Sustainable development of a breeding programme depends on having sufficient genetic variability to achieve genetic gains in each selection cycle. The aim of this study was to molecularly characterize families of the oil palm, Elaeis guineensis Jacq., of different origins using microsatellite molecular markers. The value of the observed heterozygosity was higher than that of the expected heterozygosity in all of the progenies. The coefficients (G ST= 0.207 and F ST= 0.174) and AMOVA showed genotypic differences among the evaluated families. Likewise, this was reflected in the groups obtained by the dendrogram and principal coordinate analyses. This difference could have evolved due to the enrichment of some of the families with germplasm from different origins. Therefore, genetic relationships estimated from molecular data would be convenient to select families more distant from each group and palms more distant from each family selected to reserve genetic variability. This information will guide us in the decision-making process when planning breeding programmes focused on crosses to develop new populations with an acceptable broad genetic base and adaptability. In this way, sources of resistance to biotic and abiotic factors can be identified for the development of new varieties with competitive advantages for the sector.

Rice varietal diversity was assessed in Guinea on the basis of surveys of 1679 farms located in 79 villages of the four natural regions of the country. The descriptors used were the number of known varieties, the number of cultivated varieties and Shannon's diversity and evenness index. On the basis of their use rates, varieties were classified as major or minor types at the village scale and as regionally and/or nationally eminent varieties at these scales. Varietal diversity was high, especially in forest Guinea and lower Guinea. Diversity pattern was typical of the subsistence farming system. The high share of local variety reflected the predominance of low management and low input cropping systems. The presence of improved varieties confirms farmers' openness to innovation and to the government policy of promoting improved varieties. Regional diversity reflected the agro-ecological diversity and specificities of each region, the history and the extent of rice-growing systems, and the importance of rice in the local diet. Recent dissemination of NERICA varieties has not caused any reduction of pre-existing varieties. The short-duration NERICA are mainly used as a complement to the long-duration traditional varieties and thus enhance varietal diversity. Risks of diversity erosion seem limited in the current setting of farming system and diversity structure. However, at the village level, the diversity pattern is fragile as the proportion of farmers who used each variety of the village is low and heterogeneous. A continuous monitoring of the dynamics of rice varietal diversity in Guinea is needed.

To develop synthetic varieties (Syn) of broccoli for organic agriculture, we initiated a breeding programme from a landrace (LR). A Syn was obtained through a farmer-assisted selection programme that mirrors the original LR. The diversity level of the Syn was assessed using 14 putatively neutral microsatellite markers (simple sequence repeats (SSR)) and seven SSR related to genes involved in flowering control. Four commercial F1 hybrids were also assessed. Despite the strict selection procedure applied by the farmer to reproduce the LR annually and to obtain the Syn, the detected diversity level was high and similar to that of non-selected LRs. The possible reasons for these genetic outcomes (i.e. SSR position in the genome and farmer selection methods) are discussed here.

The genebank at ICRISAT, Patancheru, India conserves a total of 19,063 pearl millet landraces from latitudes ranging from 33.00° in the Southern Hemisphere (SH) to 34.37° in the Northern Hemisphere (NH). In the present study, the NH was found to be the major region for growing pearl millet landraces (80.5%). More landraces were found at lower latitudes ( < 20°) in both hemispheres than at higher latitudes. The latitude range of 10°–15° in the NH and 15°–20° in the SH were found to be important source regions for the prevalence of pearl millet, with 39.6% and 13.1% in the world collection of landraces, respectively. Landraces from lower-latitude regions on either side of the equator varied widely for all traits. Landraces from the 5°–10°N latitude region flowered late and grew tall in the rainy and post-rainy seasons and produced more tillers. Landraces from the 10°–15°N latitude region produced few tillers and had long and thick panicles with larger seeds. Long-bristled bird-resistant landraces were considerable at latitudes of 10°–15°S and 20°–25°S. The minimum temperature at the collection sites was found to be one of the important factors for determining the patterns of the prevalence of pearl millet across the latitudes. Late-maturing, tall and high-tillering landraces from lower-latitude regions were better sources for fodder production. Early-maturing landraces producing long and thick panicles with large seeds from mid-latitude regions (15°–20°) in both hemispheres were useful for developing high-yielding cultivars. Using the latitudinal patterns of diversity in pearl millet landraces, missions may be launched to explore high-diversity, under-collected and threatened areas for the collection of materials of interest at latitudes of 15°–20°.

This paper aims to propose an international list of descriptors for Butia odorata (jelly palm), using scientific documentation methods and farmers' knowledge to allow the germplasm characterization for conservation and sustainable use. It is an attempt to promote the development of new approaches to documenting crop genetic resources using a blend of these two sources of knowledge, frequently perceived as conflicting. This long-lived and useful palm is a neglected and subutilized species, and its genetic diversity and associated knowledge are under severe erosion. A list of 11 morphological descriptors is proposed based on observations, literature review and discussions with farmers who know and use the plant. These descriptors were used to characterize 303 adult jelly palms conserved in situ. Descriptive results are presented. Only five morphological characteristics were reported by farmers as important to discriminate individual plants, indicating that farmers have simpler and more rapid ways to differentiate diversity than do the scientists based on their uses. Standard list of descriptors developed by ex situ conservationists are widely used by breeders, but they rarely reach out to farmers and other user groups, a fact that limits the full use of germplasm collections around the world. Conversely, farmer-based descriptors, which are the expression of deep knowledge of diversity and its deployment by traditional communities, are rarely considered by breeders, mainly because they are not available. In this paper, we support the idea that a blend of these two methods – in a standard format – is highly strategic to promote an effective in situ conservation-through-use approach.

Jatropha curcas (jatropha) is an important non-edible oilseed crop with potential as a raw material for biofuel production. Although J. curcas has 30–35% oil content in its seeds, it has low seed yield ( < 2 ton/ha) and thus cannot become an economically viable crop. However, jatropha has many related species and genera such as J. integerrima, J. multifida, J. podagrica and Ricinus communis that are suitable for interspecific and intergeneric hybridization. The desirable features that can be obtained from these species are high number of inflorescences from J.integerrima, large fruit size from J. multifida, high oil content from J. podagrica and raceme-type inflorescence from R. communis. We were initially successful in producing hybrids between J. curcas and these related species. Hybridity was confirmed using expressed sequence tag (EST)–simple sequence repeat markers developed from the J. curcas EST database.

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

Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

Ziziphus mauritiana Lam. is an important fruit crop of the Thar Desert of India. About 330 accessions and cultivars collected from various parts of India are currently being maintained at a farm in the Central Institute for Arid Horticulture. Utilization of such a large collection of germplasm for breeding and crop improvement is difficult. Therefore, in the present study, using a heuristic approach based on phenotypic characters, we identified 52 accessions that represented a core collection, with a coverage of 100% and a coincidence rate of 98.1%. No significant difference was observed with respect to either the Shannon–Weaver or the Nei diversity index for qualitative traits, mean values and ranges for quantitative traits or clustering patterns between the core and whole collections. The core collection represents the entire range of diversity with minimum redundancy and should be useful for the conservation and utilization of Z. mauritiana germplasm.

The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improved indica varieties/lines developed recently and/or widely used by present indica breeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improved indica varieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/lines through germplasm exchanges. Distance-based clustering revealed that Latin-American cultivated indica lines have tended to form their own ecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding, although they are still closely related to Asian indica lines. African cultivated indica lines, on the other hand, have not yet formed their own ecological cline. It was also observed that the most well-known hybrid rice parents, Zhenshan97B and Minghui63, were unexpectedly clustered in the same SG with a relatively narrow genetic distance, which suggests that a significant genetic distance between parents is not a prerequisite for all elite hybrid rice lines with high heterosis.

Spine gourd (Momordica dioica Roxb. ex Willd.) is a highly nutritious and underutilized vegetable containing high amount of protein as compared to other cucurbitaceous vegetables. Twenty-six accessions of spine gourd (M. dioica Roxb.), collected from eastern India, were evaluated to study the diversity and other genetic parameters. The estimates of genotypic coefficient of variation and phenotypic coefficient of variation for all the characters indicated that selection can be done on the basis of phenotype alone. On the basis of cluster analysis, spine gourd accessions can be categorized into three distinct groups. The accessions of spine gourd from eastern India showed an immense variation and can be used as a potential source of germplasm for crop improvement. The results presented here on nature and magnitude of genetic variability and diversity existing in this species will provide the foundation for designing an efficient spine gourd breeding programme. As spine gourd is distributed widely almost throughout India, further collections from Peninsular and Western India are suggested for maximum diversity sampling.

Landraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Assessing genetic diversity and identifying trait-specific germplasm within germplasm collections is necessary for a varietal development programme. Agronomic features were investigated in 318 diverse dry bean germplasm accessions, including check varieties. We observed a lot of genetic variability for the traits studied. A wide range of variations was noticed for days to 50% flowering, days to maturity, pod length, the number of seeds per pod and 100-seed weight (HSW). For eight of the agronomic features evaluated, the analysis of variance revealed substantial differences among the accessions. For all characters, phenotypic coefficient of variation estimations were more significant than genotypic coefficient of variation. Plant height, days to 50% flowering, seed yield (q/ha) and HSW had high heritability and genetic advance as a per cent of the mean. Association analysis revealed a significant positive relationship between HSW, plant height, pod length and seed yield (q/ha). According to a hierarchical clustering analysis based on agronomic features, the diversity of dry bean germplasm has no significant association with their geographical origin. The number of pods per plant, plant height, days to maturity, days to 50% flowering and seed yield had relatively long vectors based on principal components 1 and 2, indicating that genotypes differ significantly. Additionally, the trait-specific donors and bean common mosaic virus disease-resistant accessions, IC360831, ET4515, EC150250, IC340947, IC564797B, EC565693 and ET8409 could be of value for dry bean improvement.

Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

Bell pepper or sweet pepper (Capsicum annuum L. var. grossum) is highly susceptible to high-temperature stress (HT). Hence, search for donor across C. annuum for HT tolerance was undertaken by following Temperature Induction Response (TIR) technique. The induction and challenging temperature requirement for TIR screening were standardized in 1 d-old Capsicum seedlings. Forty Capsicum genotypes were evaluated based on the recovery growth (RG) and per cent reduction in recovery growth (%RRG) of the seedlings. The genotypes Punjab Guchhedar and Ajeet 1 were found to have maximum cellular level tolerance (CLT) to HT with higher RG and lower %RRG compared to the non-induced seedlings and HDC 75 was found to have minimum CLT. In order to confirm the findings, another experiment was conducted under managed stress and control conditions. Absolute yield obtained from both the environments were used to calculate stress tolerance indices such as heat susceptibility index, tolerance index, stress tolerance index, mean productivity, geometric mean productivity and yield stability index. Based on these tolerance indices, Punjab Guchhedar and Ajeet 1 were found to be highly tolerant and HDC 75 as highly susceptible. Further, the combined result of TIR and tolerance indices also gave the same result confirming Punjab Guchhedar and Ajeet 1 can be used as a donor for the future breeding programme aimed at evolving high-temperature-tolerant bell pepper cultivars. The result also confirms the fitness of TIR technique to screen Capsicum genotypes for tolerance to HT based on variability in acquired thermotolerance.

Jackfruit (Artocarpus heterophyllus Lam.) is a nutritious crop from the Moraceae family. The current study was undertaken to evaluate the phenotypic diversity of fruit characteristics using a set of 27 standardized fruit descriptors to describe 28 jackfruit genotypes. These data were used to identify the superior jackfruit genotype that could be used for commercial cultivation. The data revealed a wide range of differences among the genotypes for all the traits studied. Cluster analysis classified the genotypes into four major groups that confirmed the wide diversity among them. Principal component analysis (PCA) also revealed that 80.22% of the variability among the jackfruit genotypes was explained by the first five principal components (PCs). Based on the overall results, the Indian Council of Agricultural Research, Research Complex for Eastern Region (ICAR-RCER) JS 6/3 and 10/3 genotypes were found to be the most promising for table purposes (medium fruit size, pulp percentage >50 and total soluble solid (TSS) >20°Brix), whereas the ICAR-RCER JS 7/7 genotype with large fruit size, pulp percentage >50 and TSS >20°Brix was found to be suitable for processing. The coefficient of variation was the least for traits such as TSS (12.56%) and average seed length (13.56%). Hence, priority may also be given to the TSS and seed size when exploring promising genotypes and operating a selection procedure for crop improvement in jackfruit. The information generated under the study forms a potential baseline for fruit breeders to use in selecting genotypes with superior fruit qualities for jackfruit crop improvement programmes in the future.

Lentil is recognised as the most nutritious rabi pulse and, with respect to acreage, it ranks next to chickpea. It is grown throughout northern and central India. A large percentage of Indians are vegetarian and lentil has long been part of India's indigenous diet, and is a common source of protein. Of about 60 varieties released in India to date, 13 have been developed by hybridization, mostly from parents not distantly related. The narrow genetic base of the presently cultivated varieties and losses due to biotic and abiotic stress factors remain the main cause of concern. Introgression of genes between microsperma and macrosperma groups of lentil from closely related species like L. culinaris subspp. Orientalis and use of biotechnological tools, wherever necessary, have been recommended by various workers to broaden the genetic base of this crop. Direct selection for grain yield through important component traits such as pods/plant, seeds/pod, number of clusters/plant, harvest index, biological yield, early maturing and breeding for better yield quality have been suggested. Realizing the significance of plant germplasm, special efforts have been made by the national bureau to collect the genetic resources of lentil from different states of India. A large number of accessions were characterised and evaluated for various agro-morphological traits, using the lentil minimal descriptor. The core collection comprising 287 promising accessions recorded variation for seed yield and its important component traits; variation was also observed for important morphological traits, using mutation breeding approaches. These genetic resources of lentil have also been screened for tolerance to several biotic stresses and a few lines showed immunity against rust, blight and fusarium wilt and these have been utilized as donors in cross-breeding programmes. On the other hand, wild Lens species revealed substantial genetic diversity for phenological and agro-morphological characters, including some important diseases of lentil. From these genetic resources, potential donors of desirable traits have been selected after evaluation and characterization and have been utilized in the genetic improvement of cultivars.

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

Finger millet is gaining importance as a food crop with the increasing emphasis on nutritional aspects and drought resilience. However, yield improvement has stagnated. Therefore, popular varieties have been examined for the purpose of whether direct selection for grain yield can be continued or an alternate trait-based approach using the germplasm is necessary. Direct selection for grain yield over the ruling variety, cv. GPU-28 (Germplasm Unit) has not been satisfactory. The path analysis has revealed a high direct effect of mean ear weight on grain yield followed by a moderate direct effect of photosynthetic rate and leaf area index. Furthermore, backward stepwise regression analysis revealed that among the independent traits, the mean ear weight made a significant contribution (60.8%) towards grain yield, followed by the photosynthetic rate (39.2%). The regression equation predicts the inclusion of mean ear weight by 1.0 g extra (as in GE-2672) to cv. GPU-28 will increase grain yield by 4.74%. The trait-specific genotypes are superior to the cv. GPU-28 were GPU-67 (photosynthetic rate) and GE-2672 (mean ear weight) and they could be used as donors for yield improvement. Future selection would aim for genotypes having 70–75 days for flowering with 4−5 productive tillers and mean ear weight of more than 8−9 g/ear. The possible approaches for enhancing grain yield are also discussed.

Most of the modern-day improved watermelon varieties succumb to various biotic and abiotic stresses mainly because of their narrow genetic base. Insights into the genetic diversity and population structure are crucial for broadening the genetic base and improving the adaptive value. The present experiment was conducted to study the genetic diversity and population structure of a germplasm panel comprising 336 Citrullus sp. accessions. Another objective was to formulate a core collection of Indian Citrullus sp. accessions. Data from 23 highly polymorphic microsatellite markers were used for genetic diversity and population structure analysis while both molecular and phenotypic data from 17 traits were used to formulate the core set. The markers yielded a total of 69 alleles with an average of three alleles per locus. Initially, the accessions clustered into two populations and an admixture group. Intra-population analysis revealed three and two statistically distinct subpopulations in Pop I and Pop II, respectively. The exotic collections were predominant in Pop I-A, Pop II-A and Pop II-B while the Indian accessions were preponderant in Pop I-B and Pop I-C. Pop I-B recorded the maximum magnitude of gene diversity and the highest number of alleles. The well-adapted Indian landraces could be deployed in future watermelon improvement programmes. The formulated core collection (n = 46; 23.71% of the entire collection studied) would ease in maintenance of the diversity present among indigenous Citrullus sp. accessions; would ease trait search while exploring Indian diversity and can be pooled with other collection(s) to form a global core of watermelon.