five groups, namely, highly drought tolerant (1), drought tolerant (2), average drought tolerant (3), drought susceptible (4) and highly drought susceptible (5). To validate and standardized the technique, 48 genotypes of muskmelon were evaluated for two successive years. Important physiological parameters, i.e.: relative water content (RWC), electrolyte leakage, photosynthetic efficiency (Fv/Fm), chlorophyll concentration index (CCI), root and shoot length were measured and correlated to make screening results more reliable. Drought tolerance efficiency of genotypes was calculated based on yield, and drought-tolerant genotypes were identified with better yield efficiency and ranking on visual scale. Whereas, yield efficiency of some drought-tolerant genotypes were less, althouth they came under drought-tolerant scale. Being a tolerant genotype, these may not be economical for commercial cultivation. Under water-deficit condition a significant positive correlation was observed between drought tolerance efficiency, and RWC, Fv/Fm, CCI and root length. Out of 48 genotypes, 14 genotypes were came under highly drought-tolerant category based on 5 point scale.

Kamut wheat, said to have been derived from seed found in the Egyptian pyramids, appeared on the market about 25 years ago. We have investigated its taxonomic placement using microsatellite genotyping. In all, 89 accessions of 13 tetraploid wheat species, along with samples of Kamut wheat, were genotyped using two A and B genome wheat microsatellite markers per chromosome, generating 453 alleles (8–33 alleles per locus), and a mean allelic polymorphic information content (PIC) of 0.80. A diversity analysis showed that nine major accession groups could be defined, and these were inconsistent with formal taxonomic classifications of about 10% of the material. Most of these misclassifications are due to either species introgression or seed admixture. Some accessions appear to be duplicates. The Kamut wheats grouped together in a cluster containing three accessions of Triticum polonicum and three of T. durum, originating from Turkey, Iraq, Iran and Israel. We suggest that Kamut perhaps derived from a natural hybrid between T. durum and T. polonicum, which occurred in the Fertile Crescent.

Microsatellite markers (simple sequence repeats, SSRs) are used for a wide range of crop genetic and breeding applications, including genetic diversity assessment, phylogenetic analysis, genotypic profiling and marker-assisted selection. Genomic SSR (gSSR) have attracted more attention because of abundance in plant genome, reproducibility, high level of polymorphism and codominant inheritance. Recently, the availability of data for expressed sequence tags (EST), has given more emphasis to EST-derived SSRs, which belong to the transcribed regions of DNA, and are expected to be more conserved and have a higher transferability rate across species than gSSR markers. In the present study, several gSSR and EST-SSR markers were investigated for their transferability and level of DNA polymorphism in different ancestral tetraploid and diploid Triticum and Aegilops species. The same gSSR and EST-SSR markers were also evaluated for their applicability in the phylogenetic analysis of wheat. Both gSSR and EST-SSR markers showed differences for the average transferability rate and the number of alleles/locus. Phylogenetic trees based on gSSR and EST-SSR markers were in accordance with phylogenetic relations based on cytogenetic and molecular analyses.

The Mediterranean region has a rich history of domestication and cultivation of lentil (Lens culinaris Medik.). Landraces have been grown and repeatedly selected by local farmers under different agro-environments. Characterization of molecular variation and genetic differentiation helps to ensure enhanced valorization, conservation and use of these genetic resources. Nineteen Simple Sequence Repeat DNA markers were used for molecular variance analysis (AMOVA) and population structure assessment underlying 74 lentil landraces from four Mediterranean countries: Morocco, Italy, Greece and Turkey. Based on AMOVA, presence of population structure and genetic differentiation at different levels were evidenced. Genetic diversity among Turkish landraces was higher than that of other countries. These landraces were more homogeneous as shown by low genetic differentiation among individuals within each landrace. Whereas Moroccan landraces followed by Italian and Greek provenances showed higher diversity and differentiation among individuals within landraces. The wide genetic variability of these landraces could help to better adaptation to biotic and abiotic stresses. Moreover, they could provide useful alleles related to adaptive traits for breeding purposes. Based on structure analysis, we obtained indications of possible presence of two major gene pools: a northern gene pool composed of Turkish, Italian and Greek landraces, and a southern gene pool composed of Moroccan landraces. Our results could be of interest when designing future diversity studies, collection missions, conservation and core collection construction strategies on Mediterranean lentil landraces.

Bitter gourd (Momordica charantia L.) is an important market vegetable in the tropics. The objectives of this study were to (1) conduct a preliminary evaluation of genetic diversity in bitter gourd flesh (without seeds) for phytonutrient (carotenoid, ascorbic acid and tocopherol) contents with the aim to understand which phytonutrients might be increased through breeding, (2) assess the association between fruit traits and phytonutrient contents and (3) evaluate the effect of the fruit harvest stage on phytonutrient contents. A total of 17 diverse bitter gourd entries of various commercial market types were evaluated for fruit traits and phytonutrient contents for 2 years. Significant differences (P= 0.05) among the entries were detected for total carotenoids, total tocopherols, dry matter and fruit traits. Mean total carotenoid contents of the entries ranged from 10 to 1335 μg/100 g fresh weight in year 1 and 10 to 1185 μg/100 g fresh weight in year 2. Mean ascorbic acid contents were 69 and 61 mg/100 g fresh weight in year 1 and year 2, respectively. Total tocopherol contents among the entries ranged from 480 to 1345 and 445 to 2145 μg/100 g fresh weight in year 1 and year 2, respectively. Total carotenoid and ascorbic acid contents were highest at 12 days after fruit set (DAFS), but total tocopherol contents were highest from 14 to 20 DAFS. A 100 g portion of bitter gourd fruit can meet 190, 17 and 8% of the recommended daily allowances of vitamin C, vitamin E and vitamin A, respectively, for adults.

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.