Obtaining high-quality planting material for cultivation is a persisting challenge for yam (Dioscorea spp.) production in Africa. Efforts to provide a solution to this challenge have led to varying seed multiplication techniques but whose efficiency in maintaining the genetic purity of yam genotypes during the rapid multiplication process is yet unknown. Three improved varieties Swaswa, Kpamyo and Asiedu were multiplied through tissue culture, aeroponics system, field condition and vine cutting techniques. Leaf samples were collected at every stage of multiplication in the different techniques as well as the original mother plant for DNA fingerprinting. From a total of 16,922 SNP markers, an average heterozygosity of 0.091 was obtained with minor allele frequency of 0.119, and polymorphic information content of 0.166. The transition to transversion ratio was 62:38%. Hierarchical clustering of the genotypes and technologies discriminated the multiplied materials into three clusters with the first cluster consisting of only the variety Asiedu multiplied through aeroponics, vine and tubers collected from vine cutting and grown from the field. The second cluster consisted predominantly of the variety Kpamyo, with a little admixture from Asiedu. The third cluster consisted of only Swaswa. The different seed multiplication methods showed great potentials in conserving the genetic purity of genotypes used. Therefore, the use of these seed multiplication techniques could offer a lasting solution to the low multiplication ratio of yam without compromising the genetic integrity and offers a great opportunity for establishing a formal yam seed system.

Nitrogen fertilizer and water are two major nutrients required for the optimal production of rice worldwide. The utilization of different irrigation techniques to save water and fertigation to maximize rice production has been the main focus. A field experiment was conducted to explore the responses of 16 rice varieties to different irrigation and nitrogen fertilizer regimes. Two nitrogen treatments, 270 kg ha−1 and 225 kg ha−1 (urea N ≥ 46.4%), and two irrigation regimes, 8.7 t ha−1 and 5.22 t ha−1, were applied three times. Plant height and the soil and plant analyser development (SPAD) values were measured throughout the growth period. The total yield and quality characteristics of the rice varieties were also determined. Based on the yield, the 16 rice varieties were divided into three groups: high yield (I), middle yield (II) and low yield (III) using cluster analysis. A positive correlation was found between the growth period and yield of these 16 rice varieties. In the water-deficient regime, the growth period of the 16 varieties was reduced by 1.68–2.93%. Furthermore, nitrogen- and water-deficient regimes had significant effects on the polishing rate, protein content and taste values of all varieties. At maturity stage under these regimes, plant height and chlorophyll SPAD values were decreased by 1.25–6.05% and 1.60–31.48%, respectively. Deficient nitrogen fertilization, along with appropriate irrigation, is an effective method for the efficient utilization of irrigation and fertilizer resources in rice-growing areas.

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.

Germplasm innovation can provide materials for breeding sugarcane cultivars. Saccharum officinarum is the main source of high-sugar and high-yield genes in sugarcane breeding. ‘Nobilization’ is the theoretical basis for exploiting S. officinarum, and S. officinarum authenticity directly affects sugarcane nobility breeding efficiency. Herein, the authenticity of 22 SLC-series S. officinarum clones imported from Sri Lanka and preserved in the China National Germplasm Repository of Sugarcane (NGRS) was explored by four-primer amplification-arrested mutation PCR (ARMS PCR) and somatic chromosome number counting. The amplified bands from SLC 08 120 and SLC 08 131 were the same with those from S. officinarum clone Badila, i.e. a common band of 428 bp and a S. officinarum-specific band of 278 bp, hence they were tentatively assigned as S. officinarum clones. The other 20 SLC clones had both 278 bp (S. officinarum-specific) and 203 bp (S. spontaneum-specific) bands, which are hybrid characteristics. In addition, the chromosome numbers of SLC 08 120 and SLC 08 131 are both 80, belong to typical S. officinarum. While the chromosome numbers of the other 20 materials are ranging from 101 to 129, consistent with hybrids of S. officinarum and S. spontaneum. This molecular cytological characterization indicates that among the 22 introduced SLC-series clones, only two, SLC 08 120 and SLC 08 131, were S. officinarum. Future agronomic trait and resistance analyses could facilitate their use as crossing parents in sugarcane breeding.

Screening of germplasm for specific traits is a continuous pre-breeding process in deriving the drought-tolerant donors required for crop improvement. The study evaluated 17 medium-late duration finger millet genotypes under drought stress (DS) for 28 days during the reproductive stage to identify the traits and genotypes for drought tolerance using different statistical analysis. The photosynthetic rate (by 26.3%), stomatal conductance (by 26.4%), transpiration rate (by 24.8%) and grain yield (by 13.2%) were decreased and found sensitive to DS, but the leaf temperature was increased (4.7%). From the path analysis and multiple linear regression analysis, the mean ear weight and productive tillers were found to contribute to the grain yield significantly under well-watered conditions. While under DS conditions, the mean ear weight, productive tillers and threshing percentage equally contributed to grain yield. Based on the ranking of traits significantly contributing to grain yield, the genotype GE-4683 with a higher mean ear weight (10.65 g) was found superior to the popular variety, GPU-28. The Multiple linear regression equation predicts the possibility to increase the yield of GPU-28 under DS from the existing 360.0 to 459.5 g per square metre (by 29.1%) by the incorporation of three productive tillers instead of the existing two tillers per plant in the MLR equation. An additional 1.0 g of mean ear weight will be able to predict an increased grain yield from 360.0 to 392.0 gm−2, equivalent to 3.60 to 3.92 t/ha (by 9.4%).

Low molecular weight glutenin subunits (LWM-GSs) play a crucial role in determining wheat flour processing quality. In this work, 35 novel LMW-GS genes (32 active and three pseudogenes) from three Aegilops umbellulata (2n = 2x = 14, UU) accessions were amplified by allelic-specific PCR. We found that all LMW-GS genes had the same primary structure shared by other known LMW-GSs. Thirty-two active genes encode 31 typical LMW-m-type subunits. The MZ424050 possessed nine cysteine residues with an extra cysteine residue located in the last amino acid residue of the conserved C-terminal III, which could benefit the formation of larger glutenin polymers, and therefore may have positive effects on dough properties. We have found extensive variations which were mainly resulted from single-nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) among the LMW-GS genes in Ae. umbellulata. Our results demonstrated that Ae. umbellulata is an important source of LMW-GS variants and the potential value of the novel LMW-GS alleles for wheat quality improvement.

False smut of rice is an emerging disease and caused severe damage to hybrids and inbred rice cultivars grown in Asian countries. The objective of the study was to quantify of false smut resistance and identification of donors in some of the advanced breeding lines and rice varieties developed at Punjab Agricultural University, Ludhiana, India. A total of 31 genotypes were evaluated for three years in two planting date per year under field conditions. The lines were categorized into short, medium and long durations based on days to flowering. False smut was quantified using different disease variables such as per cent infected panicle, number of false smut ball per plant and disease score. Disease variables were significantly and positively correlated to each other. The infected panicle ranged 0.0–75.4% was observed among the genotypes. Three advanced lines namely RGS-2 (short), RGM-3 (medium) and RGL-3 (long) showed the lowest ranged 0.0–4.9% of infected panicle as compared to susceptible checks (47.7–75.4%). The genotypes were divided into five groups according to a component of resistance. The third group had the lowest average values (3.3%) of infected panicle as compared to the fifth group with the highest values (36.2%) of the infected panicle. The overall trend of disease variables was higher in short duration genotypes as compared to medium and long durations. Weather factors such as rain fall, rainy days and high relative humidity during the flowering period were favourable for disease development. The genotypes with lower disease variables could be utilized in diseases resistance breeding programme.

Sorghum is an important staple crop in Sub-Saharan Africa. In the Sudano-Sahelian zone of West Africa, sorghum is mainly intercropped with cowpea, but these intercropping systems are facing low-productivity problems. The overall aim of this research was to identify sorghum varieties with different agro-morphological and physiological traits that could improve the performance of the intercropping systems. We followed a two-step methodology comprising (i) identification of varieties and plant traits of interest in intercropping systems, using participatory methods, and (ii) agro-morpho-physiological characterization of 50 sorghum varieties, to examine the range of variation in traits of interest. The results show that landraces are the varieties most widely used by farmers, and that 82.5% of farmers consider the variety type they choose for intercropping to be important. Farmers mentioned plant height, number of leaves and stem diameter as important traits to consider. Analysis of variance showed significant differences between varieties for half of the 24 agro-morpho-physiological traits studied. Hierarchical clustering identified three main groups of varieties, distinguished by morphological traits such as stem diameter, total number and size of leaves (group 1), root traits (depth, growth angle, dry matter) and relative chlorophyll content (groups 2 and 3). Based on this classification, we recommend several varieties from each of the three groups, exhibiting contrasting traits, for an assessment of their performances in intercropping systems.

Availability of resistance sources among cultivated varieties helps in easy utilization as donor owing to no deleterious linkage drag. In the present investigation, 121 rice varieties were screened for their resistance against a virulent isolate of Fusarium fujikuroi (Ff-10) and genotyped using reported microsatellite markers. Among 121 varieties, only eight varieties, namely Luna Sankhi, Improved Tapaswini, Sarasa, Sadabahar, CR-311, Kshira, Wifa-10 and Binadhan-8, were found to be highly resistant (HR), seven varieties were resistant (R), 31 were moderately resistant (MR), 10 were moderately susceptible (MS), 11 were susceptible (S) and the rest 54 were highly susceptible (HS). The allele diversity of molecular markers classified the population into three clusters. The highly resistant varieties were grouped in major clusters II and III, whereas the remaining genotypes were distributed in all three clusters. Analysis of molecular variance (AMOVA) resulted in 95% of the maximum diversity within the test population and 5% diversity between populations. Population structure analysis grouped the genotypes into two sub-populations based on relatedness, where most of the resistant genotypes were grouped into one sub-population and other genotypes were distributed among sub-populations. Re-examination of reported markers' trait associations with bakanae resistance in the experimental population identified marker RM-3698 as associated with resistance accounting 8.4% explained phenotypic variation. This study shows that simple sequence repeat markers can be used to assess allelic diversity and population structure of bakanae resistance in rice varieties. The highly resistant genotypes, along with resistance markers, could be used as donors in marker-assisted bakanae improvement breeding programmes.

Ever increasing global population necessitates the need to increase availability of affordable foods with high nutritional quality. Chickpea being the second most important grain legume cultivated worldwide has the great potential to alleviate problems of protein malnutrition and hidden hunger. The objective of the present investigation was to characterize a diverse set of 402 germplasm comprising of more than 100 commercial cultivars widely cultivated and utilized by breeders for grain protein in two contrasting environments to explore the magnitude of natural genotypic diversity present in the cultivated chickpea and the scope for enhancing it and its quality through breeding. The cultivars containing more than 25 to 30.44% grain protein have been found in the study and large scale production of such protein rich cultivars is expected to increase availability as well as consumption of high quality chickpea necessary to overcome all forms of malnutrition. Trait specific germplasm containing grain protein up to 33.56% are also identified for their further utilization as potential donors in the chickpea improvement programme. The amino acid profiling of selected high and low protein containing genotypes showed considerably greater average amino acid score for all the essential amino acids than the WHO recommended requirement values and is comparable to those of the ‘complete protein’ sources of food suggesting that chickpea deserves to be considered as a ‘complete protein’ source.

Camelina (Camelina sativa (L.) Crantz), an oilseed crop, belongs to the Brassicaceae family. Two unique features of camelina in comparison with the main oil crops are an adaptation to different environments and also its unique oil composition. The development of doubled haploid plants is one of the essential methods for crop improvement. The study of genetic diversity is an important step in planning crop breeding programmes. This research was conducted to evaluate the genetic variation of 81 camelina doubled haploid lines obtained from 15 crosses by inter simple sequence repeat (ISSR) markers. The total number of amplified bands was 243, of which 239 bands (98.3%) showed polymorphism. The percentage of polymorphic bands varied between 93.75 and 100. The size of the bands ranged from 50 to 1700 base pairs. The informative ISSRs were identified by estimating marker features: polymorphism information content, effective multiplex ratio, marker index and resolving power. Three markers had higher resolving power values (9.88, 8.5 and 7.46) and were the most informative markers to identify the lines. Cluster analysis based on the complete algorithm divided the lines into five groups, indicating relatively clear configuration from the geographic distribution patterns of the parents of the doubled haploid lines. Principal coordinate analysis classified the 81 camelina doubled haploid lines into six groups. The ISSR markers detected high polymorphism to reveal the genetic variation of camelina lines. The findings of this research, along with the characterization of biochemical traits of the lines, can improve breeding programmes achieve high-yielding camelina varieties with higher and better oil content.

Maize is among major field crops which provides food, fodder and various byproducts to the industry. Development of better performing varieties is very important to enhance and strengthen the maize production system. In this study ethyl methanesulfonate (EMS) is used to induce genetic variation in maize. Mutant population was derived from two genotypes 100,003 and 100,004. EMS was applied under three different concentrations of 25, 50 and 75 mM. 25 mM was found as an ideal concentration resulting in maximum survival rate. Total 10 SSRs were used in this study, which amplified 28 alleles with average of 2.7 alleles. Analysis of molecular variance showed significant differences present among individuals. Average heterozygosity for mutants derived from 100,003 and 100,004 was 0.58 and 0.53, respectively. UPGMA analysis characterized the mutants into two main and many sub clusters. According to the principal component analysis, PC 1 and 2 contributed to 64.2% variability with eigenvalue greater than 1. Statistics showed maximum coefficients of variance in traits of leaf area, cobb height and plant height. Promising mutants were also identified and recommended for future breeding programme. In conclusion, EMS mutagenesis is an effective technique to develop novel mutants that can be exploited in future breeding programmes.

The characterisation of traditional barley varieties from North Africa is promising with respect to detect traits linked with resilience to drought. Nine Algerian barley varieties comprising the economically relevant local landraces Saïda183 and Tichedrett were genotyped by random amplifying polymorphic DNA (RAPD) and by Simple Sequence Repeat (SSR) markers to get insight into their phylogenetic relationship and to compare the efficiency of the two approaches. The SSR markers were chosen such that all chromosomes of barley were represented by at least one marker. In addition, a principal component analysis (PCA) of morpho-agronomical traits was conducted. We found that the phylogeny based on the RAPD markers reflected the geographical distribution of the tested varieties, while the phylogeny based on the SSR markers reflected the pedigree. Among the RAPD markers, the maximal polymorphism information content was obtained for BY14 with a value of 0.82, for the SSR markers, Bmg13 was most informative with a value of 0.60. The similarity matrix used to the construct the phylogenetic tree, inferred a close relationship (Jaccard Index 0.8 based on RAPD markers) between the accessions Fouara and Oued-Athmania occurring in close vicinity. The SSR markers group the autochthonous varieties Saïda183 and Tichedrett together with a Jaccard Index of 0.8. The close phylogenetic relationship between Saïda183 and Tichedrett is also supported by the PCA of morphological and agronomic traits. Our data underpin the diversity of Algerian barley varieties and lend support to the autochthonous origin of these two Algerian landraces.

Angular leaf spot (ALS) caused by Pseudocercospora griseola is a major disease of french bean (Phaseolus vulgaris L.) worldwide. A good diversity of French bean is present in the Garhwal Himalayas of Uttarakhand, India, which is unexplored. The purpose of this study was to identify ALS-resistant accessions among local landraces of French bean in this region. One hundred seventy-six local accessions were collected from different villages of Garhwal, Uttarakhand. All the accessions were screened by four SCAR primers SN02 (Phg-2), SAA19, SM02, SBA16 (Phg-3), one STS primer TGA1.1 (Phg-1) and one SSR primer Pv-at006 (Phg-5). All the accessions were also screened for ALS resistance under field condition in the years 2019 and 2020. The disease-resistant score was recorded on 1–9 scale. After field screening, 48 accessions (19 resistant, 24 moderately resistant and five susceptible) were selected for in-vitro screening under screen house condition. These 46 accessions were artificially inoculated by two different isolates of P. griseola P5 and P9, which are the most virulent pathotype characterized by microbiology lab, College of Forestry, Tehri, Uttarakhand. After in-vitro screening, seven accessions (GFB-25, GFB-26, GFB-30, GFB-32, GFB-93, GFB-97 and GFB-136) were found resistant to both the isolates P5 and P9. The P. griseola-resistant accessions may further be used in future breeding programmes to develop new and more resistant varieties of French bean against ALS.

Common bean (Phaseolus vulgaris L.) is a highly economically important crop worldwide and a particularly important source of protein and minerals for people in less developed countries. Improving yield is a vital objective to meet the increasing demand for food due to the expanding human population. The present study was undertaken to study the genetic architecture of agronomic traits of common bean in India, particularly in the north-western Himalayan region. Marker-trait association (MTA) analysis was performed in a population of 100 common bean accessions using polymorphic microsatellite markers. Population structure analysis based on SSR markers divided the accessions into three main subpopulations. Ten significant MTAs were found using general linear model (GLM) and mixed linear model (MLM) approaches. We found two markers i.e. BM142 and J04555 associated with 100 seed weight and pods per plant common in both the GLM and MLM approach markers. All the MTAs were considered as major MTAs contributing more than 25% phenotypic variation. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield and development of high yielding common beans lines.

Salinity poses a major obstacle in increasing the yield of cotton. To explore genetic material that can yield better under salt stress conditions, eight parents including 5 females and 3 testers were crossed in line × tester mating design. After successful completion of crossing, parents and their 15 crosses were evaluated for seed cotton yield, within boll yield components, fibre quality, ionic and biochemical traits under control and NaCl salt stressed conditions (10 and 20 dSm−1). Under salt stress conditions seed cotton yield, fibre length and fibre strength decreased in all genotypes whereas, lint percentage and fibre fineness increased. Among parents RH-647 and among crosses FH-214 × FH-2015 performed better for seed cotton yield while for fibre quality traits under salt stress conditions among parents KEHKSHAN, and among crosses FH-214 × KEHKSHAN performed better. Results suggested that plant height, boll weight, lint percentage, fibre length and fibre strength are reliable traits for the selection of salt tolerant genotypes in the future cotton breeding programs.

Crop germplasm conserved in genebanks, are a fundamental resource of genetic diversity for crop improvement activities, underpinning future food security and sustainable agricultural practices. However, taxonomic errors in genebank germplasm (due to misclassification, contamination and poor data collation) restrict the effective use of this material for correct purpose. Earlier studies investigating species genetic diversity using genebank germplasm, have shown varying levels of taxonomic error within the Brassica species. In response to this reported taxonomic error of global collections, together with the availability of a multiplex PCR (MPCR) marker, targeting the specific chromosomes (A, B and C) of the six Brassica species in U's triangle, this study was undertaken to confirm the taxonomic identity of accessions within the Australian Grains Genebank's (AGG) long-term Brassica collection. A total of 5161 accessions were analysed with MPCR for taxonomic identification, of which, 4842 (93.8%) were confirmed to be consistent (correct) with their labelled taxonomy, while the remaining 319 (6.2%) were identified as taxonomically inconsistent (in-error). Through the evaluation of earlier regeneration and original seed of the error accessions with MPCR, we determined that 80.9% of the taxonomic errors were traced back to the original seed, while 19.1% of errors were the result of genebank seed regeneration handling practices. Results from this study directly enhance information of the AGG Brassica collection and shape directions for distribution, acquisition and regeneration practices within the AGG and potentially other global genebanks, which will facilitate in a more effective use of these valuable genetic resources by researchers and breeders.

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.

Rice blast disease, caused by Magnaporthe oryzae, is one of the most damaging diseases of rice worldwide. Cultivation of rice varieties carrying resistance genes is the most economic and successful strategy to control the disease. In this study, 451 rice varieties from around the world including 363 Thai landrace rice varieties, 21 Thai improved rice varieties, 43 Japanese rice varieties and 24 worldwide rice varieties were screened by PCR technique using gene-specific markers for 10 rice blast resistance genes: Pi9, Piz-t, Pi50, Pigm(t), Pid2, Pid3, Pia, Pik, Pi54 and Pita. The results showed that 382 (99.48%) Thai rice varieties have at least one resistance gene and two rice varieties, ‘Hom’ and ‘Bak muay’, contained eight out of ten screened rice blast resistance genes. 320 rice varieties (83.33%) contained three or more rice blast resistance genes. The frequency of the rice blast resistance gene ranges from 87.76–9.64 per cent, of which the Pid3 gene has the highest frequency and the Pi54 gene has the lowest frequency. Two major resistance genes, found in Japanese rice varieties, are the Pik gene (76.74%) and the Pi9 gene (72.09%). While two major resistance genes, found in the international rice varieties are the Pi9 gene (66.67%) and the Pi54 gene (62.50%). The disease resistance gene profile of each rice variety obtained from this study will benefit the rice blast resistant breeding programme in the future.

Fluted pumpkin (Telfairia occidentalis Hook F.) is an underutilized indigenous leafy vegetable with enormous prospects for food security in sub-Saharan Africa. However, relatively little is known about genetic relationships and population structure in the species. In this study, 32 landraces of fluted pumpkin collected across three southern geographical regions in Nigeria were assessed for genetic diversity and population structure using 8 start codon-targeted (SCoT) makers. The polymorphic information content of the SCoT markers ranged from 0.48 in SCoT36 to 0.94 in SCoT28, with an average of 0.77. Hierarchical cluster dendrogram based on Ward's method and principal component analysis grouped the landraces into four clusters without affiliation to provenance. Overall, the mean values of the population genetic diversity parameters – Nei's gene diversity (H) and Shannon's information index (I) showed values of 0.28 ± 0.01 and 0.43 ± 0.02, respectively, implying a narrow genetic base for the landraces. The result was further corroborated by a very close Nei's genetic distance and identity among populations of the landraces. Furthermore, the south-west population exhibited the higher genetic diversity (H = 0.31 ± 0.02 and I = 0.45 ± 0.03). Population structure analysis inferred three subpopulations for the accessions with varying degrees of allelic admixture. An analysis of molecular variance revealed that almost all the genetic variation occurred within (99%) than between (1%) populations. The findings shed light on the genetic diversity of southern Nigerian fluted pumpkin and have significant implications for the characterisation, conservation, exploitation and improvement of the species.