Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing

Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.)

Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.

Nutritional and nutraceutical richness of neglected little millet genotypes from Eastern Ghats of India: implications for breeding and food value

MAIN CONCLUSION

The study provides nutritional profiling of unexploited little millets from Eastern Ghats, which has ample opportunities for future breeding programs for enhancing the food quality and holds great potential in food industry. Little millet is an important small millet native to the Indian subcontinent and their nutritional value has been underutilized compared to other cereals. It's nutritional and nutraceutical profiling is essential to integrate the plants in developmental interventions. The present study evaluated comprehensive nutritional, nutraceutical and physico-functional properties of 14 selected little millet genotypes originated from Eastern Ghats of India and compared them with an improved variety (OLM 208) of the locality. The proximate compositions (per 100 g) showed significant variations, with moisture content ranging from 4.13 to 8.48 g, ash from 1.90 to 5.15 g, fat from 2.35 to 5.74 g, protein from 10.46 to 13.83 g, carbohydrate from 70.92 to 77.89 g, fiber from 2.03 to 7.82 g and energy from 372.8 to 391.1 kcal. These little millet flours are rich in phenol 5.37-12.73 mg/g, flavonoid 1.06-8.25 µg/g, vitamin C 12.72-22.86 µg/g, antioxidants 7.22-23.17%, iron 20.38 to 61.60 mg/ kg and zinc 17.47 to 37.59 mg/ kg. The first two components of principal component analysis captures 73.0% of the total variation, which reflected huge variability among the investigated genotypes. Maximum heritability and genetic advance were recorded in flavonoid, fiber, iron, zinc, phenol and vitamin C across the populations. Taken together, some indigenous little millet genotypes such as Mami, Kalia and Bada, were exceptionally rich in fiber, protein, energy, flavonoid, vitamin C and antioxidants and are nutritionally superior compared to other varieties from the locality. These nutrition rich little millet genotypes have ample opportunities for future breeding programs to enhance the cereal quality and holds great potential in food industry for making high value functional foods.

Structure and genetic diversity of Canadian Maritimes wild hops

Studies on the northeastern American native hops (Humulus lupulus ssp. lupuloides) from the Canadian Maritimes are scarce. This study aimed to evaluate the genetic structure and diversity among 25 wild-collected hops from three Canadian Maritime provinces using microsatellite (simple sequence repeat (SSR)) markers. Based on 43 SSR markers, four distinct subgroups were found, with a low molecular variance (19%) between subgroups and a high variance (81%) within subgroups. The Nei's unbiased genetic distance between clusters ranged from 0.01 to 0.08, the genetic distance between clusters 2 and 3 being the farthest and that between clusters 1 and 2 the closest. Cluster 2 captured the highest overall diversity. A total of 18 SSR markers clearly discriminated hop clones by detecting putative subspecies-specific haplotypes, differentiating clones of native-wild H. lupulus ssp. lupuloides from the naturalized old and modern hop cultivars. Seven of the 18 SSR markers also differentiated two clones from the same site from one another. The study is the first, using molecular markers, to identify SSR markers with potential for intellectual property protection in Canadian Maritimes hops. The SSR markers herein used can be prime tools for hop breeders and growers in the region.

Millets: The future crops for the tropics - Status, challenges and future prospects

Millets are small-grained nutritious minor cereal crops that are resistant to different abiotic stresses resulting from climate change. Despite their many benefits, millets have received limited attention in agricultural research, policies, and markets. Considering the importance of millets, recently the government many tropical countries including India and Bangladesh give more emphasis to millets cultivation and improvement. Moreover, Food and Agricultural Organization of the United Nations (FAO) declared 2023 to be the "International Years of Millets". In these connections, a details and updated review of the pros and cons of millets cultivation and its improvement in this region warrant due attention. The review therefore, examines the potential and main barriers to the adoption and promotion of millet cultivation in this region. These include limited research and development efforts, inadequate infrastructure and inputs, weak market linkages and demand, and insufficient awareness and knowledge about millets' nutritional and environmental benefits. This review also highlighted the prospects and strategies for scaling up millet cultivation in this region especially in Bangladesh. These include increasing public and private investment in research and extension services, strengthening farmers' organizations and market linkages, promoting millet-based value chains and products, and integrating millets into nation's food policy. The review concludes that millets might support equitable and sustainable agricultural growth, which would contribute to global food and nutritional security and could help attain the sustainable development goals (SDGs). However, achieving this potential will require concerted efforts from multiple stakeholders, including farmers, researchers and policymakers. The review emphasizes the need for a multi-disciplinary and multi-stakeholder approach that prioritizes innovation, inclusiveness, and sustainability. Lastly, the review highlights more investigation into the socioeconomic, environmental, and nutritional effects of millet production in this region with special emphasis on Bangladesh in order to support evidence-based policies and practices.

De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.)

The genome size of the little millet Panicum sumatrense is unknown, although its genome is fairly diploid (2n = 4x = 36). Despite tremendous nutritional value and adaptability to adverse climatic conditions, P. sumatrense use was limited by their low palatability, coarse grain, and lack of variety of culinary preparations. Hence, understanding how to vary their usage to offer food and nutritional security in the continuously changing modern world, the proposed study was aimed to determine potential genes and metabolites implicated in drought resistance. The drought-resistant genotype of tiny millet OLM-203/Tarini was offered in pots under both relaxed and demanding circumstances. The experimental seedlings were 32 days old and had been under water stress for 23 days. A total of 7606 genes were compared between 23 and 32 days for roots and 7264 total genes were compared between 23 and 32 days for leaves, according to a research on differential expression genes (DEGs). Twenty essential genes for drought tolerance were up-or down-regulated in the control and treated roots of the OLM-203 genotype. For instance, the genes RS193 and XB34 were up-regulated in leaves while, WLIM1 was found to be down-regulated. Gene SKI35 was up-regulated in roots, whereas MPK6 and TCMOp1 were down-regulated in root samples. The roots and leaves of the tiny millet OLM-203 genotype expressed 36 up-regulated and 21 down-regulated serine transcripts, respectively. Gene annotations for leaf samples were classified as having "molecular function" (46%), "cellular component" (19%), and "biological process" (35%), while root sample gene annotations were categorized as having "biological process" (573 contigs), "molecular function" (401 contigs), and "cellular components" (166 contigs). Noteworthy, polyamines play a crucial role in drought stress tolerance in the genotype, and it was found that top ten DEGs encoding for polyamines were common in two tissues (leaf and root). Collectively, transcriptomics profiling (RNA-seq) unveiled transcriptional stability drought stress provide a new insight in underlying modus of operandi in little millet genotype "OLM-203/Tarini" in response to heat stress.

LMTdb: A comprehensive transcriptome database for climate-resilient, nutritionally rich little millet (Panicum sumatrense)

Little millet (Panicum sumatrense) a native of Chhattisgarh, belongs to the minor millet group and is primarily known as a climate-resilient and nutritionally rich crop. However, due to the lack of enough Omic studies on the crop, the scientific community has largely remained unaware of the potential of this crop, resulting in less scope for its utilization in crop improvement programs. Looking at global warming, erratic climate change, nutritional security, and limited genetic information available, the Little Millet Transcriptome Database (LMT^db) (https://igkv.ac.in/xenom/index.aspx) was conceptualized upon completion of the transcriptome sequencing of little millet with the aim of deciphering the genetic signatures of this largely unknown crop. The database was developed with the view of providing information about the most comprehensive part of the genome, the 'Transcriptome'. The database includes transcriptome sequence information, functional annotation, microsatellite markers, DEGs, and pathway information. The database is a freely available resource that provides breeders and scientists a portal to search, browse, and query data to facilitate functional and applied Omic studies in millet crops.

Genetic enhancement of climate-resilient traits in small millets: A review

Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.

Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches

Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.

Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC

Zanthoxylum nitidum (Roxb.) DC. (Z. nitidum) is a type of Chinese Dao-di herb, also called Liangmianzhen, which is widely used to treat arthralgia, rheumatic arthralgia, and stomach pain. However, genomic resources for Z. nitidum are still scarce. This study provides transcriptomic resources for Z. nitidum by applying single-molecule real-time (SMRT) sequencing technology. In total, 456,109 circular consensus sequencing (CCS) reads were generated with a mean length of 2,216 bp from Z. nitidum roots, old stems, young branches, leaves, flowers, and fruits. Of these total reads, 353,932 were full-length nonchimeric (FLNC) reads with an average length of 1,996 bp. A total of 16,163 transcripts with a mean length of 1,171 bp were acquired. Of these transcripts, 14,231 (88%) were successfully annotated using public databases. Across all the 16,163 transcripts, we identified 6,255 long non-coding RNAs (lncRNAs) and 22,780 simple sequence repeats (SSRs). Furthermore, 3,482 transcription factors were identified. Among the SSR loci, 1-3 nucleotide repeats were dominant, occupying 99.36% of the total SSR loci, with mono-, di-, and tri-nucleotide repeats accounting for 61.80%, 19.89%, and 5.02% of the total SSR loci, respectively. A total of 36 out of 100 randomly selected primer pairs were verified to be positive, 20 of which showed polymorphism. These findings enrich the genetic resources available for facilitating future studies and research on relevant topics such as population genetics in Z. nitidum.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.

Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication of Gevuina avellana Mol. in Central Chile

The Chilean hazelnut (Gevuina avellana Mol., Proteaceae) is a native tree of Chile and Argentina of edible fruit-type nut. We applied two approaches to contribute to the development of strategies for mitigation of the effects of climate change and anthropic activities in G. avellana. It corresponds to the first report where both tools are integrated, the MaxEnt model to predict the current and future potential distribution coupled with High-Resolution Melting Analysis (HRM) to assess its genetic diversity and understand how the species would respond to these changes. Two global climate models: CNRM-CM6-1 and MIROC-ES2L for four Shared Socioeconomic Pathways: 126, 245, 370, and 585 (2021−2040; 2061−2080) were evaluated. The annual mean temperature (43.7%) and water steam (23.4%) were the key factors for the distribution current of G. avellana (AUC = 0.953). The future prediction model shows to the year 2040 those habitat range decreases at 50% (AUC = 0.918). The genetic structure was investigated in seven natural populations using eight EST-SSR markers, showing a percentage of polymorphic loci between 18.69 and 55.14% and low genetic differentiation between populations (Fst = 0.052; p < 0.001). According to the discriminant analysis of principal components (DAPC) we identified 10 genetic populations. We conclude that high-priority areas for protection correspond to Los Avellanos and Punta de Águila populations due to their greater genetic diversity and allelic richness.

Identification and Characterization of DNA Demethylase Genes and Their Association With Thermal Stress in Wheat (Triticum aestivum L.)

DNA demethylases (dMTases) are essential proteins in plants that regulate DNA methylation levels. The dMTase genes have been explored in a number of plant species, however, members of this family have not been reported in wheat. We identified 12 wheat dMTase genes divided into two subfamilies: repressor of silencing 1 (ROS1) and DEMETER-Like (DML). The TadMTases in the same subfamily or clade in the phylogenetic tree have similar gene structures, protein motifs, and domains. The promoter sequence contains multiple cis-regulatory elements (CREs) that respond to abiotic stress, hormones, and light, suggesting that the majority of TadMTase genes play a role in wheat growth, development, and stress response. The nuclear localization signals (NLSs), subcellular localization, and SRR motifs were also analyzed. The expression profile analyses revealed that TadMTase genes showed differential gene expression patterns in distinct developmental stages and tissues as well as under heat stress (HS). Furthermore, the qRT-PCR analysis revealed that TadMTase gene expression differed amongst wheat cultivars with varying degrees of HS tolerance. Overall, this work contributes to the understanding of the biological function of wheat dMTases and lays the foundation for future investigations.

Whole-genome survey and phylogenetic analysis of Gadus macrocephalus

Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.