Trait-specific characterization of rice landraces has significant potential for germplasm management, varietal identification and mining of novel gene/allele for various traits. In the current study, we have characterized 98 unique rice landraces collected from coastal regions of India, affected by submergence and salinity, based on Sub1 and Saltol quantitative trait loci (QTL) linked microsatellite markers. Among these genotypes, four genotypes (IC536558, IC536559, IC536604 and IC536604-1) collected from Kerala and two genotypes (AC34902 and IC324589) collected from West Bengal were identified with tolerance to submergence and salinity stress. A high level of genetic diversity of He = 0.349 and 0.529 at Sub1 and Saltol QTL region was detected by QTL-linked microsatellite markers, respectively. At Sub1 region one genotype, AC34902, was detected with maximum allelic similarity with FR13A, a known submergence tolerant variety. Besides, five genotypes (IC211188-1, IC536604-1, IC536604, IC536558 and IC536559) showed comparatively close genetic relationship with the salt tolerant variety FL478 for Saltol QTL and were clustered together in the neighbour joining dendrogram. Considering the haplotype structure, five genotypes (IC203801, IC203778, IC324584, IC413608 and IC413638) were identified which did not contain any common allele similar to FR13A but were still tolerant to submergence. These individuals need further characterization for identification of new alleles responsible for their tolerance.

Cotton is one of the most important crops among natural fibres. Fibre quality determines the spinning ability, which is negatively correlated with yield and yield-contributing traits. Limited efforts have been made to improve fibre quality and yield in diploid cotton. Therefore, screening a large panel of germplasm lines can help identify genotypes with better fibre quality and yield. We evaluated 712 desi cotton genotypes for fibre quality traits. The genotypes showed a significant difference for all the traits, suggesting considerable variability for fibre quality improvement. Fibre length and strength showed high phenotypic and genotypic coefficients of variation. Heritability was high for fibre strength, length, and elongation. Fibre length and strength were positively correlated; however, micronaire was negatively correlated with these two traits. Superior accessions were identified for fibre length (11), strength (20), uniformity (7), and elongation (25) among genotypes. Most of the desi lines (71%) had medium micronaire values. Twenty accessions identified were ideal for spinning, showing the fibre strength-to-length ratio of one. Cluster analysis based on Euclidean distance grouped all 712 accessions into four major clusters. Principal component analysis biplot revealed that accessions AC3418, 360-SP1, AC3522B, Kanpur A, Gao16CB-9, and AC3370 were genetically diverse. The superior accessions for fibre quality identified in this study are potential lines for the diploid cotton improvement programme.

This study discusses some of the important aspects of laws/regulations formulated for the protection of plant varieties in Union for the Protection of New Varieties of Plants (UPOV) member states, European Community countries and India. The study also provides an insight into some of the unique features of Indian sui generis system for the protection of plant varieties. During this study, the registration of crop notified in India and in some selected UPOV member countries has been examined. Since India is not an UPOV member state, the system of plant variety protection (PVP) is independent of international scenario but aims for similar standards. The study provides useful information in order to analyse the implementation of PVP laws in UPOV member states and India. Some important features were selected for carrying out a comparative analysis. These include Intellectual Property Rights protection (patent/breeder's right), types of varieties protected, methods of testing, criteria for protection, duration of protection, exemptions (researcher/farmer's exemption), infringement and penalty and compulsory license.

There is extensive duplication of accessions among collection holders globally. To save costs, unwanted duplication should be avoided. This issue has been addressed internationally. In Europe, there are currently 35 Brassica collections located in 24 countries. Duplication may be identified not only by surveying passport data and seed transactions, but also by applying morphological or genetic characterization. Our study included two collections; one at the N. I. Vavilov Institute of Plant Genetic Resources in St. Petersburg (VIR) and one at the Nordic Genetic Resource Center (NGB). A random set of 13 accession pairs or triplets of cabbage, turnip and swede were selected on the basis of identical or similar accession names. The accessions could potentially be regarded as duplicates. Morphological characterization showed that in about 50% the pair/triplet, the accessions were identical and should thus be regarded as duplicate holding. Determining the status of the remaining accessions, which were more or less distinct but had identical or similar names, was more difficult. In this paper, possible explanations for the similarities in names are discussed, as is the need to include characterization in any duplicate assessment process.

Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

A detailed survey along the coastal regions of Southern India revealed the occurrence of seven Pandanus species, viz. P. kaida Kurz., P. odorifer (Forssk.) Kuntz., P. canaranus Warb., P. furcatus Roxb., P. thwaitesii Mart., P. foetidus Roxb and a new species P. palakkadensis Nadaf, Zanan & Wakte. The fragrance of staminate inflorescences of these species was compared with the fragrance of commercial staminate inflorescences of P. odorifer. P. thwaitesii,P. kaida and P. palakkadensis recorded comparable fragrance with that of P. odorifer. The study reveals the fragrance potential of these species, which could be exploited commercially for extraction of essential oil.

Mungbean (Vigna radiata (L.) Wilczek), also known as greengram, is the most widely cultivated Asian Vigna species. Improved mungbean cultivars have a narrow genetic base that limits yield potential and they are poorly adapted to varying growth conditions in different agro-ecological conditions. The genetic potential of landrace germplasm accessions in gene- banks therefore needs to be better exploited. Germplasm core collections are made of a reduced set of representative accessions from the entire diversity maintained by genebanks. This subset of accessions can be used for testing general combining ability with local germplasm in the search for yield enhancement. Core collections also help breeders in selecting parental material that could maximize potential genetic gain from derived hybrid populations. At the National Bureau of Plant Genetic Resources (NBPGR), India, genetic enhancement/pre- breeding studies in mungbean have been initiated involving diverse parents mainly from the cultivated gene pool, using the Bureau's core collection as starting material. Germplasm enhancement aims at widening the genetic base of breeding materials by transferring desired genes from unimproved germplasm into enhanced varieties. Mild and decentralized selected material was maintained in target sites across the country. A total of 102 progenies were advanced to F5 for further selection and use by the breeders in Delhi. The genetic potential of a few selected enhanced progenies with desired plant types and better yield-related traits is presented in this paper. The study clearly demonstrates the potential of germplasm accessions conserved in genebanks for use in large-scale base-broadening efforts in mungbean.

A collection of 18 landraces of common bean (Phaseolus vulgaris L.) from northern Portugal was evaluated for both phaseolin pattern and a set of qualitative and quantitative traits. The phaseolin Contender and Tendergreen types were the most commonly occurring, with Boyaca and Huevo de Huanchaco present, but rare. The colour of the flower standard and wing, and seed shape, colour and size were all highly variable. On the basis of morphological traits, the landraces and testers clustered into two main groups. No relationship was found between phaseolin profile and any of the quantitative traits measured. Based on phaseolin patterns, the origin of Portuguese common bean populations was probably the Andean region of South America.

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.

The Andean region of Ecuador is the place of origin of many maize landraces grouped into 24 races. Definition of priorities for maize diversity conservation in this region can be supported by the spatial identification of areas with a high eco-geographical and phenotypic diversity. Six hundred thirty-six maize samples were morphologically characterized using 14 descriptors and assigned to a distinctive race. Additionally, sampled farms were characterized by 12 environmental variables. From these data, maps of morphological and eco-geographical diversity were obtained by using techniques to determine eco-geographical and phenotypic distances and applying them to each geographical neighbourhood. The races Patillo Ecuatoriano, Racimo de Uva and Uchima exhibited high intra-racial morphological variation, particularly in the shape of the ear, kernel row layout, cob diameter and total kernel number. The highest number of different races was observed in Imbabura, Azuay and Chimborazo provinces. The highest levels of morphological diversity were found in three cells (10 × 10 km), located in Pichincha, Chimborazo and Loja provinces. Two ecological niches, located in Loja province, showed high levels of eco-geographical diversity. A comparison between diversity maps revealed shared hotspots of morphological and eco-geographical diversity in the central and southwest areas of Imbabura province. The Andean highlands of Ecuador are an optimal refuge for the conservation of maize diversity, and the criteria of eco-geographical and morphological diversity and race richness should be considered when defining priority in situ conservation areas.

Sri Lanka has a valuable repository of germplasm collection due to the availability of a large number of different traditional and improved rice varieties. Molecular techniques can increase the effectiveness of traditional technologies in assessing genetic diversity. Amplified fragment length polymorphism (AFLP) was used to evaluate the genetic diversity among rice varieties available in the germplasm collection of Plant Genetic Resources Centre, Sri Lanka. AFLP analysis of rice varieties using ten different primer combinations yielded a total of 772 polymorphic bands (98.4%). Genetic similarities were estimated using Jaccard's (J) similarity coefficient. Unweighted pair group method with arithmetic mean (UPGMA)-based dendrogram was constructed. Genetic similarities varied from 0.073 to 0.565. Cluster analysis by genetic similarity divided the accessions into four main groups. The Cophenetic correlation with r = 0.781 indicated high confidence of AFLP data to group the varieties in UPGMA clusters. Principal component analysis further confirmed the patterns obtained by the cluster analysis. The results revealed very high genetic diversity at molecular level among the Sri Lankan rice varieties used in this study.

Genetic diversity of 30 common vetch (Vicia sativa L.) lines and cultivars obtained from various resources or collected from natural flora of Turkey was evaluated by using 55 sequence-related amplified polymorphism (SRAP) and five inter-simple sequence repeat (ISSR) primer sets, and their nuclear DNA contents were determined by flow cytometer. A total of 188 polymorphic loci were detected, with an average of 3.62 loci per primer. The percentage of polymorphic loci was 82.1%. The polymorphism information content values ranged from 0.12 to 0.96, with an average of 0.63. The genetic distance coefficients were in the range of 0.112–0.627. Cluster analysis revealed that the 27 lines and three cultivars could be divided into two main groups. No polyploidy was detected within any vetch lines tested while significant (P< 0.0001) nuclear DNA content differences were determined. The present study revealed that fast and accurate fingerprinting analysis could be done using SRAP and ISSR markers, which indicated existing significant variation among common vetch lines and cultivars.

We developed a multiplex PCR DNA marker for quick and easy identification of the AAGG-genome timopheevii lineage, including Triticum timopheevii, Triticum araraticum and hexaploid Triticum zhukovskyi (AAAmAmGG), and the AABB-genome emmer wheat lineage, including Triticum durum, Triticum dicoccum and Triticum dicoccoides. Distinguishing between tetraploid AAGG- and AABB-genome wheat species based on morphology is known to be difficult. This multiplex PCR system is based on the simultaneous PCR amplification of two chloroplast regions, matK and rbcL. The matK region molecularly distinguishes the two lineages, whereas the rbcL region is a positive control amplicon. We also examined whether the simple sequence repeat is a fixed mutation within species, using genetic resources in the collection of KOMUGI, Kyoto University, which comprises accessioned species collected across diverse geographical areas. The multiplex PCR marker distinguished AAGG from AABB species with complete accuracy.

Andean arracacha (Arracacia xanthorrhiza Bancr.) is a valuable but poorly known vegetatively reproduced root crop whose origin is still unresolved. Wild tuberous forms are present in the presumed areas of domestication and have a perennial or monocarpic life history. To elucidate the origin of the cultivated form, we surveyed a molecular analysis with amplified fragment length polymorphisms (AFLPs) in a representative sample of this crop and its wild relatives from Ecuador and Peru, the presumed areas of domestication. Wild species with tuberous and non-tuberous roots were included, as well as the perennial and monocarpic forms of the presumed wild ancestor. While the two wild varieties of A. xanthorrhiza were closest to the cultivars, they were distinguished by AFLPs. Unexpectedly, two clearly distinct groups were formed among the cultivars, one of which was significantly closer to the monocarpic wild form. However, the chloroplast DNA survey revealed greater similarity between all of the cultivars and the wild perennial A. xanthorrhiza. These results combined with the morphological and life history features, confirms the hypothesis that arracacha domestication started from the wild perennial form. We suggest this scenario of domestication followed by an unsuspected introgression in the cultivation, resulting in two cryptic genetic groups, well distinguished at the molecular level. This is an important revelation with implications in genetic resource conservation and breeding standpoints in this promissory crop.

Germplasm lines with resistance to the sugarbeet root maggot (SBRM) have been developed and released to the public, providing a means to generate hybrids with resistance against the most devastating insect pest of sugarbeet in North America. Effective use of this germplasm, however, requires knowledge of relative strengths of SBRM resistance between lines and knowledge of the diversity and genetic relationships between germplasm. Therefore, field studies comparing SBRM resistance of four released SBRM-resistant germplasm lines (F1015, F1016, F1024 and F1043), a SBRM-resistant parent (PI 179180) and an unreleased SBRM-resistant population (F1055) were performed, and genetic analysis of the diversity and relationships between SBRM-resistant germplasm and their available parents was conducted using simple sequence repeat (SSR) markers. Under natural SBRM infestations, resistant germplasm exhibited significantly less SBRM damage than a susceptible control, with similar, high levels of resistance in F1016, F1024, F1043, F1055 and PI 179180 and lower resistance in F1015. SSR analysis revealed genetic similarities between F1016, F1024 and F1055, while F1015 and F1043 were genetically distinct from these lines. Among resistant genotypes, F1015 and F1043 exhibited greatest and least within-line genetic diversity, indicating greater and lesser inbreeding for F1043 and F1015, respectively. Similarities in damage ratings and genetics for F1016, F1024 and F1055 indicate that these lines are likely to be equally effective at introducing SBRM resistance into elite populations and in combining ability. In contrast, F1043, with its unique parentage and genetic dissimilarity from other resistant lines, provides a genetically distinct, but similarly effective, source of SBRM resistance.

Leaf colour characteristics of 730 sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the USDA sweetpotato germplasm collection were evaluated during 2012–2014. Colorimetry data for the abaxial and adaxial leaf surfaces were recorded using a tristimulus colorimeter and the CIE 1976 L*a*b* and CIE L*C*h* colour spaces. Most accessions (725 of 730 PIs) had dark-to-medium green leaves, but two PIs had totally purple leaves, and three PIs had yellow or yellow-green (chartreuse) leaves. For mature, field-grown green leaves, values for the red-green coordinate (a*) averaged −12.4 for the adaxial and −10.4 for the abaxial leaf surface. Values for the blue-yellow coordinate (b*) averaged 17.2 for the adaxial and 17.3 for the abaxial leaf surface. Hue angle (h*) for green leaves averaged 120.9° for the adaxial and 126.2° for the abaxial leaf surface. Colour saturation (Chroma, C*) averaged 21.3 for the adaxial and 20.2 for the abaxial leaf surface. Lightness (L*) averaged 35.4 for the adaxial and 47.2 for the abaxial leaf surface of green leaves. Late in the season, over one-half (53.9%) of the 730 PIs showed some level of purple pigmentation in the leaf lamina. Late-season purple leaves were collected and colour coordinates were recorded for 118 PIs grown in the field. For purple leaves, values for a*, b*, C*, L* and h* averaged 2.3, 6.2, 7.9, 28.2 and 64.4° for the adaxial surface and −1.0, 12.7, 13.9, 43.1 and 87.0° for the abaxial leaf surface, respectively.

Oilseed rape is a very undeveloped crop with regard to efficiency of production and the agronomic practice used to maximize its potential. The genetic potential to modify oilseed rape is limited by the narrow genetic base found within the breeding gene pool, resulting in limited novel variation available for exploitation. Novel variation is, however, present in wild diploid ancestors of oilseed rape and has been made available by developing synthetic Brassica napus. This is illustrated through the use of this material to develop an understanding of pod shattering which is one of the most agronomically important characteristics of the crop. Through a variety of approaches it is shown how progress has been made to understand this trait and how this understanding is being used to improve the crop such that efficiency of production will be enhanced.

Double ‘free-hybrids’ (DH) in alfalfa were obtained by crossing in a diallelic scheme, six multiplied simple hybrids (SH) derived from four partly inbred (S2) lines. Analysis of the specific combining ability demonstrated that the main source of variation was for dry matter yield (DMY) in DHs and supported heterosis values of DHs versus the best parent of an average +45% (ranging from +5 to +76%). Investigation at the molecular level was carried out by analysis of simple sequence repeat markers on the six parental SHs and 15 DH progenies and by comparison of gene expression profiles using microarrays of a single DH line to its parental lines. The variation of heterozygosity estimates of the DHs explained a small part (about 20%) of their variation in DMY, while the number of alleles was significantly related to DM performance (r = 0.61; P < 0.05). The microarray analysis identified genes with both significant additive and non-additive levels of expression in the hybrid compared with the parents. The majority of the variation in gene expression was additive (87%), but among the genes with a non-additive pattern of expression, the greater proportion of probe sets (86%) fell outside the parental range. Gene ontology analysis of these genes revealed the presence of a number of terms related to metabolism and genetic information processing.

The genus Limnanthes (Limnanthaceae), also known as meadowfoam, has attracted attention for industrial use due to the unique characteristics of its seed oil. Samples from wild populations showed variability in agronomically important traits involved in seed oil yield, warranting the establishment and continued development of a germplasm collection. The level of genetic diversity within the United States Department of Agriculture, Agriculture Research Service, National Plant Germplasm System (USDA-ARS-NPGS) Limnanthes collection was evaluated using 15 simple sequence repeat (SSR) markers across 62 accessions representing 7 species. Parsimony analysis separated the accessions into two main groups consistent with the traditional taxonomic sections Inflexae and Reflexae, but there was little resolution within groups. These two groups were confirmed using neighbour-joining analysis and principal coordinate analysis. SSR marker variation suggests that the Limnanthes germplasm collection is genetically diverse and the accessions within the species likely contain novel alleles, and therefore the collection contributes to the conservation of the wild Limnanthes gene pool.

Choclero is a Chilean traditional floury maize, consumed as a vegetable, with large economic and cultural value due to its culinary properties that give unique characteristics to the traditional local cuisine. Market diversification demands new materials with different ear and kernel characteristics, which are at present not fulfilled by breeders due to lack of genetic diversity. At present, the Instituto de Investigaciones Agropecuarias has a Choclero germplasm collection composed of 96 accessions, which can supply this lack of diversity, or increase the gene pool. In the present study, 34 selected Chilean Choclero landraces were characterized for 41 agromorphological traits. Phenotypic evaluation in three environments representative of the core production area revealed significant genetic variability for most of the evaluated traits, leading to the identification of several promising accessions. The greater contribution of genotype in most phenological plant, ear and kernel traits suggest their potential usefulness for breeding purposes. Principal component analysis explained over 75% of the total variation for 29 quantitative agromorphological traits. Cluster analysis separated accessions into four major groups, differentiated mainly by plant phenology and ear trait. These findings indicate a number of useful traits at an intra-racial level and a wide range of phenotypic variation that provides a good source of diversity for use in the development of new Choclero varieties.