Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(4), С. 1466 - 1466

Опубликована: Фев. 10, 2025

The advancement of multi-omics tools has revolutionized the study complex biological systems, providing comprehensive insights into molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify characterize elements that contribute to phenotypic traits. This review delves recent progress in applying approaches elucidate genetic, epigenetic, metabolic networks associated with key plants. We emphasize potential these integrative strategies enhance crop improvement, optimize agricultural practices, promote sustainable environmental management. Furthermore, we explore future prospects field, underscoring importance cutting-edge technological advancements need for interdisciplinary collaboration address ongoing challenges. bridging this aims provide a holistic framework advancing research plant biology agriculture.

Язык: Английский

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A simple and cost-effective SNP genotyping assay for marker-assisted selection of wilt resistance in castor breeding

Industrial Crops and Products, Год журнала: 2025, Номер 226, С. 120693 - 120693

Опубликована: Фев. 18, 2025

Язык: Английский

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Agro-physiological and transcriptome profiling reveal key genes associated with potato tuberization under different nitrogen regimes in aeroponics

PLoS ONE, Год журнала: 2025, Номер 20(3), С. e0320313 - e0320313

Опубликована: Март 28, 2025

Nitrogen (N) is a crucial nutrient for the growth and development of potatoes. However, excessive use nitrogen fertilizers can have detrimental effects on human health, aquatic ecosystems, environment. Therefore, understanding genes involved in metabolism essential developing future strategies to improve efficiency (NUE) plants. This study aimed identify associated with high tuber yield two contrasting potato varieties Kufri Jyoti (N inefficient) Pukhraj efficient) grown under low regimes using an aeroponics system. Both were doses (low N: 0.5 mM N; 5 N) completely randomized design (CRD) three replications over years. The phenotypic results confirmed that was more efficient compared Jyoti, particularly conditions. Additionally, transcriptome analysis produced high-quality data ( ≥ Q20), ranging from 4.35 5.46 Gb per sample. Statistically significant p ≤ 0.05) identified based reference genome. Differentially expressed (DEGs) categorized as either up-regulated or down-regulated leaf tissues. Transcriptome profiling both tissues revealed traits contributing DEGs further characterized through gene ontology (GO) annotation KEGG pathway analysis. Selected validated real-time quantitative polymerase chain reaction (RT-qPCR) In summary, several being component potatoes different These included glutaredoxin, transcription factors (BTB/POZ, AP2/ERF, MYB), nitrate transporter, aquaporin TIP1;3, glutamine synthetase, aminotransferase, GDSL esterase/lipase, sucrose synthase, UDP-glycosyltransferases, osmotin, xyloglucan endotransglucosylase/hydrolase, laccases. we overexpressed including cysteine protease inhibitor 1, miraculin, sterol desaturase, pectinesterase N stress. Our highlights these genes’ roles enhancing cultivated aeroponics.

Язык: Английский

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Exploring genomic loci and candidate genes associated with drought tolerance indices in spring wheat evaluated under two levels of drought

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 1, 2025

Wheat is a major global crop, and increasing its productivity essential to meet the growing population demand. However limited water resources primary constraint. This study aimed identify genetic factors associated with drought tolerance using diverse panel of 287 wheat genotypes evaluated under well-watered drought-stressed conditions. Water Use Efficiency (WUE) Grain Yield (GY), along indices, were assessed. A genome-wide association (GWAS) 26,814 high-density SNP markers identified loci linked these traits, 768 SNPs showing significant associations. Additionally, genomic selection (GS) was performed rrBLUP model predict trait performance across environments. Among measured traits at -log10 (P) ≥ 3, 81 mapped higher threshold 4, indicating pleiotropic QTL-by-environment interaction effects. Several novel known genes, previously reported have functions related biotic abiotic stresses response SNPs. indices evaluated, stress index (STI), geometric mean (GMP), (TOL) most reliable indicators for selecting stable, high-yielding control The same three exhibited high prediction values severe (SS) condition. Five as promising candidates breeding programs based on their superior tolerance, grain yield, nutritional value. provides valuable insights into basis in wheat, highlighting key regions improved use efficiency yield stability. findings contribute development drought-tolerant varieties optimized utilization achieve increased per unit levels, ultimately contributing sustainable agriculture food security.

Язык: Английский

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Genome-wide association study uncovers key genomic regions governing agro-morphological and quality traits in Indian mustard [Brassica juncea (L.) Czern. and Coss.]

PLoS ONE, Год журнала: 2025, Номер 20(4), С. e0322120 - e0322120

Опубликована: Апрель 24, 2025

In Indian mustard, improving agro-morphological and quality traits through conventional methods are both cumbersome resource-intensive. Marker-aided breeding presents a promising solution to these challenges. Hence, the present research aimed identify genomic regions governing using genome-wide association studies (GWAS). The GWAS panel comprised 142 diverse genotypes of mustard were evaluated for 20 different traits, revealing significant difference among genotypes. Subsequently, genotyped Brassica 90K SNP array (Illumina). Structure diversity analysis grouped into 3 sub-populations or groups, LD decay 1.05 Mb was confirmed genotypic analysis. BLINK model revealed total 49 marker-trait associations (MTAs), in which 28 21 MTAs observed during rabi 2020–21 2021–22 various respectively. Amongst them, twelve demonstrated stable with studied including days 50% flowering (DF), 100% flower termination (DFT), maturity (DM), plant height (PH), main shoot length (MSL), siliqua (SL), seeds per (SPS), oil content (OC), glucosinolates (Glu) years. Moreover, silico nearby SNPs their 31 candidate genes known be involved molecular, physiological, biochemical pathways relevant traits. These can further characterized deciphered more precise utilization programs future.

Язык: Английский

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Morphological characteristics and genome-wide association analysis among local Andrographis paniculata from Thailand under controlled environment in plant factory

PLoS ONE, Год журнала: 2025, Номер 20(4), С. e0320667 - e0320667

Опубликована: Апрель 29, 2025

Andrographis paniculata Wall. ex Nees ( A. ) is a medicinal plant widely used in Southeast Asian traditional medicine. Plant factories with artificial lighting (PFAL) provide controlled environments for optimizing growth and quality. However, the variability biomass bioactive compound production among varieties cultivated PFAL not well understood. This study investigated ten locals of accessions to assess their characteristics andrographolide (AP1) content system using hydroponic cultivation. Among accessions, TTT cultivar showed significantly higher stem height, width, above-ground yield, leaf number, AP1 compared others. Phylogenetic analyses based on SNP markers revealed that morphologically distinct but genetically similar CR, RB, PL, PC accessions. A genome-wide association (GWAS) identified two significant regions chromosome 9 associated yield content. These findings highlight potential as high-quality pharmaceutical use insights into key genes could be targeted breeding programs improve systems.

Язык: Английский

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Genome-wide association study (GWAS) combined with transcriptome analysis reveals the key genes underlying the production of seed oil, mono and poly-unsaturated fatty acids in Brassica napus

Industrial Crops and Products, Год журнала: 2025, Номер 231, С. 121205 - 121205

Опубликована: Май 21, 2025

Язык: Английский

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From wild to domesticated: exploring selection signatures caused by domestication in Carica papaya

Ecological Genetics and Genomics, Год журнала: 2025, Номер unknown, С. 100367 - 100367

Опубликована: Май 1, 2025

Язык: Английский

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Genome-wide association studies and transcriptome analysis reveal novel genes associated with freezing tolerance in rapeseed (Brassica napus L.)

PLoS ONE, Год журнала: 2025, Номер 20(5), С. e0322547 - e0322547

Опубликована: Май 27, 2025

Freezing stress is the main obstacle affecting geographical distribution, growth, development, quality, and productivity of rapeseed ( Brassica napus ) in northern China. However, there a little knowledge freezing tolerance mechanism. Here, 289 core germplasms collected from 36 countries were used to identify SNPs associated with tolerance. We RNA-seq data narrow down candidate genes identified by genome-wide association studies. The frequency distributions phenotypic values best linear unbiased estimates (BLUE) for each trait conform normal or approximately distributions, good repeatability across various locations. results showed that 594, 513, 7, 45 significantly malondialdehyde, peroxidase, soluble protein, relative electrolyte leakage, respectively. Based on these SNPs, we 4,998 genes. Crossover analysis indicated 73 overlapped between GWAS datasets, 13 involved transmission perception freeze signals, lipid metabolism, reactive oxygen species (ROS) homeostasis, antifreeze proteins synthesis, other metabolic processes. These reveal novel rapeseed, provide basis further research improvement rapeseed.

Язык: Английский

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Meta-QTL analysis for mining of candidate genes and constitutive gene network development for viral disease resistance in maize (Zea mays L.)

Heliyon, Год журнала: 2024, Номер 11(1), С. e40984 - e40984

Опубликована: Дек. 14, 2024

Язык: Английский

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