Safflower, a semiarid crop, contains a healthy oil with high unsaturated fatty acids. Genetically diverse accessions are important for genetic maintenance of safflower and breeding proposes. The objectives of present investigation were to evaluate the morphological variation of 100 safflower accessions across two years (2022 and 2023), to explore similar genotypic groups and to identify the higher contribution of traits with to the observed variability. The highest coefficient of variation (CV) was observed for seeds per secondary capitulum, number of capitula per plant and weight of lateral capitulum in the first year and the highest CV values were observed for number of capitula per plant and capitula per lateral branch in the second year. The factor analysis identified five factors in the first year and six factors in the second as yield components, height, seed yield, capitulum diameter and phonology while number of branches was identified as the extra factor in the second year. Results showed that the variation of morphologic traits was made up of from the most measured traits of safflower. We defined seven distinct clusters, which made it possible to differentiate safflower accessions based on measured traits across two years. Of 45 accessions were grouped in similar clusters across two years, without any or similar genotype by environment interaction. Some high yielding accessions like C-47 and Lesaf-175 can be entered directly in multi-environmental trials for cultivar release proposes. The recognized variation improves as a good resource, indicating an important issue for future projects for safflower germplasm maintenance and breeding.

The root-knot nematodes (RKN) (Meloidogyne graminicola) are a devastating threat to rice worldwide. The cultivated germplasm is either susceptible or moderately resistant to rice RKN. Therefore, there is a need to identify resistance sources against M. graminicola as an eco-friendly management strategy. The present study evaluated the host response of Oryza sativa genotypes comprising basmati, non-basmati improved varieties, their advanced breeding lines (83) and Oryza glaberrima accessions (42) against M. graminicola in the nematode-infested plot for two consecutive years. All O. sativa genotypes exhibited susceptible responses, while O. glaberrima accessions showed variable levels of resistance. Three of the O. glaberrima accessions (IRGC102196, IRGC102538 and IRGC102557) were highly resistant. M. graminicola significantly affected plant growth parameters in susceptible genotypes compared to resistant O. glaberrima accessions. The results were supported by histopathological studies that showed apparent giant cell formation in PR121 while penetration and development of M. graminicola juveniles were low in the O. glaberrima acc. IRGC102196. In silico analysis indicated that none of the reported nematode resistance genes from different crops had homology with the rice genome. The two anti-nematode genes (Oryzacystatin-I and Oryzacystatin-II) from O. sativa japonica revealed homology with O. sativa cv. PR121 and O. glaberrima acc. IRGC102206. Comparative analysis of these genes between PR121 and O. glaberrima acc. IRGC102206 resulted in the identification of SNPs/InDels that could be associated with nematode resistance. The identified SNPs/InDels could be validated, and further molecular studies are needed to provide insights into the resistance mechanism against rice RKN.

Twenty-nine exotic common bean germplasms and three elite cultivars were examined for phenotypic diversity in two bean-producing environments (Kanpur and Shimla) across three winter seasons and one rainy season. The estimate of genetic variability parameters revealed that the exotic bean germplasm has enough diversity for all the evaluated features. The highest genotypic and phenotypic coefficients of variation were found in seed yield, followed by 100-seed weight, pods per plant and pod length. Furthermore, seed yield was the most heritable and genetically advanced quantitative feature, followed by 100-seed weight, pod length and pods per plant. According to a trait association study, the days to maturity of phenological traits have a strong positive correlation with the days to initial flowering and the days to 50% flowering. Pods per plant and seeds per pod most strongly influence increased grain yield. The first two principal components accounted for 63.3% of the variation and demonstrated significant diversity among exotic bean lines for the traits studied, according to the principal component analysis. According to the hierarchical clustering analysis, 29 accessions and three cultivars were divided into three groups. Cluster I contains early flowering and maturing accessions, while cluster III contains high pods per plant and an increased grain yield of germplasms. The fundamental source of phenological fluctuations in both environmental circumstances is temperature. This study found four genetically divergent and stable performance accessions, including EC932021, EC932189 (earliness), and EC931452, EC931971 (high grain yield), which may aid in the establishment of a bean breeding programme.

Horseradish is a crop grown for its edible underground parts. The development of new cultivars is hindered by the species' predominant vegetative reproduction, making it essential to evaluate locally cultivated accessions to identify new types suitable for cultivation. To this end, 11 horseradish accessions from family vegetable gardens in Trentino-Alto Adige, Italy were examined using 26 qualitative and six quantitative morphological descriptors and characterized by the five major glucosinolates (GSLs) present in the rhizome compared to a reference cultivar. A wide range of variability was observed for the considered qualitative morphological traits. The rhizome's top and basal diameters were 9.9 and 6.2 cm, respectively, with an average fresh weight of 521 g. Total GSL content ranged between 79.5 and 133.5 μmol/g dry weight (DW), with sinigrin (SIN) being the primary component at an average content of 110.0 μmol/g DW. Differences among the investigated accessions were noted for quantitative traits describing their productive features and for GSL content. A positive correlation was discovered between the biometric traits of the plant's underground parts and the SIN and total GSL content, suggesting a link between the quality and yield of the edible product. According to the multivariate analysis, accessions were grouped into three main clusters: the largest of the reference cultivar and the majority of accessions with similar productive and qualitative traits; another featuring two with good qualitative and productive characteristics. The investigated accessions proved to be a valuable germplasm source for cultivating the species.

In chilli, farmer preferences for fruiting habit traits, namely fruit orientation (pendant erect) and fruits node−1 (solitary cluster), vary from region to region. For increased acceptability by farmers/consumers, cultivars should be bred with preferred fruiting habit traits in high green fruit yielding background. An investigation was carried out to study the influence of fruiting habit traits on green fruit yield and its component traits during the 2016 and 2017 rainy seasons. The F2, backcross populations and near-isogenic lines (NILs) derived from crosses involving parents differing for single or both the fruiting habit traits were grouped into fruiting habit classes (single and cluster fruiting; and clustered erect, clustered pendant, single erect and single pendant). Significance of differences in fruit yield and its component traits between/among different fruiting habit trait classes were examined using ‘t’/‘F’ tests. The significance of ‘t’/‘F’ tests was regarded as pieces of evidence for considerable effects of fruiting habit traits on fruit yield and its component traits. While results-based on F2 and backcross generations indicated a lack of effects, those based on NILs indicated significant effects of fruiting habit traits on fruit yield and its component traits. The plants bearing pendant fruits (irrespective of whether they are clustered or single) produced a large number of heavier and longer fruits than those bearing erect fruits. The results are discussed about the strategies to develop high yielding cultivars with farmer preferred fruiting habit traits.

Maize and Imperata cylindrica have been utilized globally as a pollen source for induction of haploids in wheat through chromosome elimination technique. Pollen parents with a higher haploid induction rate are desired for recovering the high frequency of haploids in wheat and related species. The present investigation was carried out with the aim to assess haploid induction efficiency of diverse germplasm of maize and I. cylindrica in different generations of intra and intergeneric crosses of hexaploid and tetraploid wheat and triticale-wheat derivatives. Crosses of twenty-six lines (female) with each of two I. cylindrica and twenty-one maize genotypes (testers) were evaluated for four haploid induction parameters viz., pseudoseed formation frequency (PFF), embryo formation frequency (EFF), haploid regeneration frequency (HRF) and haploid formation frequency (HFF). I. cylindrica outperformed maize in haploid induction rate with a frequency of embryos formed with I. cylindrica (18.39%) were significantly higher as compared to maize (4.08%). In the case of I. cylindrica genotype Ic-ye identified best with mean EFF of 30.55, 14.48 and 25.43% for hexaploids, tetraploids and triticale × wheat derivatives, respectively whereas in the case of maize genotype HPMC-60 performed best with EFF of 12.61% for hexaploids, HPMC-58 (12.58%) for tetraploids and HPMC-16 for triticale × wheat derivatives with EFF of 8.91%. I. cylindrica genotype Ic-ye and maize genotypes HPMC-14, HPMC-53, HPMC-60, HPMC-64 with significantly positive GCA for haploid induction parameters may be utilized as efficient pollen parents for recovering higher frequency of haploids in wheat.

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.

Plant height in chickpea is a multivariate, dynamic trait, and shows differences in growth rate at different stages of plant development in different genotypes. In the majority of plant-breeding experiments, the phenotypic data on a quantitative trait measured at a fixed time point (generally at maturity) are used for quantitative trait loci (QTL) mapping. However, this method can result in missing important/major QTLs which are expressed at different time points and are not expressed at maturity. In the current study, using a set of 49 desi chickpea genotypes sown at three different durations for two successive years, we observed that heritability for plant height was highest at the 2 month stage in the normal sown trial, and at the 1 month stage in late-sown trials. However, heritability drastically declines at maturity, particularly due to heat stress with an increase in temperatures during the growing period. In the association analysis, it was also observed that almost all the marker–trait associations (MTAs) identified using endpoint phenotypes were identified using data obtained at different intervals. In addition, some novel and stage-specific MTAs were identified using phenotypic data recorded at monthly intervals. The results highlight the importance of multistage phenotyping for dynamic traits like plant height in germplasm characterization programmes.

Existence of genetic divergence, appropriate characterization of breeding lines for economically important traits and determining parents with favourable alleles is the crux of crop genetic improvement programmes. This study is the first report of unravelling genetics and potential of petaloid-type cytoplasmic male sterile (pt-CMS) lines in carrot. Ten pt-CMS lines were crossed with 10 inbreds in line × tester mating fashion to generate 100 testcross progenies. Nutritional profiling of the 100 testcrosses progenies along with 20 parental types was carried out for two consecutive years for eight important traits to identify superior combiners. The pooled analysis revealed that the carotenoid content in root is under the genetic control of major genes (oligogenic). The pooled analysis revealed less than unity value of σ2A/D and σgca2/σsca2 for majority of the traits depicting preponderance of non-additive gene effects. The pt-CMS lines KT-28A, Kt-62A, KT-80A and KT-95A were identified as good combiners for carotenoids. The cross combination, KT-98A × KS-50 identified as the best heterotic combiner for CUPRAC and FRAP content over the years. Similarly, the combinations, KT-62A × KS-21, KT-80A × New Kuroda and KT-62A × KS-59 were found promising across the years for developing nutritionally rich F1 hybrids. The interaction analysis among the different antioxidant traits and plant pigments unveiled the scope of simultaneous improvement.

A better understanding of diversity in landraces is essential for planning crosses for the development of trait specific varieties with better adaptability and stability. In the present study, 120 wheat genotypes comprised of landraces, genetic stocks, released varieties and improved genotypes were evaluated in randomized block design for 14 agro-morphological traits. The clustering method and principal component analysis (PCA) programme of Statistical Package for Agricultural Research (SPAR1) was used for grouping the genotypes. These 120 genotypes were grouped into nine clusters based on agro-morphological traits. These nine clusters differed significantly on the basis of mean values for 14 agro-morphological traits. PCA showed that the two principal components (PC1 to PC2) exhibited about 49% of the total variability. Scatter plot was constructed by plotting scores of PC1 and PC2. Based on mean values obtained over two years, the diverse superior genotypes were identified for utilization in hybridization programme. From the present study, we conclude that cluster analysis grouped the landraces with greater agro-morphological similarity into one group rather than geographical isolation indicating that geographical origin may not be the only factor causing diversity. Further, released varieties exhibited superiority for grain yield, while many landraces had higher values for number of tillers in a meter, biomass and thousand-grain weight (TGW). Thus, for the improvement in TGW in released varieties, the hybridization between superior landraces for TGW from cluster ‘E’ and released wheat varieties from cluster ‘C’ could give desirable segregates.

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.

Sheath rot is one of the most destructive emerging diseases of rice in Asia and a significant loss (20–85%) to rice production is caused by this disease under temperate agro-climatic conditions of Kashmir. Disease is more prevalent in higher belts of valley where Japonica rice cultivation is more common. Also, late-maturing varieties are more likely to be attacked by sheath rot disease of rice. Information regarding the occurrence and distribution of any pathogen and its variability in the field is very much essential to devise a suitable disease management programme against the particular pathogen. The isolates of Sarocladium oryzae tested in the present study exhibited considerable variation in cultural characteristics, morphology and pathogenicity. The resistant sources for sheath rot disease of rice were identified among the temperate germplasm of rice under a relatively high inoculum concentration and disease pressure of all the variable isolates of S. oryzae. Among 219 rice genotypes screened for resistance against S. oryzae under field conditions, 42 genotypes were further evaluated under controlled epiphytotic conditions against all the 18 isolates of S. oryzae. Four genotypes (SKUA-354, ORN-V4, GS-183, GS357) were finally selected with high resistance against sheath rot disease of rice which can be utilized as potential donors for the development of disease-resistant varieties of rice against sheath rot.

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.

Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. The findings of this study reveal significant morphological variation among African tomato contributed by plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.

Core subset selection from collections hosted by seed banks, grow in importance as the number of accessions and genetic marker information rapidly increases. A data set of 20,526 single-nucleotide polymorphism (SNP) markers characterizing 7986 Mexican creole wheat landraces, was used to test 11 methods for core subset selection, through optimization criteria containing average genetic distance and genetic diversity. Allele richness was used as an additional criterion to qualify the generated core subsets. Three replications with random samples of 1500 SNP loci, each comprising a maximum of 3000 alleles, were used to perform the method evaluations through four different objective functions. The LR greedy search (LR) and LR with random first pair (LRSemi) were consistently best across all assays for maximizing the objective functions, and they performed well even for criteria not included in those functions. The Tukey's HSD (honest significant difference) multiple comparisons grouped those methods together with the sequential forward selection (SFS) and SFS with random first pair (SFSSemi) strategies as the top set of approaches. All of them are simple heuristic maximization algorithms, and outperformed two more sophisticated optimization approaches: parallel mixed replica exchange and replica exchange Monte Carlo. For their efficiency to optimize the objective functions and computing speed, the LRSemi and SFSSemi methods demonstrated to be good alternatives for core subset selection from large collections of highly homozygous accessions characterized by many biallelic markers.

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.

Bambara groundnut (Vigna subterranea (L.) Verdc) has been neglected in terms of variety selection and development which has resulted in farmers growing a mixture of landraces that are not genetically characterized and are low yielding. With the need to set up a breeding programme in Malawi, it was necessary to thoroughly understand the genetic diversity (GD) present in the available germplasm. The objectives of the study were to assess Bambara genotypes GD using agro-morphological traits and SNP markers, and to identify and select high yielding Bambara genotypes. Field trials were conducted for two seasons at Bunda College. Later, genotypes were genotyped using DartSeqLD SNP markers. All data were analysed using R Package. Significant genetic variations (P < 0.001) were observed for most traits including grain yield, which suggests that genetic variability exists in Bambara groundnuts which can be exploited in breeding programmes aimed at developing high performing varieties. Based on grain yield, the study identified 18 top performing genotypes across the evaluation seasons which will be tested under farmers’ fields’ conditions. DArTseqLD grouped the genotypes into three clusters. It was noted that majority of the genotypes from the same origin clustered together. High genetic distances were observed between genotypes from Southern African and West African regions and this has important implications in parental selection for the genetic improvement of Bambara. Our results provide valuable insights about the extent of genetic variability and how parental lines can be selected for improved genetic gain in Bambara groundnuts.

Since the 1600s, a pasta wheat locally known as Sargolla, Saragollio or Saragollo has been cultivated in central and southern regions of Italy, including Abruzzo and Puglia. To identify if distinctive Saragolla landraces are present in Abruzzo and with a view to registering them as Conservation Varieties in the Abruzzo Regional Register of Genetic Resources, a quantitative botanical characterization of 11 farm-saved seed samples from Abruzzo and a previously defined Saragolla landrace from Puglia was performed. All twelve samples were grown for two years at the CREA-CI field station in Foggia, Puglia (Italy), and were morphologically characterized according to the criteria used by the botanist Johan Percival in 1921. In the 12 samples, we identified 9 taxonomically different botanical types, the most frequent of which were the italicum (32%), found in every population from Abruzzo. The leucurum and the affine were the main components of the previously defined Saragolla from Puglia. Results of the multivariate analysis indicated that the samples collected from farms in Abruzzo are more similar to each other than to the landrace of Saragolla from Puglia and support the registration of a specific Saragolla landrace for the Abruzzo region. The diachronic comparison of the botanical diversity of the currently cultivated Saragolla, with that observed in Sicily and Algeria at the beginning of 1900, suggests that a high degree of genetic diversity still exists in the 11 Saragolla populations from the Abruzzo Region.

Common lilac (Syringa vulgaris L.) is a popular landscaping plant. Our aim was to obtain a large set of single nucleotide polymorphism (SNP) markers, to reveal the precise identities of the investigated S. vulgaris accessions, and to discover genetic relationships among them. The studied plant material included local Finnish, previously unidentified accessions, known reference cultivars, and so-called historical accessions i.e., old shrubs growing in historic cultural landscapes. We intended to verify cultivar names for some valuable local common lilac accessions and to provide insights into the history of common lilac cultivation in Finland. In the analyses, we used a set of 15,007 SNP markers. First, polymorphic information contents were calculated (mean 0.190, range 0.012–0.500 per marker). Then, to investigate genetic relationships among genotypes, a phylogenetic tree was constructed, and a principal coordinate analysis was conducted. A Bayesian analysis of population structure was performed to determine the number and distribution of genetic clusters among samples. Genetic marker data combined with existing historical and phenotypic knowledge revealed novel information on the unidentified cultivars and on the genetic relationships among studied accessions and solved the arrival and early history of common lilac in Finland. Overall, such comprehensive genomic characterization and deep understanding of genetic relationships of S. vulgaris can be used when utilizing present cultivars and developing new ones in future breeding programs.