Introgressions lead to reference bias in wheat RNA-seq analysis

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Март 7, 2024

Abstract Background RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of quantification and thus conclusions made downstream. Reference bias analysis has to be explored complex polyploid genomes despite evidence that they often mosaic wild relative introgressions, which introduce blocks highly divergent genes. Results Here we use hexaploid wheat as model polyploid, using both simulated experimental data show alignment suffers widespread largely driven by introgressed This leads underestimation gene expression incorrect assessment homoeologue balance. By incorporating models ten genome assemblies into pantranscriptome reference, present novel method reduce readily scaled capture more variation new transcriptome becomes available. Conclusions study shows presence introgressions lead analysis. Caution should exercised researchers non-sample for methods, such one presented here, considered.

Язык: Английский

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Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (Triticum aestivum L.)

Agronomy, Год журнала: 2025, Номер 15(1), С. 169 - 169

Опубликована: Янв. 11, 2025

A chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide unique DNA markers are urgently needed marker-assisted selection. In this study, 11,016 primer pairs targeting 5036 indel sites were successfully designed E6015-3S, average density of 0.36 indels per Mbp. These believed to be and polymorphic in genome; as gathered from evidence, (i) 76.18 99.34% yielded a single hit during sequence alignment 18 sequenced genomes, (ii) 83.59 90.98% 1042 synthesized amplified band 16 accessions, (iii) 59.69 99.81% tested between 15 individual accessions. also anticipated excellent resolvability on agarose or polyacrylamide gels, since most them have sizes 46 bp, amplicon 141 250 polymorphism ratios 6.0 25.0%. Collectively, these CSSL development more broad applications, germplasm classification, seed purity testing, genetic linkage mapping, breeding wheat, owing their uniqueness, polymorphism, easy-to-use characteristics.

Язык: Английский

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Genomics-guided landscape unlocks superior alleles and genes for yellow rust resistance in wheat

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Март 11, 2025

Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to wheat production worldwide. Breeding resistant cultivar is crucial for managing this disease. However, understanding of the genetic mechanisms underlying YR resistance remains fragmented. To address this, we conducted comprehensive analysis with variome data from 2,191 accessions worldwide and over 47,000 response records across multiple environments pathogen races. Through genome-wide association studies, established landscape 431 loci, providing rich resource (R) gene deployment. Furthermore, cloned genes corresponding three namely Yr5x effective against Pst races, Yr6/Pm5 that conferred two species, YrKB (TaEDR2-B) conferring broad-spectrum without yield penalty. These findings offer valuable insights into basis in lay foundation engineering durable disease resistance.

Язык: Английский

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Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

Genome biology, Год журнала: 2024, Номер 25(1)

Опубликована: Июль 1, 2024

Abstract Background The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while huge complex genome polyploid wheat hinders efficient genotyping abundant varieties towards accurate identification, management, exploitation germplasm resources. Results We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in at pan-genome level, demonstrating CNVb can serve as an ideal DNA fingerprinting marker for discriminating varieties, with accuracy validated by PCR assay. then construct digitalized map across 1599 global accessions. Key markers are linked trait-associated introgressions, such 1RS·1BL translocation 2N v S translocation, beneficial alleles, end-use quality allele Glu-D1d (Dx5 + Dy10) semi-dwarf r-e-z allele. Furthermore, we demonstrate these tagged promote stable cost-effective strategy evaluating resources ultra-low-coverage sequencing data, competing SNP array applications new management collections gene banks, describing manner. also user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), exploring profiles over ever-increasing accessions, propose QR-code-like representation individual digital fingerprint. This platform allows uploading comparison stored varieties. Conclusions CNVb-based approach provides low-cost high-throughput enabling modern breeding precise practical decision-making.

Язык: Английский

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Reconciliation of wheat 660 K and 90 K SNP arrays and their utilization in dough rheological properties of bread wheat

Journal of Advanced Research, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

High-density Wheat 660K and 90K SNP arrays are powerful tools for understanding the genetic basis of wheat traits. However, their inconsistantly physical positions that were caused by different versions Chinese Spring genome during developing confused inconvenient further application. With repid development geonome sequencing, we aim to reconciliate in modern cultivar reveal dough rheological properties bread wheat. We refined currently popular AK58 was released more recently. next performed genome-wide association studies (GWAS) linkage analysis identify important loci related quality traits using updated un-updated arrays, respectively. Refining results showed 92.3% 83% SNPs precisely mapped genome, respective. GWAS indicated 26 intervals composed 1032 significant associated with 9 multiple environments. The interval stability time on 1D narrowed into an 8.4-Mb region whereas is 405 Mb arrays. Linkage revealed QTL QST.henau-1D.2 1.64 Mb. Integration 6.46 containing 35 annotation genes collinearity analysis. After T-test, gene expression analysis, seven them potential candidate thus favorable haplotypes identified benefit marker-assisted selection. A reconciliation promote efficient applications. Important this study provided valuable information breeding.

Язык: Английский

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Genome-wide identification and expression analysis of phytochrome gene family in Aikang58 wheat (Triticum aestivum L.)

Frontiers in Plant Science, Год журнала: 2025, Номер 15

Опубликована: Янв. 21, 2025

Phytochromes are essential photoreceptors in plants that sense red and far-red light, playing a vital role regulating plant growth development through light signal transduction. Despite extensive research on phytochromes model like Arabidopsis rice, they have received relatively little attention wheat. In this study, we employed bioinformatics methods to identify eight TaAkPHY genes the Aikang58 wheat variety. Based gene structure, conserved domains, phylogenetic relationships, family exhibits high degree of conservation. Synteny analysis revealed evolutionary history PHY Chinese Spring ( Triticum aestivum L.), barley Hordeum vulgare rice Oryza sativa maize Zea mays quinoa Chenopodium Willd.), soybean [ Glycine max (L.) Merr.], thaliana Heynh.]. Among these species, is most closely related barley, followed by maize. The cis -acting element indicates promoter regions contain large number CAT-box, CGTCA-motif, GC-motif, etc., which mainly involved development, hormone response, stress response. Gene expression profiling demonstrated exhibit varying levels across different tissues induced various conditions treatments. Co-expression network suggested may specifically regulate downstream associated with responses, chloroplast circadian rhythms. Additionally, least absolute shrinkage selection operator (LASSO) regression algorithm machine learning was used screen transcription factors such as bHLH, WRKY, MYB influenced genes. This method helps quickly extract key influencing from amount complex data. Overall, findings provide new insights into growth, laying foundation for future

Язык: Английский

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Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1-B of Chinese Wheat Accessions Using Pan-Genome

Plants, Год журнала: 2025, Номер 14(4), С. 504 - 504

Опубликована: Фев. 7, 2025

The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog Viviparous-1 (VP-1) gene maize and was reported to confer resistance pre-harvest sprouting (PHS) in wheat. In this study, structure analyzed using wheat pan-genome consisting 20 released cultivars (19 are from China), 3 single nucleotide polymorphisms (SNPs), which were identified at 496 bp, 524 1548 bp CDS region, respectively. Haplotypes analysis showed that these SNPs complete linkage disequilibrium only two haplotypes designated as hap1 (TGG) hap2 (GAA) present. Association between PHS four experiment environments revealed average accessions with significantly better than hap2, infers effects resistance. To further investigate impacts alleles locus resistance, SNP region converted KASP marker, used for genotyping 304 Chinese cultivars, whose evaluated three environments. rates (SRs) 135 lower 169 validating present study provided breeding-friendly marker functional variants can be genetic improvement

Язык: Английский

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Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 23, 2025

Abstract Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than diversity. The strategy of using single genome reference RNA-seq analysis could not handle introgression bias, especially hexaploidy wheat. Here, we conducted 328 wheat lines, including representative diverse landraces and elite cultivars from China the United States, to investigate role variation shaping agronomic traits. Using pan-genome resources, identified 20,615 more transcripts ‘Chinese Spring’ alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed wild relatives were under tight genetic control. Genes responding environmental stress show higher activity after into genome, how long-term breeding selection impacted regulation targeted introgression. Multi-omics modeling 231 high-confidence candidate 34 field traits seedling resistance phenotypes 8 powdery mildew isolates. More one fifth those candidates have no homolog genome. By utilizing indexed KN9204 EMS library, 80% showed significant trait difference between type mutant lines. Furthermore, directional shifts which changed by improvement demonstrated distinct adaptations local environments. Our study correct bias reads mapping studies revealed patterns within their mechanisms, highlighted impact world’s most important crop.

Язык: Английский

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Fine mapping of stripe rust resistance gene YrAn1589 in common wheat using Wheat660K SNP array and BSR-Seq

Theoretical and Applied Genetics, Год журнала: 2025, Номер 138(3)

Опубликована: Март 1, 2025

Язык: Английский

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The Genome of the Lima Bean Variety Baiyu Bean Highlights Its Evolutionary Characteristics

Ecology and Evolution, Год журнала: 2025, Номер 15(3)

Опубликована: Фев. 28, 2025

ABSTRACT The baiyu bean ( Phaseolus lunatus ), also known as the lima bean, is a plant belonging to Fabaceae family, has long and distinguished history of cultivation in China highly regarded local variety bean. In current study, we present reference genome variety, which scaffold N50 length 47.545 Mb. A comparative genomic analysis was conducted using genomes seven legume species, results demonstrated that 1564 1275 genes exhibited expansion contraction, respectively. Moreover, 543 were identified exclusive adaptive evolution revealed presence 61 under between P. common vulgaris . An examination branch model five undergoing branch. Additionally, evolutionary selective pressure acting on other branches plants analyzed. comprehensive structural variations (SVs) G27455 conducted, resulting identification 5549 SVs. Among these, 333 high‐impact SV genes. acquisition sequence this excellent will facilitate exploration utilization its characteristics, providing foundation for genetic improvement

Язык: Английский

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