Guinea grass (Megathyrsus maximus Jacq.) is an important forage species in vast rangelands/grasslands of India and several tropical countries owing to its high biomass yield, good nutritional quality and wide adaptation. Evaluation of the existing natural variation and selection of desirable genotypes is the most plausible breeding method for this apomictic and polyploid grass. Developing a core sub-set to narrow down the number of germplasm required for future genetic studies is also pertinent. The present study involved characterization of 152 diverse M. maximus germplasm representing collections from different agro-ecological zones of India as well as those procured from Africa and Brazil; and development of a core sub-set. Nineteen metric, seven non-metric and nine nutritive traits together established the presence of wide variability among the genotypes. Clustering of the genotypes resulted in eight distinct clusters. The largest cluster included genotypes from Ethiopia, north India, north-western India, south India and north-eastern hill region, thus represented the highest diversity. Eleven of the total 26 Ethiopian genotypes clustered together. Non-metric morphological traits effectively differentiated the genotypes, and were associated with nutritional quality also. Genotypes which flowered once in a year showed slightly better crude protein and digestibility. The clusters were further sub-clustered and representatives were selected to develop the core sub-set of 23 genotypes comprising 20 indigenous and three exotic accessions. Comparison of the range of diversity and mean value for traits as obtained in the core sub-set and that in the total germplasm indicated successful capturing of maximum diversity in the core sub-set.

‘Broccolo fiolaro’ (Brassica oleracea L. convar.Italica) is a typical vegetable produced in a restricted hill country area around Creazzo(Vicenza) in north-eastern Italy. The cultivation of this vegetable dates back severalcenturies ago, but a very few farms are still involved in the production.‘Broccolo fiolaro’ is a variety of broccoli highly valued for itsagronomic and organoleptic features.

Four ‘Broccolo fiolaro’ selections were characterized by simplesequence repeats (SSRs) molecular markers and compared with other five cultivatedvarieties of broccoli of the Italica group in order to reconstruct their genetic structureand evaluate the degree of similarity among and within populations. The analysis of 12 SSRpolymorphic loci pointed out a low genetic variability among the four ‘Broccolofiolaro’ selections. Moreover, the whole ‘Fiolaro’ groupshowed significant differentiation from the other broccoli cultivars and could be easilydistinguished by cluster analysis. An assignment test on ~30 genotyped plants randomlychosen from each broccoli population correctly recognized the proper accession 88% of thetime, proving this method to be useful for cultivar identification.

Melon (Cucumis melo L.) is an economically important vegetable crop worldwide. Karnataka state of southern India is rich in melon landraces and wild relatives, which are potential sources of genetic diversity for crop improvement. Here we report on the collection, characterization and documentation of previously unexplored landrace and wild material to broaden the availability of this genetic diversity for use in melon improvement. Accessions of botanical groups, momordica, kachri, chandalak, reticulatus, acidulus and indicus, intermediate forms of acidulus and momordica, and three melons of an unknown group were sourced directly from farmers of eight agro-ecological regions. Twenty-three representative melon landraces and wild relatives, along with four reference varieties of different botanical groups, were evaluated for agronomic traits during the year 2016. Very wide and distinctive genetic variations were observed among the melon accessions for ovary characters, sex expression, days taken to first fruit maturity, external and internal fruit traits, and fruit cracking (splitting). The remarkable variability displayed among the melon accessions as observed from the study demonstrates the importance of them as a valuable genetic reservoir for melon improvement.

Oaks are model species due to their importance in various ecosystems, worldwide distribution, high economic value and emerging genomic resources. As such, knowledge on population differentiation across their distribution range is of high importance for sustainable forest management. As in most angiosperms, chloroplasts are maternally (via seeds) inherited in oak species and acorns are dispersed over comparably short distances. Consequently, chloroplast markers reveal comparatively high differentiation between populations, making them highly viable for the analysis of historic migration patterns and the certification of reproductive material. Despite the existence of various white oak (section: Quercus) chloroplast markers, red oak (section: Lobatae) chloroplast markers remain limited. Northern red oak is one of the most important North American oak species and a widespread non-native plantation tree species in European forests. We took advantage of chloroplast genomes of Q. rubra L. and related oak chloroplast genomes to develop a set of robust and easy-to-use chloroplast microsatellite primers for northern red oak. Furthermore, we tested transferability of those novel red oak primer pairs to Q. robur L. and Q. petraea Matt. Liebl. The new set of fifteen polymorphic chloroplast microsatellite markers revealed three additional northern red oak haplotypes after screening 80 northern red oak individuals representing seven haplotypes, identified based on formerly available markers. Therefore, they provide a higher resolution of haplotypes as compared to currently available markers.

Embryogenic callus induction and regeneration are useful in many aspects of plant biotechnology, especially in the functional characterization of economically important genes. However, in sugarcane, callus induction and regeneration vary across genotypes. Saccharum spontaneum is an important wild germplasm that confers disease resistance and stress tolerance to modern sugarcane cultivars, and its genome has been completely sequenced. The aim of this study was to investigate the effect of genetic variations on embryogenic callus induction and regeneration in S. spontaneum and to screen genotypes having high tissue culture susceptibility. The study was performed using nine genotypes of S. spontaneum and the following five parameters were assessed to determine the response of genotypes to embryogenic callus induction and regeneration: callus induction, embryogenic callus ratio, embryogenic callus induction, embryonic callus regeneration and regeneration capacity. All the genotypes varied significantly (P < 0.01) in all the parameters, except for embryonic callus regeneration, which was high (>80%) for all the genotypes. High broad-sense heritability (86.1–96.8%) indicated that genetic differences are the major source of genotypic variations. Callus induction was found to be strongly positively correlated with embryogenic callus induction (r = 0.890, P < 0.01) and regeneration capacity (r = 0.881, P < 0.01). Among the nine tested genotypes, VN2 was found to be the most responsive to tissue culture and could therefore be used to characterize functional genes in S. spontaneum. We also suggested an approach with potential applications in facilitating the rapid identification of sugarcane genotypes susceptible to tissue culture.

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.

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.

Aegilops tauschii, the D genome donor of wheat, is an invaluable source of genetic variability, which can be utilized for broadening the wheat gene pool. Linked leaf rust resistance and non-glaucousness genes transferred from Ae. tauschii to cultivated wheat variety WH542 were mapped in the present study. Genetic analysis in an F2 population from a BC3 plant derived from the cross Triticum durum cv. PBW114/Ae. tauschii acc. pau14195//4*T. aestivum cv. WH542 revealed monogenic dominant inheritance for both the traits. The leaf rust resistance and the non-glaucousness gene were tentatively named LrT and IwT, respectively. Leaf rust resistance gene exhibited all stage resistance. SSR markers Xbarc124, Xgdm5, Xgdm35, Xcfd51 and EST-derived markers Xcau96 and Xte6 on chromosome 2DS were linked with both genes. Chromosomal assignments of the genes were confirmed by testing linked SSR markers on Chinese Spring nulli-tetrasomics lines. SSR markers Xcau96 (1.6 cM) and Xbarc124 (0.6 cM) flanked LrT and Xgdm35 (4.1 cM) and Xte6 (2.5 cM) flanked non-glaucousness gene. LrT and IwT showed a recombination distance of 3.4 cM. Hence, IwT can be used as an easy to score morphological marker of LrT during its transfer to other glaucous backgrounds.

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.

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.

Asian palmyrah palm (Borassus flabellifer L.) is a multipurpose, economically important tree widely distributed in the Indian subcontinent and Southeast Asia. The multifaceted uses (~800 uses) of the tree as food, wood and medicine make it a viable industrial crop. However, the dioecious nature of the tree coupled with long juvenile phase (12–20 years to initiate flowering), long stature and considerable variations in the productivity of male and female trees necessitates the application of new biotechnological tools for crop improvement. This review provides comprehensive information on the extent of genetic diversity of the crop, problems associated with palmyrah cultivation along with its multifaceted application and research gaps to be addressed for the effective utilization and conservation of palmyrah palm genetic resources.

Improvement in multi-cut forage sorghum varieties that can perform better than SSG 59-3, a sweet Sudan grass released in 1974, has been a challenge. Efforts were made to create variability in SSG 59-3 through mutagenesis using both physical and chemical mutagens. Fifteen such mutants were evaluated for 2 years in different locations in India. Considerable variability was observed for important fodder yield and quality traits. SSG 237 flowered 10 d early than SSG 59-3. SSG 231, SSG 260, SSG 232 and SSG 237 had high protein percentage and in vitro dry matter digestibility (IVDMD) values compared with SSG 59-3. Hydrocyanic acid (HCN), a major anti-nutritional factor, was low in six mutants, the lowest being in SSG 226. This variability can be used in different breeding programmes aimed at improving multi-cut forage sorghum varieties. The lines with improved fodder quality (low HCN, high protein and IVDMD) can be used in the breeding programme for the improvement in multi-cut forage sorghum varieties.

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.

Drought tolerance is a highly complex trait and one of the important components of yield stability in wheat. An experiment was therefore conducted to study the drought tolerance status of 14 high-yielding wheat varieties based on morphological characteristics under a randomized complete block design following factorial arrangement with three replications. Variety × Treatment × Year interactions of wheat genotypes were studied for various morphological traits under normal and drought stress conditions for 2 years in plants grown in pots. Significant differences were observed among the 14 varieties of wheat. Sutlej-86 was found to be highly affected by drought, with maximum reductions in plant height, spike length and number of spikelets/spike. The variety with the maximum tolerance to drought was Bahawalpur-97; this variety also had the lowest reductions in the number of fertile tillers/plant, the number of spikelets/spike, spike weight, the number of grains/spike, 1000-grain weight, grain yield/spike, total biomass and stress susceptibility and tolerance indices. Stronger correlations among the studied attributes under drought stress over normal conditions further highlighted drought stress adversities. The studied traits are thus recognized as drought tolerance indicators for varietal selection, and varieties showing less reduction under drought could be used as a standard check in breeding programmes to identify lineages with drought tolerance and could be recommended for drought-stressed areas.

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.

Theobroma cacao L. (cacao) is an important tropical crop used to produce chocolate. Evolutionary relationships between cultivated and wild cacao genotypes and their genetic diversity are poorly understood. Exploring phylogenetic diversity and spatial patterns of both cultivated and crop wild relatives can improve the knowledge of the evolutionary history of a crop, giving insights into its cultivation, breeding programmes and conservation. This study identifies biodiversity priority areas in Colombia by calculating phylogenetic diversity indices using a set of 87 single nucleotide polymorphism markers. These were sourced from 279 genotypes conserved in the Corporación Colombiana de Investigación Agropecuaria (Agrosavia) germplasm collection. The Caribbean and North Andes areas exhibited the highest phylogenetic diversity and significantly high relative phylogenetic diversity. We propose that those regions where wild cacao occurs should be prioritized as conservation areas. Besides, cacao lineages that have recently diverged and are present in Arauca, Huila and Nariño areas, with significantly low relative phylogenetic diversity, should be prioritized for breeding programmes. The Amazonia genotypes were closer to the root of the phylogenetic tree, suggesting an older origin than those found in the Andes region. Our study highlights the importance of using T. cacao germplasm from the Amazonia region as a priority to recover relict diversity in breeding programmes and broaden the gene pool of modern cultivated cacao.

In this work, 10 processing type Hungarian tomato gene bank accessions were investigated in a 3-year open-field experiment together with three commercial varieties for quantifying the genotype × environment interaction for their total soluble solids, total acid, dry matter, lycopene, total polyphenol content and antioxidant activity. Results showed remarkable differences of accessions in phytonutrient content over the 3 years (environments). Genotype main effect plus genotype × environment interaction biplots were created for the visualization of the best performing samples and of their relation to a theoretical best variety. Obovate fruit-shaped accessions (especially RCAT031257 and RCAT060349) reached outstanding nutritional results in every environment. According to extremities in weather conditions, two landraces (RCAT060348 and RCAT060349) with higher drought tolerance, and two (RCAT031257 and RCAT029837) less prone to excessive rainfalls were identified. The results can contribute to the enrichment of tomato nutritional phenotypic data banks, facilitating the utilization of gene bank accessions in genomic studies.

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.

Rice blast caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice production worldwide. Information on rice varieties with the blast disease resistance gene is important for rice cultivar development. This study identified rice blast resistant genes in 226 rice cultivars including 203 Thai landrace rice cultivars (19 upland rice cultivars from the North, 99 lowland rice cultivars from the Northeast, 45 floating rice cultivars from the Northeast and 40 cultivars from the South), 21 recommended rice varieties and two susceptible varieties ‘KDML105’ and ‘Nipponbare’ by using gene-specific markers for the blast resistant genes Pid3, Pi54 and Pigm. Results showed that 159 cultivars have at least one resistant gene and four cultivars have all three resistant genes. These results indicate that Thai landrace rice is a valuable source of rice blast resistant genes for rice breeding programmes.