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

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 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.

Language: Английский

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Genome-wide identification of copy number variation in diverse black pepper accessions

Planta, Journal Year: 2025, Volume and Issue: 261(4)

Published: March 8, 2025

Language: Английский

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Identification and validation of a major QTL, QFhb-6AL, for Fusarium head blight resistance on chromosome 6AL in wheat

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(4)

Published: March 15, 2025

Language: Английский

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Development of molecular markers for total soluble solids in tomato fruits

Scientia Horticulturae, Journal Year: 2025, Volume and Issue: 344, P. 114111 - 114111

Published: March 1, 2025

Language: Английский

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Genome-wide atlas of loci involved in chromosomal recombination in common wheat

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Nov. 26, 2024

Chromosomal recombination is a pivotal biological mechanism for generating novel genetic diversity, essential plant breeding and research endeavors. This study investigated the loci involved in chromosomal through analyzing five published recombinant inbred line (RIL) populations four double haploid (DH) populations. Great phenotypic variations frequency were observed between chromosomes. A total of 29 QTL mapped, which predominantly located on B genome. Notably, one chromosome 6AL was identified from two RIL 3B both DH Additionally, map delineating hotspot regions developed, these all chromosomes except 6B. Recombination tended to locate 1D, 3A, 3B, 6A, 7D compared 1B, 5B, In addition, most at termini, with some clustering specific regions. Besides factors, also explored impact chip size population type number identifiable events. Overall, this work improves our understanding molecular mechanisms rate may contribute optimization strategies wheat.

Language: Английский

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

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 25, 2024

Language: Английский

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A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits

Plant Communications, Journal Year: 2024, Volume and Issue: unknown, P. 101226 - 101226

Published: Dec. 1, 2024

Language: Английский

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