Cordia sinensis, locally known as ‘Goondi’ in India, is an underexploited multipurpose fruit species found in hot arid regions that is well adapted to drought, salt and hot conditions. The present study was undertaken to collect fruit samples from different locations in the Kachchh region of Gujarat, India, and to determine their field establishment for characterization, conservation and utilization. The maximum distribution of the species was observed in Bhuj (45%) and Mandvi (25%). Field boundaries (35%) and scrub forests (30%) had greater frequencies, whereas backyards had rarer frequencies (10%). The species most commonly occurred on levelled topography (60%) with a soil pH in the range of 8–8.5 (63%). Morphological data of three-year-old plants in the field gene bank showed a maximum coefficient of variation in the number of leaves per plant (66.6), followed by the number of branches per plant (45.62) and collar diameter (27.69). Wide variations were recorded in plant height (121.67–212 cm), spread (118–223 cm2) and the number of branches per plant (6–24.33). Specific accessions were identified for fodder (CBCG-12, CBCG-13 and CBCG-16), early flowering and fruiting (CBCG-12, CBCG-13 and CBCG-14), easier propagation by seeds (CBCG-12 and CBCG-13) and salt tolerance (CBCG-15 and CBCG-16). Preliminary findings and information provided about this species' utilization and other aspects might be useful for future research on its domestication, sole plantation and conservation aspects, improving the exploitation of this species by present and future generations.

Microsatellite markers specific to Cheirostylis yunnanensis Rolfe were developed using an enriched genomic DNA library technique. The library was constructed using (AG)20 and (CAG)20 oligonucleotide repeats. A total of 48 primer pairs were designed and tested with 48 C. yunnanensis Rolfe samples, resulting in 11 polymorphic loci. The number of alleles per locus ranged from 2 to 12, with an average of six alleles. The observed and expected heterozygosity ranged from 0.0426 to 0.8085 and 0.0421 to 0.9078, respectively. Of the 11 polymorphic loci, three showed a significant deviation from Hardy–Weinberg equilibrium and one exhibited linkage disequilibrium. Cross-species amplification was tested with five samples of Cheirostylis of unknown species resulting in eight loci that could be amplified, with the number of alleles ranging from one to two. The microsatellite markers developed in this study will be useful for the genetic analysis of C. yunnanensis in order to differentiate species as well as to establish a conservation plan for this species.

The genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India holds a collection of 542 accessions from the Caribbean and Central American (CCA) regions, of which 424 were evaluated for eight qualitative and 17 quantitative traits at ICRISAT farm. A hierarchical cluster analysis was performed using the scores of the first nine principal components that resulted in four clusters. The accessions of these four clusters exhibited the following good characteristics: cluster 1 had high pod-bearing length and high seed protein content; those of cluster 2 had high degree of branching, large number of pods per plant and high seed yield per plant; those of cluster 3 had long pods; and those of cluster 4 had larger seeds. In the whole collection of accessions, diversity was found to be maximum (H′ = 0.630+0.026) for plant height and minimum for tertiary branches per plant (H′ = 0.259+0.026). The highest correlation coefficient was observed between racemes per plant and pods per plant (r= 0.914) followed by between pods per plant and seed yield per plant (r= 0.744), and between shelling percentage and the harvest index (r= 0.703). In view of the poor representation of the world collection of pigeonpea (13,771 accessions) from the CCA regions, launching of collection missions in these countries has been suggested to fill gaps and increase the variability. Multi-location evaluation of the collections for agronomic traits at potential locations in the CCA regions and systematic evaluation for nutritional traits and resistance to biotic and abiotic stress could result in the identification of useful genotypes, particularly vegetable types, for use in breeding programmes to develop high-yielding cultivars as well as to release as varieties in these regions.

During recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

Chinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembled de novo by a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.

In this study, a near-isogenic line (BC4F10) CR572 developed by introgressing a chromosomal segment from Oryza rufipogon (accession no. 105491) into the Oryza sativa subsp. japonica cv. Hwaseong was found to exhibit a significant increase in the number of spikelets per panicle (SPP) and grain weight compared with the recurrent parent Hwaseong. Quantitative trait locus (QTL) analysis in F2 generation derived from the cross between CR572 and Hwaseong revealed that two QTLs, qSPP1 and qTGW1, were linked to a simple sequence repeat marker, RM283, on chromosome 1. The additive effect of the O. rufipogon allele at qSPP1 was 13 SPP, and 21.6% of the phenotypic variance was explained by the segregation of RM283. The qTGW1 QTL explained 19.1% of the phenotypic variance for grain weight. Substitution mapping was carried out with five F3 lines derived from F2 plants having informative recombination breakpoints within the target region. Substitution mapping indicated the linkage of qSPP1 and qTGW1. The grain yield of CR572 was 18.2 and 15.8% higher than that of Hwaseong at two locations, respectively, mainly due to the increase in 1000-grain weight and SPP. These results are very useful for QTL cluster transfer by molecular marker-assisted selection in rice breeding programmes and for QTL gene cloning by map-based cloning.

Dongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

The search for disease resistance in wild types is continuing, in order to introduce resistant genes from wild relatives. In this study, we found that the wild melon Cucumis prophetarum was comparably more tolerant to salinity, the damping-off disease caused by the fungus Rhizoctonia solani and the root-knot nematode Meloidogyne incognita. The percentage of wild melon survival was 60% compared to that of the cultivated cucumber Cucumis sativus, which was 15%, when irrigated with NaCl at a concentration of 2500 ppm; and 96% for the wild melon compared with 44% for the cultivated cucumber when irrigated with CaSO4.2H2O at a concentration of 1000 ppm. Wild melon plants were more tolerant to R. solani attack, as only 20% of the plants were infested compared with 100% of infestation observed for the cultivated cucumber. The average number of nematode galls was 250 per plant on the cultivated cucumber when compared with 6.3 per plant on the wild species. Wild melon could be a potential source of resistant or tolerant genes that can be transferable to cultivated cucumbers.

Kerala, a humid tropical southern state, is the third largest producer of Tamarind (Tamarindus indica L.) in India. This tree spice is an important livelihood option for the rural society, especially in Palakkad district which is the lead producer of tamarind in the state with a few accepted primitive cultivars, viz. ‘valanpuli’, ‘madhurapuli’ and ‘thenpuli’. A survey was conducted to identify the fruit variability and document the sweet tamarind types of Palakkad. This study revealed the variability and weight of 30 fruits was seen to be the most indicative variable of tamarind in Kerala. The pod length varied from 5.28 to 23.41 cm and fruit weight from 4.83 to 43.40 g. Hierarchical clustering on principal component analysis resulted in six clusters. The clusters I, IV and V represented collections with fruit weight more than 20 g. Box plot diagrams revealed the high real pulp value in sample KTJ 162 (9.57) and high fruit length in KTJ 44 (21.68 cm). Among 113 collections, 18 samples were collected as perceived sweet types based on local enquiry. In the scatter plot between total soluble solids and ratio between total soluble solids and total titrable acidity, two samples were spotted as sweet types with acidity below 8%. Further molecular characterization and systematic crop improvement programmes are required for conserving the eroding gene pool of tamarind in Kerala and to develop sweet types for commercial production.

An integrated approach based on the use of bioinformatics and gene expression analysis tools was carried out to evaluate the organ-specific transcription modulation of nine genes relevant to sugar metabolism of Beta vulgaris L. plantlets of the autumn cv. Franca and spring cv. Bianca, in response to low-temperature (LT) treatments. Different growth cycles imply different plant capability to adapt to the environment that includes variations in gene expression of key metabolic enzymes. The transcriptional response was evaluated by quantitative PCR analysis before, during and after the LT treatments. The results were correlated with the LT-induced electrolyte leakage measure and the carbohydrate content. Stress-induced transcript level alterations were detected in the two cultivars, suggesting a modulation of sucrose synthesis and carbohydrate partitioning. Cold stress induced deep changes in the autumn cultivar, especially in fructose-1,6-biphosphatase gene expression, irrespective of temperature or exposure time. These differential features of expression profiles constitute first clues on the molecular basis of the differential LT response of sugarbeet autumn and spring cultivars.

Triggered by the need to develop inter-seasonal, multi-cut cereal forage crops, this study aimed at the exploitation of phenotypic variations among the rich pearl millet (Pennisetum glaucum L.) collections in Sudan for possible utilization in forage-type breeding programmes. A total of 100 pearl millet accessions were used in three field trials grown in rainy, winter and summer seasons (2008–2009) at the Gezira Research Station Farm and the Gezira University Experimental Farm. Wide diversity and highly significant differences in the total dry forage yield, days to harvest, plant height, number of tillers/plant and leaf/stem ratio were found among the accessions. At an 80% morphological similarity level, the 100 accessions of pearl millet were clustered into four main groups. In the rainy and winter seasons, 71 and 56% of the accessions produced forage yield of more than 5 t/ha, respectively. In contrast, 77% of the accessions produced less than 5 t/ha in the summer season. Among the top-ranking 25 accessions, two accessions (HSD 2190 and HSD 2236) were common in dry matter yield in the three seasons, whereas 11 accessions were identified in at least two seasons. The presence of such common accessions in more than one season is encouraging for growing pearl millet as a multi-cut crop for a longer period. These results indicated the possibility of the development of forage-suited varieties of pearl millet directly through further evaluation of those common accessions or indirectly through a crop breeding programme.

Plant viruses pose a threat to the acquisition, maintenance and distribution of lupin germplasm (genus Lupinus, family Fabaceae). The availability of sufficient quantities of healthy and virus-free seeds from maintained lupin collections is mandatory for conducting lupin research. The objective of this research was to determine which lupin species were potentially infected with potyviruses (presumably seed-borne) upon germination in the greenhouse. The procedure for screening lupin seedlings in the greenhouse for potyviruses incorporated enzyme-linked immunosorbent assay followed by elimination or segregation of infected seedlings from the population before transplantation into the field plots for regeneration and accession characterization. None of the accessions in this evaluation had been tested previously for virus. From 2002 to 2005, 15 perennial (30 accessions) and 6 annual lupin species (213 accessions) were evaluated on site at the Western Regional Plant Introduction Station in Pullman, WA, USA. While none of the greenhouse perennial seedlings tested positive for potyvirus, seedlings in three annual species (Lupinus albus, Lupinus angustifolius and Lupinus luteus) were infected by potyviruses, presumably by seed transmission. Future testing may focus on the annual species, thus saving limited germplasm maintenance resources.

In India, the restriction of genetically modified (GM) crops and derived products not approved in the country necessitates surveillance for transgene(s) in plant material/products imported into the country. CDC Triffid expressing acetolactate synthase (ALS) conferring tolerance to sulphonylurea herbicide is the only GM flax event that has got approval in Canada in 1990s and subsequently deregistered in 2001. In spite of deregistration, the unexpected and unauthorized detection of traces of GM flax in the consignments imported from Canada to Europe has further necessitated the stringent monitoring of flax shipments from Canada for suspected GM incidents. This study reports on the detection of transgenic elements being present in GM flax employing polymerase chain reaction assays, in a set of 123 flaxseed accessions imported from Canada for research purpose. Based on the tests conducted, none of the transgenic elements, namely, nos promoter (P-nos), nos terminator (T-nos), nptII marker gene, ALS transgene, as present in the GM flax CDC Triffid were detected in any of the tested accessions. The well-known herbicide tolerance gene cp4-epsps, being employed in Roundup® Ready events of other crops, was also not detected in these samples. This case study has demonstrated the importance of monitoring the presence of transgene(s) in flaxseed imports, and such studies need to be carried out for the imported seeds from the country where GM events of respective crop are being approved whereas they have not been approved in the country of import as a part of precautionary approach.

Diversity in agronomically important traits of wild emmer wheat, Triticum dicoccoides, the progenitor of most cultivated wheats, was examined in l60 genotypes representing 16 populations derived from a wide ecogeographical spectrum of climate, soil and water availability in Israel and Turkey. The analysis included 14 quantitative economic characters including heading date, culm length, biomass, grain yield and its components, and grain protein percentage.

The results led to two major conclusions: (i) agronomically important traits varied genetically: ecogeographic diversity in these traits is dramatically displayed when populations are grown in a relatively standardized environment; and (ii) genetic diversity is revealed not only between, but also within populations. Thus, genotypes excelling in some of these characters were found in several populations.

Adzuki bean (Vigna angularis [Willd.] Ohwi & H. Ohashi) is one of the most important legume crops cultivated in East Asia and northern South Asia. Despite its agronomic importance, the lack of available sequence information has made it difficult to improve important agronomic traits. In the present study, we performed de novo assembly of transcript sequences produced by short-read sequencing to construct 59,860 full-length protein-coding sequences in adzuki bean. These genes were subjected to a BLASTP search to identify putative homologues of the 84 Arabidopsis genes involved in the circadian clock and photoperiodic flowering pathway. A large proportion of these Arabidopsis genes were found to be conserved in adzuki bean. However, there were no homologues of six genes including FLOWER LOCUS D (FD) and LEAFY (LFY). Furthermore, the phylogenetic relationships of 25 highly homologous matches to CONSTANS (CO) or CONSTANS-LIKE (COL) of Arabidopsis indicated the lack of a CO orthologue in adzuki bean. FLOWER LOCUS T (FT) and its homologues were found to have two homologous counterparts in adzuki bean. This study provides primary genetic resources that may be useful for producing adzuki bean with improved flowering and fruiting performance in response to environmental changes.

Chickpea is a cool season, photothermal-sensitive crop, that is adversely affected by high temperatures (>35°C) and whose flowering is promoted by long-day conditions (>12 h). This prevents horizontal crop spread under a variety of agro-climatic conditions and the development of insensitive genotypes that perform well in all seasons. Therefore, a study was conducted to identify genotypes that are mature early, insensitive to photoperiod, high temperature and tolerant to drought stress. A set of 74 genotypes was evaluated under rainfed conditions in Kharif 2021 (off-season) to select eight promising early-maturing genotypes with high-yielding capacity. Then further investigations were conducted in five different seasons Late Kharif 2021, rabi 2021, summer 2022, early Kharif 2022 and Kharif 2022 to identify the genotypes with photothermo-insensitivity among the selected eight genotypes. With the exception of rabi 2021, each of these seasons were distinct from the chickpea's typical growing season. Among these eight, the stable genotypes which are performed better in all the seasons, especially in summer were considered, such as IPC 06-11, MNK-1, JG-14 and ICE 15654-A as a photothermo-insensitive, were able to flower and set pods with higher seed yield and, resulting in early maturity in a temperature range of 41.4/9.3°C with photoperiods of 13.1/10.9 h to reach in all seasons throughout the year. The heritability was more than 60%. Hence, these genotypes can be used as donor aids in the development of early maturing, drought stress tolerant and photothermo-insensitive chickpea.

Biotechnological techniques comprise useful tools for the conservation of endangered plant genetic resources. In the present work, polymorphism and usefulness of amplified fragment length polymorphism (AFLP) markers in assessing the genetic diversity in populations of Billbergia zebrina were investigated in nodular cultures and adult plants of the species. AFLP markers revealed moderate-to-high genetic diversity based on the estimations of Nei's gene diversity (mean He = 0.28), Shannon index of diversity (mean HS = 0.48) and the number of polymorphic fragments (mean of 56.17 polymorphic fragments over six primer pairs). In comparison to published studies of population genetics performed in other bromeliad species, the present study suggests that natural populations of B. zebrina likely maintain high levels of genetic diversity, an important feature towards conservation of plant genetic resources. The results obtained reveal that AFLP markers comprise a powerful tool in order to assess the levels of genetic diversity in natural populations of this endangered species. Integrating AFLP markers with in vitro propagation techniques is understood as an adequate strategy for conservation programmes of this species.

Lutein has significant nutritional benefits for human health. Therefore, enhancing soybean lutein concentrations is an important breeding objective. However, selection for soybeans with high and environmentally stable lutein concentrations has been limited. The objectives of this study were to select soybeans with high seed lutein concentrations and to determine the stability of lutein concentrations across environments. A total of 314 genotypes were screened and 18 genotypes with high lutein concentrations and five genotypes with low lutein concentrations were selected for further examination. These 23 genotypes and two check varieties were evaluated under six environments (two planting dates for 2 years at one location and two planting dates for 1 year at another location). Lutein concentrations were influenced by genotype, environment and genotype × environment interactions. Genotypes with late maturity and low lutein concentrations were more stable than those with early maturity and high concentrations. Early (May) planting resulted in greater lutein concentrations than late (June) planting. Among the genotypes evaluated, PI603423B (7.7 μg/g) and PI89772 (5.8 μg/g) had the greatest mean lutein concentrations and exhibited medium and high stability across the six environments, respectively. Thus, these genotypes may be useful for breeding soybeans with high and stable seed lutein concentrations.