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.

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.

This is the first report of a pasture plant collecting mission to the highlands of Eritrea and a preliminary examination of the potential of species for both Eritrea and southern Australia. In 2004, seeds from 53 legume species were collected from 58 locations in the southern highlands between Keren, Adi Quala and Senafe. Strains of Rhizobium from 18 species were also collected. Seed collections of 11 species with Rhizobium were established in germplasm nurseries at the Medina Research Station, Western Australia between 2005 and 2010. Observations on their growth, flowering and seed production were recorded. Based on a climate match analysis and observations from germplasm nurseries, it was suggested that species with most promise for parts of southern Australia include the annual legume Biserrula pelecinus ssp. leiocarpa and the perennial shrub Colutea abyssinica. The greatest potential, however, is reserved for the highlands of Eritrea where germplasm is well adapted. Species found low in the landscape including from the genera Lotus, Trifolium and Medicago appeared well utilized. Different species found higher in the landscape including from the genera Indigofera, Tephrosia, Crotalaria, Trifolium schimperi, B. pelecinus ssp. leiocarpa and C. abyssinica were much less common, appeared under-utilized and may be under threat from genetic erosion. Animal production on the non-arable dry hillsides of the highlands would benefit from better utilization of these species through replanting some areas, careful grazing management and demonstration of the benefits of increasing the native legume component of these wild pastures.

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.

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.

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.

The plant Camellia fascicularis, belonging to family Theaceae, has high ornamental and medicinal value, and rare gene resources for genetic improvement of Camellia crops, but is currently threatened with extinction because of the unique and extremely small wild populations. Molecular markers have clarified the wild plant species’ genetic diversity structure, new gene resources and relationship with crops. This will be beneficial for conservation of these valuable crop-related wild species and crop improvement. In this study, we identified 95,979 microsatellite loci from 155,011 transcriptome unigenes, and developed 14 polymorphic expressed sequence tag-derived simple sequence repeat (EST-SSR) microsatellite markers for C. fascicularis. The number of alleles (Na) per locus was 2–8 with a mean of 4.86. The genetic diversity of 40 individuals from four natural populations of C. fascicularis was analysed using these polymorphic markers. The number of alleles (Na) for EST-SSR ranged from 2 to 5, with the expected heterozygosities (He) and observed heterozygosities (Ho) in all loci ranging from 0.183 to 0.683, and from 0.201 to 0.700, respectively, implying a rich genetic variation present in wild C. fascicularis populations. Moreover, the phylogenetic analysis among four populations, using the 14 EST-SSR markers developed in this study, grouped 40 individuals into three groups, which coincide with their geographic distribution. These results showed that 14 EST-SSR markers are available for the analysis of genetic variation in C. fascicularis populations and genetic improvement of new Camellias cultivars by interspecific hybridization, and are beneficial for conservation of the endangered species.

Although morphological plasticity has been widely known in various cactus genera, few studies have investigated the origin and molecular relationship between morphological variants from cacti. Morphological variants are relevant specimens because atypical, exotic and generally unique forms are preferred by cactus traders and collectors. The current study investigates the molecular relationship between the tortuosus and monstruosus ornamental variants of Cereus peruvianus used in landscapes. Polymorphisms in loci of simple-sequence repeats in DNA were used as molecular markers. The variants tortuosus and monstruosus, and plants with typically columnar and erect shoots cultivated in southern Brazil were retrieved from public parks and home gardens. High polymorphism, an indicative of vegetative propagation, and a moderate genetic divergence were detected at the molecular level in monstruosus and tortuosus plants. Artificial selection and vegetative propagation of the ornamental variants of Cereus may be inducing a moderate genetic divergence and formation of two heterologous groups with conservative genetic diversity. Polymorphism in Cereus variants revealed groups with contrasting genes among the variants tortuosus and monstruosus which may be useful for breeding to generate new and different new variants.

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.

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.

In Ethiopia, the low productivity of garlic is largely due to a shortage of high yielding and stable varieties. To address this issue, thirteen garlic genotypes were evaluated for yield stability and performance across six different environments in central and southeast Ethiopia. The genotypes were analysed using Additive Main effects and Multiplicative Interaction (AMMI) and genotype-by-environment interaction (G × E) methods. Results showed that the genotypes differed significantly for bulb yield performance and morphological traits, with G-020/03 and G-054/03 producing the highest bulb yield with 25.39% and 18.39% yield advantages over the check variety, Kuriftu, respectively. Furthermore, G-020/03 demonstrated better yield stability across most environments, while G-054/03 exhibited specific adaptability. GGE biplot analysis confirmed that these two genotypes were among the three winning genotypes in terms of yield performance and relative stability. Therefore, G-020/03 and G-054/03 have been selected as candidate varieties for release, potentially improving garlic productivity in Ethiopia.

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.

The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir (Abies sibirica Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (Abies alba Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of A. alba and a small sample of eight Nordmann fir (Abies nordmanniana (Steven) Spach) trees.

Cattleya walkeriana, one of the most improved Brazilian Cattleyas, is a popular tropical orchid endemic from Brazil and currently endangered. In the present study, for the first time microsatellite markers were developed for C. walkeriana and their transferability was tested for the species C. loddigesii and C. nobilior. The markers were used for genotyping 26 C. walkeriana specimens from different growers and from different levels of improvement. The transferability was successful, with five polymorphic loci transferred to C. loddigesii and six polymorphic loci to C. nobilior. Eight loci were polymorphic, revealing a maximum of two to ten alleles per locus in C. walkeriana and two to four and two to five in C. loddigesii and C. nobilior, respectively. There was no significant linkage disequilibrium in the studied loci. For C. walkeriana, the observed and expected heterozygosities ranged from 0 to 0.963 and from 0.138 to 0.841, respectively. These markers identified polymorphisms and may be used to study the genetic diversity, gene flow or hybridization of these species.

Valtrate is the major active component of iridoids in Valeriana jatamansi plants, and has been widely used for the treatment of various diseases, giving rise to rapidly increasing market demands. The gene VjG10H from V. jatamansi encoding geraniol 10-hydroxylase (G10H) was introduced into V. jatamansi hairy roots and a transgenic hairy root culture system of V. jatamansi with good valtrate production ability was successfully established for the first time. The valtrate content of VjG10H-transformed lines ranged from 8.12 to 10.77 mg/g, with an average valtrate content (9.52 mg/g) of all the four G lines being higher than the non-transgenic hairy root line. Overexpression of VjG10H significantly improved valtrate production, indicating that G10H played an important role in stimulating valtrate accumulation. MeJA treatment stimulated valtrate accumulation in all of the VjG10H overexpression recombinant lines compared to untreated cultures, indicating that methyl jasmonate treatment was another effective regulation target for metabolic engineering of valtrate biosynthesis in V. jatamansi. Thus, transgenic hairy root technology coupled with elicitor treatments may be a promising strategy to increase valtrate yield in V. jatamansi.

Soil moisture deficit is the major constraint for sesame crop production during its main rainfed and summer cultivation seasons. In summer cultivation, the crop frequently gets exposed to soil moisture deficit at various crop growth stages. Therefore, it is essential to identify the traits along with promising genotypes adapted to soil moisture deficit. A set of 35 sesame genotypes with checks was used to quantify the variation in morpho-physiological, yield, and quality traits under irrigated (WW) and deficit soil moisture stress (WS) conditions in the summer seasons of 2021 and 2022. The analysis of variance revealed the presence of high variability among the genotypes for various measured traits. The mean performance indicated that WS negatively affects the growth, development, yield and quality traits. Moreover, the correlation, path analysis and D2 analysis studies suggested that the traits, viz. leaf area (LA), total dry matter (TDM), canopy temperature (CT), number of branches per plant (NBP) and number of seeds per capsule (NSC) were significantly associated with seed yield under both the conditions. Quality traits like palmitic acid and oleic acid correlated positively with seed yield, particularly under WS. Furthermore, the genotypes with lower canopy temperatures were found to be better seed yielders under WS. In addition, mean performance and cluster analysis suggested that the genotypes: IC- 205776, JSCDT-112, JCSDT-26, IC-205610, and IC-204300, secured higher seed yield along with superior agronomical traits and net photosynthetic rate. These selected genotypes were most promising and could be used in future sesame crop improvement programmes.

Sugarcane brown rust, caused by Puccinia melanocephala, is one of the main diseases of sugarcane in China. The identification and discovery of new resistance genes have important theoretical and practical significance for preventing outbreaks of brown rust and ensuring the sustainable production of sugarcane. To screen for polymorphic simple-sequence repeat (SSR) molecular markers for localization of brown rust resistance genes, we used two populations that are suitable for genetic linkage map construction and mapping of new resistance genes to construct resistant and susceptible genetic pools. We then screened 449 pairs of primers to identify polymorphic SSR markers in the parental lines and the resistant/susceptible genetic pools. The results showed that 25 pairs of primers directed amplification of polymorphic DNA fragments between the parents of the cross combination ‘Yuetang 03-393’ × ‘ROC 24’, and 16 pairs of primers amplified polymorphic fragments between the parents of the cross combination ‘Liucheng 03-1137’ × ‘Dezhe 93-88’. Four pairs of primers (SMC236CG, SCESSR0928, SCESSR0636 and SCESSR2551) amplified polymorphic DNA fragments between the parental lines and the resistant/susceptible genetic pools in ‘Yuetang 03-393’ × ‘ROC 24’. The results of this study will establish a solid foundation for the mapping of new brown rust resistance genes, genetic linkage map construction and the development of closely-associated molecular markers in sugarcane.