Smart breeding driven by advances in sequencing technology

Modern Agriculture, Год журнала: 2023, Номер 1(1), С. 43 - 56

Опубликована: Март 1, 2023

Abstract Crop breeding has undergone numerous advancements throughout history with the next revolution being uncertain. This review provides an overview of techniques from traditional selective and crossbreeding to modern based on molecular marker‐assisted genomic selection. Systematic analysis mainstream genotyping approaches principle, application scenario supporting software revealed that changes in technology have led explosion data. data expansion will drive a breakthrough sequencing integrate artificial intelligence automation. The also discusses technological associated during big era, including models, technologies future intelligent breeding, provide references for crop breeders. paper highlights potential smart driven by advances technology, which lead development new strategies accelerate process.

Язык: Английский

---

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2023, Номер 50(11), С. 846 - 860

Опубликована: Авг. 21, 2023

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progresses in studying on genome are substantially trailed behind those other two major crops, rice maize, at least a decade. With rapid advances assembling reduced cost high-throughput sequencing, emerging de novo assemblies whole-genome sequencing data leading paradigm shift research. Here, we review recent progress dissecting germplasm evolution since release first high-quality genome. New insights have been gained during domestication modern breeding progress, genomic variations multiple scales contributing diversity germplasm, transcriptional epigenetic regulations functional genes polyploid wheat. Genomics databases bioinformatics tools meeting urgent needs genomics research also summarized. The ever-increasing omics data, along with advanced well-structured databases, expected accelerate deciphering gene resources future advances.

Язык: Английский

---

Future of durum wheat research and breeding: Insights from early career researchers

The Plant Genome, Год журнала: 2024, Номер unknown

Опубликована: Май 17, 2024

Abstract Durum wheat ( Triticum turgidum ssp. durum ) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate growing world population, need to significantly increase production meet anticipated demand paramount. This review summarizes recent advancements in research, encompassing exploitation of existing novel genetic diversity, exploration potential new diversity sources, breeding climate‐resilient varieties, enhancements management practices, utilization modern technologies cultivar development. In comparison bread T. aestivum ), community area are considerably smaller, often comprising many small‐family farmers, notably African Asian countries. Public programs such as International Maize Wheat Improvement Center (CIMMYT) Agricultural Research Dry Areas (ICARDA) play a pivotal role providing adapted cultivars these small‐scale growers. We spotlight contributions others this review. Additionally, we offer our recommendations on key areas research explore addressing challenges posed by change while striving enhance sustainability. As part Initiative, Expert Working Group Genomics Breeding recognizes significance collaborative efforts advancing toward shared objective. hope insights presented stimulate future deliberations trajectory genomics breeding.

Язык: Английский

---

A review of BioTree construction in the context of information fusion: Priors, methods, applications and trends

Information Fusion, Год журнала: 2025, Номер unknown, С. 103108 - 103108

Опубликована: Март 1, 2025

Язык: Английский

---

Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

---

A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 7, 2025

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. encompassing 14.51 billion base pairs featuring all 21 centromeres 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays 5,611 rDNA units. Genome-wide rearrangements, elements, transposable element expansion segmental duplications were deciphered during tetraploidization hexaploidization, providing understanding subgenome evolution. Among them, insertions hexaploidization greatly influenced gene expression balances, thus increasing genome plasticity transcriptional levels. Additionally, generated 163,329 full-length cDNA sequences proteomic data that helped annotate 141,035 high-confidence protein-coding genes. T2T reference (CS-IAAS), along with its transcriptome proteome, represents significant step in our complexity provides insights for future research breeding.

Язык: Английский

---

Evaluating Genome Assemblies for Optimized Completeness and Accuracy of Reference Gene Sequences in Wheat, Rye, and Triticale

Plants, Год журнала: 2025, Номер 14(7), С. 1140 - 1140

Опубликована: Апрель 6, 2025

Recent years have witnessed a surge in the publication of dozens genome assemblies for Triticeae crops, which significantly advanced gene-related research wheat, rye, and triticale. However, this progress has also introduced challenges selecting universally efficient applicable reference genomes genotypes with distant or ambiguous phylogenetic relationships. In study, we assessed completeness accuracy triticale using comparative benchmarking universal single-copy orthologue (BUSCO) analysis transcript mapping approaches. BUSCO revealed that proportion complete genes positively correlated RNA-seq read mappability, while frequency internal stop codons served as significant negative indicator assembly data mappability wheat. By integrated alignment rate, covered length, total depth from data, identified SY Mattis, Lo7, Mattis plus Lo7 most robust references studies triticale, respectively. Furthermore, recommend D sequence be incorporated bioinformatic analyses introgression, translocation, substitution into frequently occurs during breeding. The could help evaluating correctness published future, other findings are expected to support closely related species.

Язык: Английский

---

Deletion of wheat alpha-gliadins from chromosome 6D improves gluten strength and reduces immunodominant celiac disease epitopes

Theoretical and Applied Genetics, Год журнала: 2025, Номер 138(5)

Опубликована: Апрель 8, 2025

Язык: Английский

---

Genome-wide association analysis identifies seven loci conferring resistance to multiple wheat foliar diseases, including yellow and brown rust resistance originating from Aegilops ventricosa

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

Опубликована: Апрель 15, 2025

We assembled a European bread wheat (Triticum aestivum L.) association mapping panel (n=480) genotyped using 90,000 single nucleotide polymorphism array, with the aim of identifying genetic loci controlling resistance to four fungal diseases: yellow (stripe) rust (YR), brown (leaf) (BR), Septoria tritici blotch (ST) and powdery mildew (PM). Simulations showed our have good power detect loci, >50% probability as little 5% variance when heritability was 0.6 or more. Using disease infection data collected across 31 trials undertaken in five countries, genome-wide studies (GWAS) identified 34 replicated (20 for YR, 12 BR, two PM, 0 ST), seven associated more diseases. Construction analysis eight bi-parental populations enabled selected locus YR_2A010 (chromosome 2A) YR_6A610 (6A), be independently cross-validated, along development markers track alleles at these loci. Notably, chromosome 2A corresponds 2NvS introgression from wild species, Aegilops ventricosa. found evidence strong selection over recent breeding history, being present 48% most cultivars panel. Collectively, we define architectures major diseases under field environments, provide resources exploit new improved resistance.

Язык: Английский

---

Progress and innovations of gene cloning in wheat and its close relatives

Theoretical and Applied Genetics, Год журнала: 2025, Номер 138(5)

Опубликована: Апрель 29, 2025

Abstract Key message Wheat and its close relatives have large complex genomes, making gene cloning difficult. Nevertheless, developments in genomics over the past decade made it more feasible. The genomes of cereals, especially bread wheat, always been a challenge for mapping cloning. recent advances led to significant progress this field. Currently, high-quality reference sequences are available major wheat species their relatives. New high-throughput genotyping platforms next-generation sequencing technologies combined with genome complexity reduction techniques mutagenesis opened new avenues In review, we provide comprehensive overview genes cloned so far discuss strategies used these genes. We highlight advantages drawbacks individual approaches show how particular genomic contributed A wide range resources increase number successful projects decade, demonstrating that is now feasible perform rapid agronomically important genes, even as wheat.

Язык: Английский

---