These findings confirm low genetic diversity within C. sativa populations, which has significant implications for breeding strategies aimed at improving yield and resilience in industrial applications and genome-wide association studies and marker-assisted selection to enhance genetic gains.
Abstract
Background
Camelina sativa, an oilseed crop from the Brassicaceae family, has gained attention over the past two decades due to its resilience to harsh environments, short growth cycle, low input needs, and high omega-3 fatty acid content. These traits make it a promising candidate for industrial and bio-based applications, including edible and industrial oils, biofuels, and soil enhancement. This study aimed to identify and genotype SNPs on a genome-wide scale to assess genetic diversity and population structure for breeding programs and conservation efforts.
Results
Using Genotyping-by-Sequencing (GBS) technology, we investigated 86 C. sativa doubled haploid lines from 15 crosses, mapping 5,872 high-quality SNP markers across the genome. Population structure analysis revealed two main subpopulations, with evidence of genetic exchange likely influenced by geographic factors and human activity. AMOVA results indicated that 90% of variation occurred within subpopulations, with a low Fst value (0.096) suggesting high gene flow (Nm = 2.343). Hierarchical cluster analysis (HCA) based on genetic distances grouped the lines into two main clusters, each further subdivided into two distinct subgroups, highlighting the existence of a well-defined genetic structure within the population.
Conclusions
These findings confirm low genetic diversity within C. sativa populations, which has significant implications for breeding strategies aimed at improving yield and resilience in industrial applications. This research provides crucial insights for future genetic studies and breeding efforts in Camelina, particularly regarding genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gains.
This review critically evaluates the transition from conventional phenotypic selection to data-driven breeding strategies, examining genomic selection (GS), genome-wide association studies (GWAS), multi-omics integration, CRISPR/Cas9 genome editing, and high-throughput phenotyping (HTP) within the context of polyploid crop improvement.
Muhammad Abu Bakar Ghalib, Ayesha Khawar, M. Ramzan et al.· Discover Plants· 0 citations
Background Advances in next-generation sequencing have accelerated genome-wide exploration of genetic diversity in underutilized oilseed crops. Salvia hispanica L. (chia), a high-nutrient pseudocereal rich in omega-3 fatty acids, is increasingly valued for its health benefits and commercial potential, yet it remains poorly characterized at the genomic level. Understanding the scale and nature of genomic variation is essential for improving complex traits such as oil yield, stress tolerance, and seed quality. Methods Two contrasting chia genotypes, Black-chia (CACH-B) and White- chia (CACH-W), were resequenced using the Bio-Resequencing Toolkit (BRT) pipeline. High-coverage sequencing, with a mapping rate exceeding 99% and an average depth of approximately 28×, facilitated the detection and annotation of single-nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy-number variations (CNVs), and structural variants (SVs). The functional classification of variant impacts enabled the identification of genes potentially linked to metabolic and adaptive traits. Results A total of 1.97 million SNPs, 401,493 InDels, 836 CNVs, and 15,288 SVs were identified across the chia genome. Notably, approximately 53% of exonic SNPs were non-synonymous (dN/dS ≈ 1.28), predominantly affecting lipid metabolism, transcriptional regulation, and stress response pathways, potentially altering key agronomic traits. In addition, CNV hotspots were concentrated in chromosomes 3 and 6, overlapping MYB, WRKY, and bZIP transcription factor loci, may potentially be involved in stress tolerance and yield. Furthermore, structural rearrangements, including inversions and duplications within the FAD2, FAD3, and CYP450 gene clusters, were potentially associated with seed pigmentation and omega-3 biosynthesis, pointing to their potential breeding relevance. Observed heterozygosity (Hₒ ≈ 0.71) and nucleotide diversity (π ≈ 7 × 10−3) indicated moderate to high allelic richness. In addition, the low FST value (0.038) indicates substantial genomic similarity between the two genotypes. Conclusion This study presents the first comprehensive map integrating SNPs, CNVs, and SVs in S. hispanica L. The results reveal a structurally dynamic genome characterized by substantial sequence and structural variation, providing valuable insights into genomic diversity and potential adaptive mechanisms in chia. The coexistence of high SNP diversity and abundant structural variation underpins chia's nutritional specialization and environmental resilience. These results deliver a foundational genomic resource for marker-assisted breeding, genome-wide association studies, and the development of climate-resilient chia cultivars.
C. Azzam, M. Rizk, R. Arafa et al.· Journal of Genetic Engineeri...· 0 citations
This comprehensive review demonstrates that shifting from reactive field evaluation to marker-driven, genomics-assisted precision design provides the definitive molecular framework required to engineer high-yielding, climate-resilient, and disease-proof cacao cultivars, thereby permanently safeguarding the long-term economic sustainability of global cocoa supply chains.
Atharva Gangurde, Adesina Christiana, Franc Olivier Nzogang· International Journal of Inn...· 0 citations
Hyacinth bean (Lablab purpureus (L.) Sweet), commonly known as lablab, is an underutilized legume with potential for improving food and nutritional security in smallholder farming systems. Although it is adapted to low-input and drought conditions, genetic improvement of lablab is constrained by limited knowledge of its genetic diversity, despite extensive germplasm collections. Moreover, additional diversity maintained in farmers’ fields is currently not well documented or conserved. This study assessed the genetic diversity and population structure in a global panel of 281 lablab accessions, including newly collected farmer cultivars from Tanzania. Genotype-by-sequencing yielded 15,125 high-quality single nucleotide polymorphisms (SNPs). Observed heterozygosity exceeded expected heterozygosity, suggesting partial outcrossing in this predominantly self-pollinating species. The bimodal distribution of individual heterozygosity, with two peaks corresponding to accessions exhibiting low (< 15%), and high (> 15%) heterozygosity, supports the possibility of partial outcrossing, which may be facilitated by insect pollination. Population structure analyses revealed seven distinct genetic clusters which were not correlated with geography, suggesting historical seed exchange and germplasm movement across regions. Tanzanian farmer collections harbor genetic variation that is not represented in local seedbanks, underscoring the significance of on-farm conservation and the need for future collection efforts. These findings pave the way for further genome research in marker-assisted breeding, which will contribute to future food security and sustainable livelihoods.
Elice Godson Lekasio, K. Mtei, X. Argout et al.· Genetic Resources and Crop E...· 0 citations
Cowpea (Vigna unguiculata L. Walp.) is a multifunctional species originating from Africa, where it plays a key role in food security and sustainable agriculture. In Morocco, it remains a marginal crop that has been scientifically overlooked, despite its crucial role in food security, which limits its integration into genetic improvement programs and compromises the sustainable conservation and valorisation of this plant genetic heritage. A field experiment was conducted during the 2023 cropping season using a randomized complete block design with three replications to evaluate the agro-morphological diversity of 19 cowpea landraces collected from different regions of Morocco. A total of 50 qualitative and quantitative traits (morphological, phenological, and agronomic) were assessed at different growth stages. The results revealed a considerable level of variation across most assessed traits, supported by a high total phenotypic diversity (HT = 0.53) and a mean within-population diversity (Hs̄ = 0.45±0.20) that exceeded the among-population phenotypic diversity (GST = 0.16). The average phenotypic diversity (Hp̄) across landraces was 0.45, with no significant differences among landraces. principal component analysis (PCA) revealed significant variation among the 19 cowpea landraces, enabling their grouping based on similarities independently of their geographical origin, with landraces BH3, CF2, HG and TK1 being distinguished by a combination of desirable traits. These results show a considerable level of intra- and inter-landrace diversity among Moroccan cowpea landraces, providing essential information for their conservation, sustainable use, and incorporation into breeding and selection programs, which is particularly relevant as a strategic crop in the current context of climate change.
Zineb Moudni, Y. Hmimsa, E. Lazaridi et al.· Notulae Scientia Biologicae· 0 citations
Brassica junceae (L.) Czern. (Indian mustard) plant is one of the world’s most vital agricultural crops that is also known as cruciferous oilseed crops. This study characterises ten Brassica genotypes from Rajasthan, India, using integrated morphological, biochemical and molecular approaches. Nine morphological traits were assessed using a randomized complete block design (RCBD) with 3 replicates. Biochemical profiling was assessed and quantified for glucosinolates, antioxidants, β-carotene, vitamin E, erucic acid and oil content. The DNA barcoding genes matK and rbcL loci, were analysed through Sanger sequencing following through phylogenetic reconstruction (UPGMA/ML/NJ; Kimura 2-parameter model). Principal component analysis (PCA) further explains 69.2 % morphological variation, with yield components dominating in PC1. Control genotype PM-21 exhibited superior performance (199 siliqua/plant, 5.56 cm siliqua length, 5.485 g yield), while control genotype PM-30 showed relatively high β-carotene (2.315 ppm) and vitamin E (25.17 mg/g). Parallelly glucosinolate content ranges from 15.7–83.7 µmol/g. Genetic parameters revealed moderate to high GCV (16–29 %) and PCV (32–72 %). The DNA barcoding confirms the species identity (99–100 %, GenBank; ON556533-ON556542). This study identifies a promising genotype (PM-21, PM-30) for better yield and nutritional breeding for preliminary single-location characterisation. Future research should integrate these nuclear markers simple sequence repeats (SSRs)/single nucleotide polymorphisms (SNPs) and multi-location trials to translate this variation into practical breeding applications.
Sogarwal Purnima, S. Anubhuti, C. Arjun· Plant Science Today· 0 citations