Jul 2026· Agricultural Science Digest - A Research Journal· 0 citations· 27 references
TL;DR
Variants associated with stress-responsive transporters, kinase signalling proteins, transcription factors and regulatory genes were also detected, indicating potentially important adaptive genomic signatures within the Iluppai Poo Samba genome.
Abstract
Background: Traditional rice landraces represent valuable reservoirs of genetic diversity associated with agronomically important traits, stress adaptation, nutritional quality and regional adaptation. Iluppai Poo Samba (Oryza sativa L.) is a traditional South Indian rice landrace cultivated in Tamil Nadu, India, valued for its characteristic aroma, grain quality and adaptation to local agroecological conditions. However, genomic information for this cultivar remains limited. The present study aimed to characterize genome-wide sequence variation in Iluppai Poo Samba through whole-genome sequencing (WGS). Methods: High-quality paired-end sequencing libraries were prepared using the NEXTflex Rapid DNA Sequencing platform and sequenced using Illumina chemistry. Sequence reads were subjected to quality assessment, genome alignment, variant calling, genome-wide SNP density analysis and functional annotation of genomic variants. Result: Sequencing quality assessment demonstrated high-quality reads with Q20 values exceeding 97% and Q30 values exceeding 94%, with an average GC content of approximately 45%. A total of 1,410,690 SNPs and 138,431 InDels were observed across the genome. Genome-wide SNP analysis revealed extensive chromosomal variation, heterogeneous SNP distribution patterns and distinct polymorphic hotspot regions. Functional annotation detected widespread intergenic, intronic and coding-region polymorphisms, including 44,070 synonymous and 51,380 non-synonymous SNPs. Transition/transversion (Ts/Tv) ratios ranging from 2.24 to 2.50 supported the reliability of variant identification. Variants associated with stress-responsive transporters, kinase signalling proteins, transcription factors and regulatory genes were also detected, indicating potentially important adaptive genomic signatures within the Iluppai Poo Samba genome.
This study provides new insights into the pangenome of Magnaporthe oryzae and introduces a method for the identification of functionally important genes in fungal species.
Yi Wang, Qi Wu, Jin-bin Li et al.· Journal of Advanced Research· 0 citations
Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding.
Yang Lv, Hao Wu, M. Asad et al.· Plants· 0 citations
Leiwuqi yak is an important indigenous yak genetic resource distributed in eastern Tibet, but its genomic characteristics and adaptive evolutionary features remain poorly understood. In this study, whole-genome resequencing was performed on 110 Leiwuqi yaks, and these data were integrated with publicly available genomic data from other domestic and wild yak populations to investigate the genetic diversity, population structure, and candidate genomic regions potentially associated with local adaptation of Leiwuqi yak. After quality control and variant filtering, a total of 19,966,141 high-quality SNPs were identified across all samples. Most SNPs were located in intronic and intergenic regions, with a transition/transversion ratio of 2.47. Although sequencing depth differed between newly sequenced (3.87×) and public (9.04×) data, all samples were processed through a unified pipeline with stringent filtering criteria. Genetic diversity analyses showed that Leiwuqi yak retained relatively abundant nucleotide diversity, whereas runs of homozygosity and genomic inbreeding coefficient analyses suggested possible effects of local isolation or recent inbreeding. Population structure analyses based on principal component analysis and ADMIXTURE revealed that Chinese domestic yak populations shared a broadly similar genetic background with wild yak, whereas Indian yak exhibited clear genetic differentiation. Although Leiwuqi yak did not form a completely independent genetic cluster at the genome-wide level, selective sweep analysis identified localized genomic differentiation in this population. A total of 466 protein-coding genes were detected within candidate selected regions. Functional enrichment analyses showed that these genes were mainly associated with the Wnt signaling pathway, NF-kappa B signaling pathway, pathways in cancer, light absorption, and receptor-mediated endocytosis. These findings suggest that developmental regulation, immune and stress responses, environmental perception, and cellular homeostasis may contribute to the adaptive differentiation of Leiwuqi yak. Overall, this study provides new genomic evidence for understanding the genetic uniqueness and adaptive evolution of Leiwuqi yak and offers a scientific basis for its conservation and sustainable utilization.
Chenbo Shi, Lin Fu, Tengxiang Wang et al.· Frontiers in Veterinary Scie...· 0 citations
The first draft genome assembly of the MHR genome is presented, providing a foundation to understand the genetic architecture underlying key phenotypic traits and identifying potential novel gene sources in MHR for rice improvement in the Caribbean region.
Uddesh M. Sahadeo, Omar Ali, A. Ramsubhag et al.· BioTech· 0 citations
Alfalfa (Medicago sativa L.) yield is a complex quantitative trait shaped by multiple yield components and strong genotype-by-environment interactions. In this study, we combined multi-environment phenotyping with deep whole-genome resequencing to dissect the genetic architecture of six agronomic traits in 198 half-sib families. Field trials conducted across two contrasting locations over three years revealed extensive variation in plant height, stem diameter, stem number, fresh weight, dry weight, and leaf-to-stem ratio. Deep resequencing generated an average of 39.4 Gb clean data per accession, with an effective sequencing depth of 42.14×, and identified 10.37 million high-quality SNPs densely distributed across the alfalfa genome. Using multi-environment BLUP values for GWAS, we detected 1137 trait-associated SNPs and prioritized candidate genes by integrating variant effects, haplotype differentiation, functional annotation, and expression patterns. A non-synonymous SNP in MsBG42, encoding beta-glucosidase 42, was associated with stem diameter. For biomass-related traits, MsG0780040381.01, designated MsFBL, encodes an F-box/FBD/LRR-repeat protein and was associated with both fresh and dry weight, with root-preferential expression. Hairy root-based functional validation further showed that MsFBL positively regulates root and whole-plant biomass. These findings provide a high-resolution genomic resource and identify MsFBL as a functionally supported target for alfalfa biomass improvement.
Bao Ao, Yang-Yang Han, Pan Xu et al.· Horticulture Research· 0 citations
Indigenous chickens play a critical role in food security and climate resilience in smallholder systems, yet their genomic diversity and adaptive potential remain insufficiently characterised. This study employed low-pass whole-genome sequencing (LP-WGS; 0.2–1.99×) to investigate genomic diversity, population structure, inbreeding and candidate environment-associated genomic variation in 33 chickens from highland, midland, and lowland agroecologies in the Tigray region of northern Ethiopia. After imputation and stringent filtering, 23.4 million high-confidence SNPs were retained, including ~ 17% novel variants, indicating substantial uncharacterised genetic diversity in these populations. SNP density (13.8 ± 8.6 SNPs/kb) was comparable to values reported from high-coverage Ethiopian chicken datasets, demonstrating the suitability of LP-WGS for population genomics in resource-limited settings. Marked differences in genomic diversity were observed among ecotypes: midland chickens showed the highest nucleotide diversity (π = 0.00267), followed by lowland (π = 0.00233), whereas highland chickens showed the lowest diversity (π = 0.00203) and elevated genomic inbreeding (FROH and FHOM ≈ 0.18). Population structure analyses revealed clear genetic separation among ecotypes. PCA (13.91% variation explained) distinguished lowland chickens along PC1 and separated highland from midland along PC2, while ADMIXTURE and FST patterns supported three major ancestral genomic backgrounds. Functional annotation of private missense variants uncovered distinct adaptive signatures reflecting the contrasting agroecological conditions. Highland chickens showed enrichment of candidate genes potentially involved in physiological processes relevant to high-altitude environments, including cold response, angiogenesis, cardiovascular regulation and metabolic homeostasis (eg., PARP1, ACOX2, ITGB3, EDNRB, SOX8, and SOX10). Midland chickens exhibited candidate signals of selection in genes with known roles in innate antiviral immunity, bacterial defence and inflammatory regulation (eg., BAK1, CLSTN1, CYSLTR1, CYSLTR2, CXCR7, GIPR, DSCAM, GDAP1, TLR3, TLR4, TLR7, IFIH1, ADORA1, EPHB1, and TMPRSS2). Lowland chickens displayed candidate variants associated with heat-stress response, DNA damage repair, oxidative balance and cardiovascular support under extreme temperatures (e.g., MLH1, BDKRB1, GPR19, FLT1, CCL18, TGM2, and RAMP3). Overall, the results indicate substantial genomic differentiation among ecotypes and suggest candidate environment-associated genetic divergence across Tigray’s diverse agroecological zones. These populations may represent important reservoirs of adaptive genetic variation for climate-resilient poultry breeding, warranting further functional validation and conservation-oriented management.
Gebreslassie Gebru, G. Belay, Tsadkan Zegeye et al.· Scientific Reports· 0 citations
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