Phoebe cooperiana U.N Kanjilal ex A. Das is an indigenous forest tree species yielding fruits consumed widely across the state of Arunachal Pradesh, India. As part of an initiative to domesticate the species, phenotypic variation in fruit and seed morphology as well as the biochemical properties of the pulp were assessed for 14 populations within the state. Nine fruit and seed characters were measured and 12 biochemical parameters of the fruits were analysed. Five trees were selected from each population and a minimum of 30 fruits were collected from each tree. Analysis of variance indicated significant variation in all fruit and seed morphological parameters. The coefficient of variation for fruit weight was reported to be 5.02%, seed weight 5.60%, pulp weight 5.36% and pulp fruit ratio 4.14%. Among biochemical parameters which are of nutritive value, crude protein, vitamin E and A were higher than that found in most common fruits and vegetables. These traits also showed significant variation among the 14 selected populations with crude protein values ranging between 5.99 and 10.76%, vitamin E between 4.80 and 7.33 mg/100 g and vitamin A between 1.88 and 3.13 mg/100 g. The fruits are also high in phenol with a mean value of 22.19 mg/g and displayed promising 2,2-diphenyl-1-picrylhydrazyl radical scavenging properties averaging 56.94% antioxidant activity. However, cyanogen content in the fruits was higher than the permissible amount for human consumption, for which processing is recommended before use. The opportunities for domestication are discussed and some promising traits and populations that can be utilized in the domestication programme are identified.

Development of a representative and well-diversified core with minimum duplicate accessions and maximum diversity from a larger population of germplasm is highly essential for breeders involved in crop improvement programmes. Most of the existing methodologies for the identification of a core set are either based on qualitative or quantitative data. In this study, an approach to the identification of a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data was proposed. For this purpose, six different combined distance measures, three for quantitative data and two for qualitative data, were proposed and evaluated. The combined distance matrices were used as inputs to seven different clustering procedures for classifying the population of germplasm into homogeneous groups. Subsequently, an optimum number of clusters based on all clustering methodologies using different combined distance measures were identified on a consensus basis. Average cluster robustness values across all the identified optimum number of clusters under each clustering methodology were calculated. Overall, three different allocation methods were applied to sample the accessions that were selected from the clusters identified under each clustering methodology, with the highest average cluster robustness value being used to formulate a core set. Furthermore, an index was proposed for the evaluation of diversity in the core set. The results reveal that the combined distance measure A 1 B 2 – the distance based on the average of the range-standardized absolute difference for quantitative data with the rescaled distance based on the average absolute difference for qualitative data – from which three clusters that were identified by using the k-means clustering algorithm along with the proportional allocation method was suitable for the identification of a core set from a collection of rice germplasm.

Six distinct market samples of Dacryodes edulis (safou/African plum) with different fruit colour were characterized in terms of morphological, sensory and nutritional traits that can guide the selection of high-value individual trees for cultivar development. The morphological characteristics assessed were: fruit length, fruit width, fruit and flesh weights, flesh thickness and pulp/fruit ratio, while the sensory characteristics were: acidity, aroma astringency, bitterness, oiliness, preference, fibrousness and sourness. In addition, the biochemical composition (carbohydrates, ash, protein, lipids, dietary fibres, vitamin C, iron, calcium and phosphorus contents) was determined. These attributes all showed great variability, suggesting their importance in the identification of multi-trait ideotypes for potential cultivar development.

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

Huauzontle (Chenopodium berlandieri ssp. nuttalliae) is a locally important vegetable crop native to the highland valleys of Central Mexico and a potential source of genes for improving its Andean sister crop, quinoa (Chenopodium quinoa). A previous work involving two huauzontle lines identified one waxy genotype that lacked amylose due to mutations in granule-bound starch synthase I (GBSSI), major amylose-synthesis genes with two constituent subgenomes, A and B. We conducted this study to determine the extent of waxy genotypes and cryptic GBSSI mutations in 11 huauzontle accessions or landrace populations extending from Puebla in the southeast to Jalisco in the northwest. This represents one of the first published studies of genetic variation in C. berlandieri ssp. nuttalliae. Accessions were phenotyped for opaque versus translucent seed morphology and their seed starches were stained with Lugol's Stain. In addition, complete or partial GBSSI genes from their A and B genomes were polymerase chain reaction (PCR)-amplified, cloned and sequenced. Seven accessions were either wholly or partially non-waxy while six were either entirely or partially waxy. All waxy accessions carried the same putatively null alleles, designated gbssIa-tp (A-genome) and gbssIb-del (B-genome). The identification of publicly available genotypes carrying gbssIa-tp and their potential use in breeding waxy grain quinoa is discussed.

The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.

A germplasm panel of 52 six-rowed barley landraces from northern Morocco was analysed by a Cleaved Amplified Polymorphic Sequences (CAPS) assay of a fragment of the elongation factor G (EF-G) gene. Forty-nine of these accessions carried allele A, and the other three carried allele D. The latter all originated from a narrow region close to the border with Algeria, whereas the former were represented across the whole collection area. Since six-rowed D allele carriers are present in North Africa, along with both two-rowed cultivated and wild barleys, it is likely that the European six-rowed barley varieties carrying the D allele have Moroccan parentage.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

A study was conducted to collect and characterize the indigenous Kala zeera (Bunium persicum Boiss. Fedtsch.) accessions from the hills of northwestern Himalayan sates of Jammu and Kashmir, Himachal Pradesh and Uttarakhand. Around 1000 accessions were collected during this exploration mission, out of which diversity of 252 accessions was established through morphological characterization. The morpho-agronomic characterization and the analysis of trait data revealed significant variability in number of branches per plant, number of umbelets per umbel, number of seeds per plant, seed yield per plant and 1000 seed weight. The collection and characterization of these diverse accessions can prove useful in future Kala zeera improvement programmes in the world as this is the first such comprehensive report of the crop from northwestern Himalayan region of India.

Nine characters contributing to seed yield were measured on 20 accessions of horse gram (Macrotyloma uniflorum (Lam.) Verd), and subjected to genetic divergence analysis using Mahalanobis statistic and mapping using DIVA-GIS. The accessions were collected from two eco-geographical regions of Andhra Pradesh (India) – North Coastal and Rayalaseema. Based on D2 values the genotypes were grouped into five clusters. Genetic diversity was not related to eco-geographical distribution. The greatest inter-cluster distance separated clusters II and V, followed by clusters IV, and V, III and IV. Entries in clusters V and II appear suitable as parents for horse gram improvement. The Rayalaseema region is the source of useful variation for days to flowering, maturity and yield.

Farmers in local communities have a considerable amount of information on their genetic resources both at the individual and community level. The farmers' knowledge is interweaved into their daily practices as a reserve accumulated over the generations. The Farmer Field Fora approach (FFF) has been conceptualized in order to activate farmers to identify the existing resources both in the crops they cultivate and in their knowledge, to recognize its value and to start using it more consciously. The FFF approach links the use of existing diversity to the possibility of having new varieties and to improving productivity. In weekly meetings farmers observe changes in the field between varieties, debate on them and draw conclusions. In every session a theme on plant development is debated among farmers with the aid of a facilitator. Close contact with researchers allows involvement with the breeding practices and enables the aims and conduct used in research to be understood. This empowers farmers to participate in a more active way in research, to apply more precise ways of observing and managing their genetic resources, and to link their work to conservation activities at the national and local level. The results of the FFF trial, which was carried out in 10 villages in the region of San in Mali in 2001, show an increased interest among farmers to observe varieties. The appreciation criteria used is multiple including yield, earliness, strong tillers, high number of tillers, and resistance for diseases and Striga. It seems obvious that even though the goal of the approach is on-farm conservation of plant genetic resources, it must be closely linked to farmers' interest. The variation of the results between villages demonstrates variability of climatic condition in this region and a high genotype—environment interaction. Further modifications of the approach are required in order to improve equitable participation of different stakeholders and improve the institutionalization of on-farm conservation.

Knowledge of the genetic diversity of germplasm of breeding material is invaluable in crop improvement programmes. Frequently, qualitative and quantitative data are used separately to assess genetic diversity of crop genotypes. While assessing diversity based on qualitative and quantitative traits separately, there may occur a problem when the degree of correspondence between the clusters formed does not agree with each other. This study compares five different procedures of clustering based on the criterion of weighted average of observed proportion of misclassification in black gram genotypes using qualitative, quantitative traits and mixture data. The INDOMIX- and PRINQUAL-based clustering procedures, i.e. INDOMIX and PRINQUAL methods in conjunction with the k-means clustering procedure, show better performance compared with other clustering procedures, followed by clustering based on either quantitative or qualitative data alone. The use of the INDOMIX- and PRINQUAL-based procedures can help breeders in capturing the variation present in both qualitative and quantitative trait data simultaneously and solving the problem of ambiguity over the degree of correspondence between clustering based on either qualitative or quantitative traits alone.

It is generally accepted that high-oleic crops have at least 70% oleate. As compared to their normal-oleic counterparts, oil and food products made from high-oleic peanut have better keeping quality and are much healthier. Therefore, high-oleic peanut is well recognized by processors and consumers. However, owing to the limited availability of high-oleic donors, most present-day high-oleic peanut varietal releases merely have F435 type FAD2 mutations. Through screening of a mutagenized peanut population of 15L46, a high-yielding peanut line with desirable elliptical oblong large seeds, using near infrared model for predicting oleate content in individual single seeds, high-oleic peanut mutants were identified. Sequencing FAD2A and FAD2B of the mutants along with the wild type revealed that these mutants possessed G448A FAD2A (F435 type FAD2A mutation) and G558A FAD2B (non-F435 type FAD2B mutation). Expression of the wild and mutated type FAD2B in yeast verified that the functional mutation contributed to the high-oleic phenotype in these mutants. The mutants provided additional high-oleic donors to peanut quality improvement.

Beachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.

In a search for high-quality jute (Corchorus olitorius) fibre using phenotypic marker(s), a single plant from CRIJAF accession OIJ 154 was isolated on the basis of its unique red-tinted pale green stem, which becomes crimson red at maturity, and was given a code name, PPO4. Progenies from this selection bred true with respect to morphological characters. It has a slightly lower height at maturity, but has comparable yield and a higher harvest index when compared to the most popular high-yielding variety JRO 524. In spite of having lower chlorophyll per unit weight of leaf tissue, the photosynthetic rate per unit chlorophyll, the relative growth rate of PPO4 was higher than JRO 524. A composite analysis of quality parameters indicated that the genotype is of higher grade (between TD2 and TD3) with very fine (1.5 tex) fibre of high tensile strength (19.7 g/tex). The lignin content (ca 14%) of the fibre was also less than that of JRO524 (ca 17%) under standard assay conditions. This plant type, with distinct morphological markers, could be utilized in breeding programmes for the genetic improvement of jute.

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Grewia tenax locally known as ‘Gangerun’, is an important multipurpose underutilized shrub and potentially threaten species of the Thar Desert of India. Owing to its importance, naturally available germplasm was collected and evaluated for its sustainable utilization in future. Data on individual mother plant, seed characters and soil profile were investigated. Habitat occurrence of G. tenax was found in patches with dominant association of Euphorbia caducifolia across the four districts of western Rajasthan. Individual plant on unprotected area portrayed far lower average height (0.95 m) and canopy area (1.75 m2) than protected area (2.63 m and 13.89 m2) signifying level of browsing pressure on this species in Jaisalmer. Soil samples belonging to Pali region have high organic carbon and low electrical conductivity content than Jaisalmer and Jodhpur. The statistical analysis of seed characters revealed the presence of high coefficient of variation (%) in 100-seed weight (HSW; 27.36) followed by seed length (SL; 8.06) and least in seed breadth (SB; 5.85). The range and mean values of HSW, SL, SB and length:breadth ratio (LBR) were (2.02–7.00 and 3.34 g), (4.36–6.15 and 5.36 mm), (3.73–4.68 and 4.25 mm) and (1.11–1.44 and 1.27), respectively. Significantly positive correlation was observed between SL and LBR (0.73) followed by HSW and SL (0.66). Along with these findings, its economic importance, utilization and conservation are detailed in this paper as to hasten further research on its various aspects for its successful conservation and utilization.

Direct sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

The technique of inter-simple sequence repeat-polymerase chain reaction (ISSR-PCR) was used to fingerprint blackgram (Vigna mungo) genotypes in order to differentiate them at a molecular level. Twenty-four primers were used to analyse 11 blackgram genotypes. The genotypes used in the study could be differentiated based on combined amplification profiles generated by two primers (UBC primer numbers 808 (AG)8C and 826 (AC)8C). It was observed that 3′-anchored repeat primers based on (AG) and (GA) repeats amplified a greater number of bands than 3′-anchored repeat primers of (CA) and (AC) repeats. This result perhaps indicates that GA/AG repeats are more frequent than CA/AC repeats in the blackgram genome.