Aquaculture, Год журнала: 2025, Номер 599, С. 742125 - 742125
Опубликована: Янв. 7, 2025
Язык: Английский
Molecular Plant, Год журнала: 2022, Номер 15(11), С. 1664 - 1695
Опубликована: Сен. 7, 2022
The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, incorporation molecular marker genotypes. However, performance or phenotype (P) is determined the combined effects genotype (G), envirotype (E), and environment interaction (GEI). Phenotypes can be predicted precisely training a model data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, enviromics across time space). Integration 3D information profiles (G-P-E), each with multidimensionality, provides both tremendous opportunities great challenges. Here, we review innovative technologies breeding. We then evaluate multidimensional that integrated strategy, particularly envirotypic data, which have largely been neglected in collection are nearly untouched construction. propose smart scheme, genomic-enviromic prediction (iGEP), as an extension genomic prediction, multiomics information, big technology, artificial intelligence (mainly focused machine deep learning). discuss how to implement iGEP, models, environmental indices, factorial structure cross-species prediction. A strategy proposed prediction-based crop redesign at macro (individual, population, species) micro (gene, metabolism, network) scales. Finally, provide perspectives translating into gain through integrative platforms open-source initiatives. call coordinated efforts institutional partnerships, technological support.
Язык: Английский
Процитировано
164
Trends in Plant Science, Год журнала: 2022, Номер 28(2), С. 199 - 210
Опубликована: Сен. 21, 2022
Язык: Английский
Процитировано
82
Frontiers in Public Health, Год журнала: 2021, Номер 9
Опубликована: Дек. 21, 2021
Radiation mutation breeding has been used for nearly 100 years and successfully improved crops by increasing genetic variation. Global food production is facing a series of challenges, such as rapid population growth, environmental pollution climate change. How to feed the world's enormous human poses great challenges breeders. Although advanced technologies, gene editing, have provided effective ways breed varieties, editing single or multiple specific target genes, enhancing germplasm diversity through still indispensable in modern classical radiation because it more likely produce random mutations whole genome. In this short review, current status radiation, accelerated particle space discussed, molecular mechanisms radiation-induced are demonstrated. This review also looks into future development breeding, hoping deepen our understanding provide new vitality further breeding.
Язык: Английский
Процитировано
83
Theoretical and Applied Genetics, Год журнала: 2024, Номер 137(8)
Опубликована: Июль 9, 2024
Rust diseases, including leaf rust, stripe/yellow and stem significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding deployment of cultivars with genetic resistance is the most effective sustainable approach to control these diseases. The toolkit for breeders select rust has rapidly expanded a multitude loci identified using latest advances in genomics, mapping cloning strategies. goal this review was establish genome atlas that provides comprehensive summary reported associated resistance. Our mapped quantitative trait (QTL) characterised genes three rusts from 170 publications over past two decades. A total 920 QTL or were positioned across 21 chromosomes based on reference (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple suggesting they could have pleiotropic effects more We discuss range strategies exploit wealth information efficiently utilise sources resistance, stack desirable develop enhanced disease.
Язык: Английский
Процитировано
13
Aquaculture, Год журнала: 2023, Номер 577, С. 739979 - 739979
Опубликована: Авг. 9, 2023
Язык: Английский
Процитировано
20
Animal Research and One Health, Год журнала: 2024, Номер 2(2), С. 204 - 216
Опубликована: Март 29, 2024
Abstract Large‐scale genotyping at a low cost is crucial for molecular breeding of livestock. In this study, the Cattle110K capture chip was developed, based on by target sequencing system. The panel included 112,180 single necleotide polymorphisms (SNPs), from potential functional regions screened genome‐wide associated BayesB, expression quantitative trait loci‐mapping, ATAC‐seq, and reported markers. All SNPs were distributed evenly cattle genome, with more than 99% markers having minor allele frequency greater 0.05. Assessment results indicated that total 1.2 M high‐quality identified in 110 K regions, averaging approximately 10 per sequence. genotype consistency repetitive samples using liquid 99.21% while concordance between Illumina BovineHD BeadChip averaged 98.17%. A significant association signal slaughter weight carcass length 37.3–41.5 Mb chromosome 6, pinpointing NCAPG‐LCORL locus. This locus has previously been meat traits cattle. Additionally, novel candidate around 3.4 13 73.5 8, significantly correlated hip height marbling score, respectively. We compared accuracy genomic estimated values chip. demonstrated had comparable ability prediction to BeadChip. Advances cost‐effective are expected accelerate genetic progress coming years.
Язык: Английский
Процитировано
7
BMC Genomic Data, Год журнала: 2024, Номер 25(1)
Опубликована: Май 7, 2024
China has thousands years of goat breeding and abundant genetic resources. Additionally, the Hainan black is one high-quality local breeds in China. In order to conserve germplasm resources goat, facilitate its improvement further protect diversity goats, it urgent develop a single nucleotide polymorphism (SNP) chip for goat.
Язык: Английский
Процитировано
7
Frontiers in Plant Science, Год журнала: 2024, Номер 15
Опубликована: Июнь 25, 2024
Introduction Pepper ( Capsicum spp.) is a vegetable that cultivated globally and has undergone extensive domestication, leading to significant diversification in its agronomic traits. With the advancement of genomics pepper reduction sequencing costs, high-throughput detection single nucleotide polymorphisms (SNPs) small insertions-deletions (indels) become increasingly critical for analyzing germplasms improving breeding programs. As result, there pressing need cost-effective, high-throughput, versatile technique suitable both foreground background selection breeding. Methods In present study, Python-based web scraping scripts were utilized systematically extract data from published literatures relevant sequence databases focusing on genomes. Subsequent extraction, SNPs indels meticulously identified filtered. This process culminated delineation core polymorphic sites, which instrumental development specific probes. Following this, comprehensive phenotypic genotypic analyses conducted diverse collection 420 germplasms. Concurrently, genome-wide association study (GWAS) was elucidate genetic determinants helical fruit shape peppers. Results this 45K Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip developed GenoBaits platform. composed 45,389 probes, 42,535 are derived sites (CPS) landscape, while 2,854 associated with traits, spanning across 43 The CPS probes spaced at an average interval 68 Kb. We have assessed performance germplasms, successful capture target DNA fragments by 45,387 Furthermore, probe ratio surpassed 70% 410 tested. Using chip, we efficiently genotyped 273 spiciness levels elucidated relationships among Our results allowed precise clustering sister lines C. chinense addition, through GWAS shape, three quantitative trait loci (QTLs): heli2.1, heli11.1, heli11.2. Within heli11.1 QTL, encoding tubulin alpha chain identified, suggesting potential role growth pattern fruits. Discussion summary, GBTS offers robust promising tool advancing research into germplasm new varieties.
Язык: Английский
Процитировано
7
Journal of Integrative Plant Biology, Год журнала: 2024, Номер unknown
Опубликована: Окт. 28, 2024
ABSTRACT The past decade has witnessed rapid developments in gene discovery, biological big data (BBD), artificial intelligence (AI)‐aided technologies, and molecular breeding. These advancements are expected to accelerate crop breeding under the pressure of increasing demands for food. Here, we first summarize current methods discuss need new ways support efforts. Then, review how combine BBD AI technologies genetic dissection, exploring functional genes, predicting regulatory elements domains, phenotypic prediction. Finally, propose concept intelligent precision design (IPDB) driven by technology offer ideas about implement IPDB. We hope that IPDB will enhance predictability, efficiency, cost compared with technologies. As an example IPDB, explore possibilities offered CropGPT, which combines techniques, bioinformatics, art from breeders, presents open, shareable, cooperative system. provides integrated services communication platforms biologists, bioinformatics experts, germplasm resource specialists, dealers, farmers, should be well suited future
Язык: Английский
Процитировано
7
Scientific Reports, Год журнала: 2025, Номер 15(1)
Опубликована: Янв. 21, 2025
Abstract White lupin ( Lupinus albus L.) is an ancient grain legume that still undergoing improvement of domestication traits, including vernalization-responsiveness, providing frost tolerance and preventing winter flowering in autumn-sowing agriculture, vernalization-independence, conferring drought escape by rapid spring-sowing. A recent genome-wide association study highlighted several loci significantly associated with the most contrasting phenotypes, deletions promoter FLOWERING LOCUS T homolog, LalbFTc1 , some DArT-seq/silicoDArT loci. The present aimed to develop validate a versatile PCR marker array enabling molecular selection spring- winter-type white ecotypes. Candidate DArT-seq silicoDArT were transformed into cleaved amplified polymorphic sequence (CAPS) or derived CAPS markers. Developed markers, together those previously published for INDELs quantitative trait from linkage maps, implemented screening germplasm panel subjected 2-year phenotyping phenology traits. Three DArT-seq, two seven INDEL markers positively validated, constituting convenient PCR-based assay accurate reselection towards early thermoneutrality late as well tracking high genetic phenotypic diversity within landraces, revealed study.
Язык: Английский
Процитировано
1