Horticulture Research, Год журнала: 2024, Номер 11(4)
Опубликована: Апрель 1, 2024
, an extremely rare population of apricots, originated in warm South-East China and is excellent material for genetic breeding. However, most apricots two related species (
Язык: Английский
Genes, Год журнала: 2023, Номер 14(7), С. 1484 - 1484
Опубликована: Июль 21, 2023
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The is posing increased demand for food, thereby pushing an acceleration in agricultural production. Furthermore, anthropogenic activities have resulted environmental pollution such as water soil degradation well alterations the composition concentration of gases. These affecting not only biodiversity loss but also physio-biochemical processes crop plants, resulting a stress-induced decline yield. To overcome problems ensure supply food material, consistent efforts being made develop strategies techniques increase yield enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication initially remained dependent on phenotype-based selection improvement. But it has grown through cytological biochemical methods, newer contemporary methods based DNA-marker-based help agronomically useful traits. now supported by high-end molecular biology tools like PCR, high-throughput genotyping phenotyping, data from morpho-physiology, statistical tools, bioinformatics, machine learning. After establishing its worth animal breeding, genomic (GS), improved variant marker-assisted (MAS), way into crop-breeding programs powerful tool. novel innovative marker-based models genetic evaluation, GS makes use markers. can amend complex traits shorten period, making advantageous over pedigree (MAS). It reduces time resources required plant while allowing gain attributes. been taken new heights integrating advanced technologies speed learning, environmental/weather further harness potential, approach known integrated (IGS). This review highlights IGS strategies, procedures, approaches, associated emerging issues, with special emphasis cereal crops. In this domain, highlight potential cutting-edge innovation climate-smart crops endure abiotic stresses motive keeping production quality at par global demand.
Язык: Английский
Процитировано
57
Genome biology, Год журнала: 2023, Номер 24(1)
Опубликована: Янв. 26, 2023
Abstract Background A pangenome aims to capture the complete genetic diversity within a species and reduce bias in analysis inherent using single reference genome. However, current linear format of most plant pangenomes limits presentation position information for novel sequences. Graph have been developed overcome this limitation. bioinformatics tools graph genomes are lacking. Results To problem, we develop strategy construction downstream pipeline (PSVCP) that captures variants’ while maintaining linearized layout. Using PSVCP, construct high-quality rice 12 representative analyze an international panel with 413 diverse accessions as reference. We show PSVCP successfully identifies causal structural variations grain weight height. Our results provide insights into population structure genomic diversity. characterize new locus ( qPH8-1 ) associated height on chromosome 8 undetected by SNP-based genome-wide association study (GWAS). Conclusions demonstrate constructed our combined presence absence variation-based GWAS can additional power analysis. The genome sequence variants data valuable resources genomics research improvement future.
Язык: Английский
Процитировано
53
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Янв. 2, 2025
Global food security depends heavily on a few staple crops, while orphan despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes later pangenomes. Recent advances DNA sequencing enabled pangenome construction for several offering more comprehensive understanding genetic diversity. Orphan crop research has now entered pangenomics era applying these pangenomes with advanced selection methods genome editing technologies can transform neglected species into broader agricultural significance. A reference is not enough to harness full variation species. Here, authors review principles, applications improvement, discuss possible ways support pangenomics-driven molecular breeding.
Язык: Английский
Процитировано
2
Nature Genetics, Год журнала: 2025, Номер unknown
Опубликована: Фев. 3, 2025
Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed barley using 20 inbred genotypes representing domesticated by generating analyzing short- long-read RNA-sequencing datasets tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific (RTDs) integrated these into linear pan-genome framework to create pan-RTD, allowing categorization as core, shell or cloud. Focusing on core (expressed all genotypes), observed significant abundance variation among tissues between driven partly RNA processing, gene copy number, structural rearrangements conservation promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations frequent functional diversification. complement pan-transcriptome, comprehensive cultivar (cv.) Morex gene-expression atlas illustrate how combined can be used guide biological inquiry.
Язык: Английский
Процитировано
2
BMC Biology, Год журнала: 2024, Номер 22(1)
Опубликована: Апрель 23, 2024
Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, comprehensive genetic pool encompassing all variations within species, serves as an invaluable tool, unaffected by confounding factors intraspecific diversity. This allows for more nuanced exploration TE evolution.
Язык: Английский
Процитировано
8
Genome Biology and Evolution, Год журнала: 2024, Номер 16(4)
Опубликована: Апрель 1, 2024
Abstract A pangenome captures the genomic diversity for a species, derived from collection of genetic sequences diverse populations. Advances in sequencing technologies have given rise to three primary methods construction and analysis: de novo assembly comparison, reference genome-based iterative assembly, graph-based construction. Each method presents advantages challenges processing varying amounts structures DNA data. With emergence high-quality genome assemblies advanced bioinformatic tools, is emerging as an exploring biological functional implications variations.
Язык: Английский
Процитировано
8
Horticultural Plant Journal, Год журнала: 2024, Номер 10(6), С. 1274 - 1290
Опубликована: Авг. 14, 2024
The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled annotated genomes of maternal (PsbM) paternal (PsbF) lines hybrid 'Yuluxiang' constructed pangenome 1.15 Gb by combining these two with five previously published representing cultivated wild germplasm. Using pangenome, identified 21 224 gene PAVs (Presence-absence variation) 1 158 812 SNPs (Single Nucleotide Polymorphism) in non-reference genome that were absent PsbM reference genome. Compared SNP markers, PAV-based analysis provides additional insights into population structure. In addition, some genes associated fruit quality traits have differential occurrence frequencies expression between Asian European populations. Moreover, our revealed a mutated an insertion promoter region PsbMGH3.1 potentially enhance sepal shedding 'Xuehuali' which vital quality. may play role IAA pathway, contributing to distinct low-auxin phenotype observed plants heterologously overexpressing this gene. This research helps capture populations genomic resources accelerating breeding.
Язык: Английский
Процитировано
8
Plant Biotechnology Journal, Год журнала: 2025, Номер unknown
Опубликована: Янв. 29, 2025
Summary Improving cold tolerance at the flowering stage (CTF) in rice is crucial for minimising yield loss, making identification and application of cold‐tolerant genes QTLs imperative effective molecular breeding. The long lead time, dependence on treatment conditions, inherent complexity trait make studying genetic basis CTF challenging. To date, fine‐mapping or cloning specific to has not yet been achieved. In this study, single segment substitution lines (SSSLs) were constructed using HJX74 as recipient IR58025B, known good CTF, donor. This approach led two QTLs, qCTF3 qCTF6 , rice. promising breeding potential. Further, we identified causal gene CTF1 underlying through map‐based . which encodes a conserved putative protein, SNPs within its coding sequence that influence Additionally, variations promoter also contributes CTF. Thirteen variant sites four SSSLs are consistent with IR58025B. Moreover, analysed 307 accessions characterise haplotypes based 13 variation sites, identifying five distinct haplotypes. selection evolutionary analysis indicate haplotype newly generated mutation undergone japonica during domestication. study only provides novel favourable but highlights potential advancing
Язык: Английский
Процитировано
1
Plant Biotechnology Journal, Год журнала: 2023, Номер 22(3), С. 544 - 554
Опубликована: Ноя. 14, 2023
Summary Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting expression recombination rates. However, compared with other variations, their roles in functional biology crop improvement remain largely unexplored. In this review, we highlight technological methodological advancements that have allowed comprehensive understanding inversion variants through the pangenome framework machine learning algorithms. Genome editing is an efficient method for inducing or reversing mutations plants, providing effective mechanism to modify local Given potential inversions breeding, anticipate increasing attention on from scientific community future research breeding applications.
Язык: Английский
Процитировано
14
Rice, Год журнала: 2023, Номер 16(1)
Опубликована: Янв. 17, 2023
Grain shape is a key trait in rice breeding. Although many QTLs and genes of grain have been identified, how different combinations alleles these affect largely unknown. It important to understand the effects gene for breeding by design. In present study, we performed genetic dissection shapes Guangdong Simiao varieties, popular kind South China, identify effective their combination We selected two hundred nineteen indica accessions with diverse fifty-two varieties long slender genome-wide selection analysis. The results showed that four (GS3, GS5, GW5 GL7) twenty fall into regions varieties. Allele analysis frequency distribution GS3allele3 GW5allele2 accounted 96.2%, GL7allele2 GS5allele2 76.9% 74.5% respectively. Further allelic 30 were identified whole panel, 28 found international 6 There mainly three (combinations 17, 18 19) 19 (GS3allele3 + GS5allele2) having highest percentage (51.9%). All carried GW5allele2, while 17 (GL7allele1) (GL7allele2) significant differences both length length/width ratio due GL7 alleles. Pedigree Guang8B, maintainer first released male sterile line Guang8A, parent lines Guang8B GS5allele2, allele differed, resulting size. suggest specific GS3, are used improvement. Combination predominant Our current study dissect genetics will facilitate molecular
Язык: Английский
Процитировано
13