In South Europe, rice is grown as an irrigated crop in river deltas where it plays an important role in soil desalinization. Specific varieties are needed for these tough conditions. We analyzed the genetic structure of a set of 305 varieties coming from the European Rice Germplasm Collection (ERGC) with 90 single nucleotide polymorphisms and compared it with a reference set representative of the diversity of Oryza sativa (mini-Germplasm Bank (GB)). These accessions had been characterized for their grain type and growth cycle duration. The polymorphism information contents of the ERGC were lower than those of the mini-GB, indicating a narrower genetic basis. Indeed, almost all ERGC accessions belong to the japonica group. Within the japonica group, both a dendrogram and a Bayesian clustering identified two major clusters. The first cluster encompassed tropical japonicas and American varieties from USA and Argentina characterized by long and narrow grains and medium to long duration. On a finer level, tropical japonicas appear separated from the other accessions. The second cluster is composed of European varieties mostly early or medium in duration and Asian temperate accessions, with a subgrouping based on grain format. A set of 200 accessions was composed for association mapping studies on traits such as salt tolerance.

Soil salinity is a major limitation to legume production in many areas of the world. Identification of the genetic source of salt tolerance is critical in soybean breeding for improving soybean production in salt-affected regions. Vietnam has unique sources of soybean germplasm and varieties are grown in the area where exposure to salinity is frequent. However, there is little research on the identification of salt tolerant sources in the Vietnamese gene pool. The present study compared 18 Vietnamese soybean cultivars for their differences in salt tolerance. Under a range of NaCl stress from 0 to 200 mM NaCl, there was a large variation in salt tolerance among the 18 soybean lines evaluated. The soybean accession PI 675847 A (Vietnamese variety DT2008), was identified as a useful source of salt tolerance. During vegetative growth, PI 675847 A had lower leaf scorch scores, higher cell membrane stability, better photosynthesis and biomass accumulation under NaCl stress than the other 17 strains evaluated. In addition, PI 675847 A maintained better growth and seed yield in salt-affected soils compared with the sensitive lines. Analyses of ion contents in plant leaves under saline conditions showed that PI 675847 A was able to limit uptake and transport of Na+ and Cl−. Because of its higher productivity under saline conditions, PI 675847 A will be a useful germplasm source in soybean improvement programs for salt tolerance.

A total of 54 horsegram landraces collected from three altitudinal zones (lower hills, mid hills and higher hills) of Himalayan region were characterized and evaluated for nine quantitative characters. Accessions collected from lower and higher hills were more diverse and differed significantly from mid hills accessions for characters viz., days to flowering, days to physiological maturity, plant height and grain yield per plant. The plotting of first and second principal component axes scores revealed that there was dispersion among the accessions collected from different altitudinal groups. It reveals a less variability among the landraces collected from same altitudinal group but high variability among the landraces collected from different altitudes. This suggests that the horsegram landraces are adapted to specific zone due to different selection pressure practiced by the farmers at different altitudes. Farmers in lower and higher hills select the landraces having high grain yield coupled with less reproductive phase duration and taller in nature.

Roselle (Hibiscus sabdariffa L.) is an economically important plant in Niger. Little is known about its genetic diversity and population structure. In this study, we performed the first diversity assessment of a collection of 124 roselle accessions and 16 accessions of its close relatives Hibiscuscannabinus and Abelmoschusesculentus. Our study was based on ten agromorphological traits and 267 amplified fragment length polymorphism markers. We identified two major distinct groups in H. sabdariffa using a Bayesian method. These two genetic groups were associated with statistical differences for three phenological characteristics: number of days to flowering, 100-seed weight and calyx size. However, the calyx colour, i.e. a morphological characteristic often used to classify different local ecotypes, did not superimpose this separation. Our findings suggested that roselle diversity is genetically structured; the two different groups were clearly associated with morphological differences but were not commonly used by farmers for their classification. The impact of the perceived ecotype structure and its consequence on farmer management is discussed.

Using microsatellite loci, we assessed the mating system and genetic diversity of the dioecious tropical tree Genipa americana in a natural population (NP) and a progeny test (PT). For NP, we also estimated the paternity correlation within and among fruits and mean pollen dispersal distance. As expected for dioecious species, all offspring originated from outcrossing (t = 1). Mating among relatives (1 − ts) and paternity correlation (rp) were variable among progenies (1 − ts = 0.03–0.19; rp = 0.04–0.40), but greater in NP than in PT. Fixation index (F) was generally significant and lower in adults than in offspring, indicating selection against inbred individuals. Paternity correlation was higher within (0.40) than among (0.26) fruits, indicating a lower effective number of pollen donors (Nep) within (2.5) than among (3.8) fruits. Due to the higher rp in NP, the effective size within progenies (Ne) was lower (2.69) than PT (3.27). The pollen dispersal pattern was strongly leptokurtic, suggesting long-distance pollen dispersal (mean of 179 m). The results show that both populations can be used for seed collection in environmental reforestation programmes; however, considering that PT is structured in maternal progenies, NP is more suitable for seed collection due to the lower probability of mating among related trees.

Southern Sudan has a low population density, abundant land and tremendous agricultural potential. A large number of domesticated crops are grown in the region in a range of cropping systems. There are also numerous useful wild plant genetic resources. Little collecting work has been done in the region, there are few accessions from southern Sudan stored ex situ and publications on the actual and potential plant genetic resources for agriculture are sparse. The region has been a centre of civil conflict with little respite since independence in 1956. The farmers’ fields and natural environments represent in situ genebanks, which following the cessation of hostilities will become extremely important for the rehabilitation of subsistence agriculture, the promotion of cash crop production and the revitalization of the regional economy. Several wild plant species are highly nutritious and merit the attention of plant scientists. This article describes some of the domesticated, semi-domesticated and wild plant genetic resources of the area, and suggests why these are important for agricultural rehabilitation following implementation of a peace accord.

Ever increasing global population necessitates the need to increase availability of affordable foods with high nutritional quality. Chickpea being the second most important grain legume cultivated worldwide has the great potential to alleviate problems of protein malnutrition and hidden hunger. The objective of the present investigation was to characterize a diverse set of 402 germplasm comprising of more than 100 commercial cultivars widely cultivated and utilized by breeders for grain protein in two contrasting environments to explore the magnitude of natural genotypic diversity present in the cultivated chickpea and the scope for enhancing it and its quality through breeding. The cultivars containing more than 25 to 30.44% grain protein have been found in the study and large scale production of such protein rich cultivars is expected to increase availability as well as consumption of high quality chickpea necessary to overcome all forms of malnutrition. Trait specific germplasm containing grain protein up to 33.56% are also identified for their further utilization as potential donors in the chickpea improvement programme. The amino acid profiling of selected high and low protein containing genotypes showed considerably greater average amino acid score for all the essential amino acids than the WHO recommended requirement values and is comparable to those of the ‘complete protein’ sources of food suggesting that chickpea deserves to be considered as a ‘complete protein’ source.

Genetic diversity identified in the Capsicum genepool has been utilized extensively to improve pepper disease resistance, fruit quality and varied yield attributes. Little attention has been dedicated to evaluating the breadth of potential diversity within Capsicum for fresh-cut attributes and genetic enhancement of fresh-cut fruit quality. We evaluated fresh-cut attributes in pepper accessions with diverse fruit phenotype selected from available cultivars and the USDA, ARS Capsicum genebank. Subjective assessment of product quality and objective measurement of package atmospheric composition, tissue juice leakage and membrane electrolyte leakage after 7, 10 and 14 d of storage identified significant differences for fresh-cut attributes among as well as within sweet bell, large elongate, jalapeno and serrano germplasm. Sweet bell and large elongate fruited accessions generally exhibited increasing electrolyte leakage over days of storage, whereas jalapeno and serrano accessions maintained stable electrolyte leakage levels. Jalapeno and serrano fruit classes were typified by faster decline in package headspace O2 and accumulation in CO2 partial pressures in comparison to sweet bell and large elongated fruit classes. Regression analysis demonstrated a relationship between overall visual quality and electrolyte leakage after 14 d of storage for sweet bell and large elongated fruit classes. The results demonstrate extensive variation in Capsicum germplasm to improve pepper for fresh-cut applications and facilitate research to better understand physiological and heritable determinants of fresh-cut product quality.

Hydrangea and Schizophragma are popular horticultural and ornamental plants. This study was designed to identify unknown accessions of Hydrangeaceae that have leaf morphological characters different from Hydrangea anomala subsp. petiolaris and Schizophragma hydrangeoides in Jeju, Korea. A total of 29 accessions of Hydrangea and Schizophragma from the wild were collected and analyzed using randomly amplified polymorphic DNA (RAPD) and single nucleotide polymorphisms (SNPs) from the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene. Morphological characteristics of leaves and shoot apices of several accessions were also examined. Based on the RAPD markers, SNPs of the (rbcL) gene and morphological characteristics of apical buds, the unknown accessions were identified as H. anomala var. petiolaris.

Sweet cherries can be grafted onto a wide range of rootstocks belonging to the genus Prunus. The identification of sweet cherry rootstocks using morphological traits is almost impossible particularly during the dormant season, yet it is very important for the grower to know exactly the rootstock as this has a major influence on cultivar performance and agricultural practices. However, DNA-based molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides a good opportunity to reliably distinguish the rootstocks. Herein, we have integrated high-resolution melting (HRM) analysis, coupled with five simple sequence repeat (SSR) markers, in order to facilitate the identification of the most popular sweet cherry rootstocks in Greece. The five SSR loci used were highly informative and generated a unique melting curve profile of microsatellites for each of the six sweet cherry rootstocks tested. In particular, one marker, BPPCT002, with six HRM profiles was sufficient to discriminate all the sweet cherry rootstocks studied, highlighting its potential use for rootstock identification. Hence, this assay provided a flexible, cost-effective and closed-tube microsatellite genotyping method well suited to sweet cherry rootstock identification.

The range-wide genetic structure of the highly productive and valuable timber species Sequoia sempervirens (D. Don) Endl. is still insufficiently studied, although published data based on different genetic markers (nuclear and chloroplast microsatellites, AFLP, RFLP and isozymes) demonstrated relatively low population structure. However, more genetic markers are needed to increase the efficiency of population genetic studies in coast redwood. Therefore, we developed seven nuclear and five chloroplast microsatellite or simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) and the complete chloroplast genome sequence, respectively. All selected markers were tested in a range-wide sample representing trees from 16 locations. They are highly polymorphic microsatellite loci with the number of alleles ranging from 3 to 17, and the number of effective alleles from 1.1 to 2.48. Coast redwood is a hexaploid species, and its chloroplasts are paternally inherited. Therefore, the chloroplast SSR markers are especially useful for this species, because their genotyping is not affected by nuclear genome ploidy. Moreover, they showed high gene diversity for each locus within and across all populations and can be used to study range-wide population genetic structure, pollen-based gene flow and long-distance gene transfer. Coast redwood can propagate clonally, and nuclear polymorphic EST-SSRs can be used for clonal identification. They are linked with expressed genes and their variation can reflect variation in genes under selection, including those that could be potentially important for local adaptation of coast redwood considering the threat of climate change.

Potato (Solanum tuberosum L.) has been cultivated in Latvia since the 17th century, and formal breeding programmes have been established since the start of the 20th century. The Latvian potato genetic resource collection consists of 83 accessions of Latvian origin, including landraces, old cultivars released starting from the 1930's, modern cultivars and breeding material. These are maintained in field and in vitro collections. Pedigree information about the potato cultivars is often limited, and the use of hybrids of local cultivars as parents is common in the Latvian potato breeding programme. Ninety-four Latvian potato varieties and breeding lines and some commonly used foreign accessions were genotyped with the potato DNA diversity array technology. Analysis of the Latvian potato genetic resources collection revealed that the amount of genetic diversity has increased in the modern cultivars in comparison with the old cultivars.

This paper examines the fate of alleles and changes of genetic diversity in old (ca 1930s) versus more modern (ca 1990s) UK bread wheat varieties using 14 mapped DNA microsatellite (simple sequence repeat, SSR) loci and morphological markers. The allelic constitution of varieties belonging to three time periods (early, intermediate, late) was determined. While at certain loci one or more SSR alleles were gained between early and late periods, at others the allelic representation remained constant, although a shift in allelic frequencies could sometimes be detected. No locus showed a clear, net loss in the total number of alleles over the time period. In a further group of loci, there was neither clear gain nor loss, but rather a dynamic flux of alleles. A comparison of the allelic constitution of the UK variety set with a larger genetic pool (non-UK varieties) showed that some loci were rather similar in allelic constitution, while others possessed additional diversity. Certain SSR alleles appeared to be associated with old or modern varieties, possibly indicating associations with chromosome regions under selection pressure. The same exercise was conducted on the basis of 14 of the morphological characteristics recorded in the course of distinctness, uniformity and stability testing of varieties. Overall, this analysis generated a similar picture of changes in diversity to that obtained from the microsatellite data.

Kenya lies within sorghum centre of diversity. However, information on the relative extent of diversity patterns within and among genetically defined groups of distinct ecosystems is lacking. The objective was to assess the structure and phenotypic diversity of wild sorghum populations across a range of geographical and ecological conditions in the country. Sixty-two wild sorghum populations (30 individuals per population) sampled from four distinct sorghum growing regions of Kenya and covering different agroecologies were characterized for ten qualitative traits. Plant height, number of tillers, panicle sizes and flag leaf dimensions were also recorded. Frequencies of the phenotypic classes of each character were calculated. The Shannon diversity index (H′) was used to estimate the magnitude of diversity. Principal component analysis was used to differentiate populations within and between regions. Wild sorghum is widely distributed in Kenya, occurring in sympatric ranges with cultivated sorghum, and both have overlapping flowering windows. All characters considered displayed great phenotypic diversity. Pooled over characters within regions, the mean H′ ranged between 0.60 and 0.93 in Western and Coast regions, respectively. Wild sorghum was found to show a weak regional differentiation, probably reflecting the importance of seed-mediated gene flow in shaping the wild sorghum population structure. Trait distribution was variable among regions, but there was no conspicuous distribution of the traits studied in any given region. Spontaneous hybridization and introgression of genes from cultivated to wild sorghum seems to be likely, and may already have occurred for a long time, although undocumented. Implications for in situ and ex situ genetic resources conservation are discussed.

The aim of the study was to develop the system of polymerase chain reaction (PCR)-based markers for the assessment of genetic diversity and population genetic studies of Gentiana lutea L. as well as to determine the utility of two indices of marker informativeness. The informativeness was determined for 40 PCR primers of different types (random amplified polymorphic DNA, inter simple sequence repeat, inter-retrotransposon amplified polymorphism, resistance gene analog polymorphism and conserved DNA-derived polymorphism markers) by evaluating discriminating power (DL) and resolving power (Rp) in a sample of 30 plants from two populations. Analysis of correlation between the index value and the number of differentiated pairs of genotypes in the given sample revealed that DL is more efficient than Rp; therefore, we selected primers based on the DL value. In total, 12 primers with the largest values of DL were chosen. Analysis of genetic relationship among 86 plants from six populations showed that the number of bands produced by the three of selected primers was sufficient to give average bootstrap support across six key nodes in the dendrogram higher than 85%, while using six of the primers resulted in average bootstrap value exceeding 99%. Thus, a minimal set of three to six selected primers are sufficient for a quick assessment of genetic diversity of G. lutea populations, depending on the sample size and degree of differentiation between populations, while the rest of the primers with DL values above 0.8 may be used for ecogenetic surveys. Preliminary results obtained with selected primers indicate the moderate level of genetic variation within the species and significant differentiation among individual populations.

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Português de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

The rising need for crop diversification to mitigate the impacts of climate change on food security urges the exploration of crop wild relatives (CWR) as potential genetic resources for crop improvement. This study aimed at assessing the diversity of CWR of the Indian Ocean islands of Mauritius and Rodrigues and proposing cost-effective conservation measures for their sustainable use. A comprehensive list of the native species was collated from The Mauritius Herbarium and published literature. Each species was assessed for the economic value of its related crop, utilization potential for crop improvement, relative distribution, occurrence status and Red List conservation status, using a standard scoring method for prioritization. The occurrence data of the priority species were collected, verified, geo-referenced and mapped. A total of 43 crop-related species were identified for both islands and 21 species were prioritized for active conservation. The CWR diversity hotspots in Mauritius included Mondrain, followed by Florin and Le Pouce Mountain. Although a wide diversity of CWR has been recorded on both islands, most do not relate to major economic crops in use, therefore only a few species may be gene donors to economic crops at the regional and global level. For example, coffee, a major global beverage crop, has three wild relatives on Mauritius, which could potentially be of interest for future predictive characterization.

Powdery mildew (PM) is one of the most severe fungal diseases of cucumber that limits its production worldwide. In this study, 140 genotypes of cucumber were screened for disease resistance under field and artificial conditions, and then validated with eight known SSR markers linked to PM resistance. Among these genotypes, genotype GS140 was found resistant (R), whereas GS148, GS16 and GS70 were moderately resistant, and GS169 was found to be tolerant. Of all the eight markers, only C31, C80, C162, SSR16472 and SSR16881 amplified the reported linked allele. The 127 bp allele of SSR16881 was found to be associated with the lowest disease severity of 37.65%. The associated markers could further be verified for their usability using linkage studies and the contrast genotypes in the present study could serve as a tool for selection in future marker-assisted selection breeding strategies for PM resistance.

A global survey was conducted among a wide range of stakeholders to gain insight into the state of on-farm management (OFM) as a strategy for enhancing the conservation and sustainable use of plant genetic resources for food and agriculture (PGRFA). The results show that OFM is not considered a priority in national PGRFA programmes (NPGRPs), and that OFM practitioners and their organizations are not always aware of, or involved in, NPGRPs. The survey also highlighted the lack of awareness, understanding and collaboration between OFM practitioners and the managers and policy-makers associated with NPGRPs. The outcome of the analysis supports a hypothesis that OFM is, to a large extent, supported by stakeholders who are not directly engaged in the conservation and use of PGRFA, and therefore not associated with NPGRPs. This should be taken into consideration when seeking to improve the performance and impact of national programmes, and their commitment to safeguard PGRFA and contribute to food security, poverty alleviation and sustainable agriculture.

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.