Genomic selection in plant breeding: Key factors shaping two decades of progress

Molecular Plant, Год журнала: 2024, Номер 17(4), С. 552 - 578

Опубликована: Март 12, 2024

Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in past two decades, effectively accelerating genetic gains plant breeding.This article provides a holistic overview key factors that have influenced GP breeding during this period.We delved into pivotal roles training population size and diversity, their relationship with population, determining accuracy.Special emphasis was placed on optimizing size.We explored its benefits associated diminishing returns beyond an optimum size.This done while considering balance between resource allocation maximizing accuracy through current optimization algorithms.The density distribution single-nucleotide polymorphisms, level linkage disequilibrium, complexity, trait heritability, statistical machine-learning methods, non-additive effects are other vital factors.Using wheat, maize, potato as examples, we summarize effect these for various traits.The search high GP-theoretically reaching one when using Pearson's correlation metric-is active research area yet far from optimal traits.We hypothesize ultra-high sizes genotypic phenotypic datasets, effective methods support omics approaches (transcriptomics, metabolomics proteomics) coupled deep-learning algorithms could overcome boundaries limitations achieve highest possible accuracy, making selection tool breeding.

Язык: Английский

---

Stability of grain zinc concentrations across lowland rice environments favors zinc biofortification breeding

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Фев. 13, 2024

Introduction One-third of the human population consumes insufficient zinc (Zn) to sustain a healthy life. Zn deficiency can be relieved by increasing concentration ([Zn]) in staple food crops through biofortification breeding. Rice is poor source Zn, and countries predominantly relying on rice without sufficient dietary diversification, such as Madagascar, priority. Methods Multi-environmental trials were performed Madagascar over two years, 2019 2020, screen total 28 genotypes including local imported germplasm. The conducted highlands Ankazomiriotra, Anjiro, Behenji Morovoay, location representative coastal ecosystem. Contributions genotype (G), environment (E), G E interactions (GEIs) investigated. Result grain [Zn] Malagasy varieties was similar internationally established baseline 18–20 μg/g for brown rice. While several breeding lines reached 50% our target set at +12 μg/g, only few met farmers’ appreciation criteria. Levels stable across E. effects accounted main fraction variation, 76% 83% variation year 1 2 trials, respectively, while GEI comparatively small, contributing 23% 9%. This contrasted with dominant yield. Our results indicate that tested contained alleviate malnutrition, developing new Zn-biofortified should therefore GGE analysis did not distinguish mega-environments [Zn], whereas least three existed yield, differentiated presence limiting environmental conditions responsiveness improved soil fertility. Discussion conclusion reveals seems under strong genetic control agro-climatic Madagascar. We could identify interesting potential donors program, among those BF156, relatively (AMMI stability value (ASV) = 0.89) reaching (>26 μg/g). selection general adaptation, would have rely multi-environment testing, centralized earlier generations.

Язык: Английский

---

Proof of concept and early development stage of market-oriented high iron and zinc rice expressing dicot ferritin and rice nicotianamine synthase genes

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Янв. 12, 2023

Abstract Micronutrient deficiencies such as iron (Fe), zinc (Zn), and vitamin A, constitute a severe global public health phenomenon. Over half of preschool children two-thirds nonpregnant women reproductive age worldwide have micronutrient deficiencies. Biofortification is cost-effective strategy that comprises meaningful sustainable means addressing this issue by delivering micronutrients through staple foods to populations with limited access diverse diets other nutritional interventions. Here, we report on the proof-of-concept early development stage collection biofortified rice events high density Fe Zn in polished grains been pursued further advance for product release. In total, eight constructs were developed specifically expressing dicot ferritins nicotianamine synthase 2 ( OsNAS2 ) gene under different combinations promoters. A large-scale transformation these Bangladesh Philippines commercial indica cultivars subsequent molecular screening confined field evaluations resulted identification pool ten concentrations up 11 μg g −1 37 , respectively. The latter has potential reduce prevalence inadequate intake childbearing 30% 50%, respectively, compared current prevalence. To our knowledge, first biotechnology public-sector adopts cycle phase-gated approach, routinely applied private sector.

Язык: Английский

---

Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica)

Theoretical and Applied Genetics, Год журнала: 2024, Номер 137(8)

Опубликована: Июль 17, 2024

Язык: Английский

---

Next Generation Nutrition: Genomic and Molecular Breeding Innovations for Iron and Zinc Biofortification in Rice

Rice Science, Год журнала: 2024, Номер 31(5), С. 526 - 544

Опубликована: Май 17, 2024

Global efforts to address malnutrition and hidden hunger, particularly prevalent in low- middle-income countries, have intensified, with a focus on enhancing the nutritional content of staple crops like rice. Despite serving as for over half world's population, rice falls short meeting daily requirements, especially iron (Fe) zinc (Zn). Genetic resources, such wild species specific varieties, offer promising avenues Fe Zn content. Additionally, advancements molecular breeding approaches identified key genes loci associated accumulation grains. This review explores genetic resources mechanisms underlying The functional genomics involved uptake, transport, distribution plants revealed OsFRO1, OsIRT1, OsNAS3. Similarly, uptake translocation, including OsZIP11 OsNRAMP1, been identified. Transgenic approaches, leveraging transporter gene families genome editing technologies, Moreover, strategies reducing phytic acid (PA) content, known inhibitor mineral bioavailability, explored, identification low-PA mutants natural variants. integration genomic information, whole-genome resequencing pan-genome analyses, provides valuable insights into basis micronutrient traits facilitates targeted efforts. Functional studies elucidated translocation Furthermore, transgenic techniques shown promise grains through manipulation genes. Overall, multi-omics holds significant addressing global hunger by quality rice, thereby contributing improved food security worldwide.

Язык: Английский

---

Digital tools and technologies used in food fortification: A scoping review

Annals of the New York Academy of Sciences, Год журнала: 2025, Номер unknown

Опубликована: Янв. 14, 2025

Abstract Food fortification (i.e., industrial and biofortification) increases the micronutrient content of foods to improve population nutrition. Implementing effective programs requires generation use data inform decision making. The digital tools technologies (DTTs) for such purposes in broader nutrition is growing; however, there limited consolidation those used fortification. This scoping review aimed identify describe DTTs programs. We searched peer‐reviewed gray literature conducted 17 stakeholder surveys. then mapped identified against value chains. Of 11,741 articles identified, 158 met inclusion criteria. From included surveys, 125 were across three categories: software tooling ( n = 58), information lifecycle 50), hardware infrastructure 17). Gaps processing, post‐harvest storage, aggregation, transport nodes chain, prioritization, translation/dissemination, decision‐making chain. have potential address challenges faced by stakeholders generate program making nutritional impact. Further work needed standardize terminology, relevant from other sectors, explore needs.

Язык: Английский

---

The Contribution of Zn Uptake and Grain Zn Loading Intensity to Achieving Zn Biofortification Breeding Targets in Rice

Journal of Plant Nutrition and Soil Science, Год журнала: 2025, Номер unknown

Опубликована: Апрель 27, 2025

ABSTRACT Background Increasing Zinc (Zn) concentrations in rice grains is targeted Zn‐biofortification breeding but most varieties have grain Zn far below targets. Aims High‐Zn donors been identified and our aim to investigate whether higher these were the result of superior uptake during reproductive stage, loading intensities or caused by an extended period. Methods Field experiments comparing two high‐Zn low‐Zn modern conducted over seasons Madagascar tissue content determined from heading maturity. Results between maturity was not limiting concentrations. Neither did studied genotypes differ significantly duration loading, which peaked 8–12 days after flowering strongly decreased thereafter, even donors. Instead, intensity filling differed with peak rates exceeding 60 ng day −1 compared 13–37 varieties. This high further evident when biomass compared. Donor IRIS‐9368 loaded up 40 mg 12–21 resulted a zinc harvest index 47.7% 26.1% for local variety X265 despite similar reproductive‐stage uptake. Conclusions We hypothesize that xylem‐to‐phloem transfer at upper nodes more efficient donor IRIS‐9368.

Язык: Английский

---

Genomic approaches for improving grain zinc and iron content in wheat

Frontiers in Genetics, Год журнала: 2022, Номер 13

Опубликована: Ноя. 8, 2022

More than three billion people worldwide suffer from iron deficiency associated anemia and an equal number zinc deficiency. These conditions are more prevalent in Sub-Saharan Africa South Asia. In developing countries, children under the age of five with stunted growth pregnant or lactating women were found to be at high risk deficiencies. Biofortification, defined as breeding develop varieties staple food crops whose grain contains higher levels micronutrients such zinc, one most promising, cost-effective sustainable ways improve health resource-poor households, particularly rural areas where families consume some part what they grow. Biofortification through conventional wheat, for iron, have made significant contributions, transferring important genes quantitative trait loci (QTLs) wild related species into cultivated wheat. Nonetheless, quantitative, genetically complex nature wheat limits progress breeding, making it difficult attain genetic gain both yield mineral concentrations. Wheat biofortification can achieved by enhancing uptake, source-to-sink translocation minerals their deposition grains, bioavailability minerals. A QTLs major minor effects those traits been detected wheat; introducing effective lines will increase New approaches achieve this include marker assisted selection genomic selection. Faster need combined simultaneously content lines.

Язык: Английский

---

New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(9), С. 4667 - 4667

Опубликована: Апрель 25, 2024

Lysine is an essential amino acid that cannot be synthesized in humans. Rice a global staple food for humans but has rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying content crucial to increase accumulation. In this study, five grain three leaf datasets 4,630,367 single nucleotide polymorphisms (SNPs) 387 rice accessions were used perform genome-wide association study (GWAS) by ten statistical models. A total 248 71 common QTNs associated with grain/leaf identified. The accuracy genomic selection/prediction RR-BLUP models was up 0.85, significant correlation between number favorable alleles per accession 0.71, which validated reliability additive effects these QTNs. Several key uncovered fine-tuning Additionally, 20 30 QTN-by-environment interactions (QEIs) detected grains/leaves. QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted gene-by-environment interaction identified grains. These findings suggested application multi-model GWAS facilitates better understanding accumulation rice. hold potential lysine-rich normal phenotype.

Язык: Английский

---

Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Март 22, 2023

Breeding staple crops with increased micronutrient concentration is a sustainable approach to address malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected agronomic (115) (41) traits, which higher in number but smaller effects compared single population analysis. The MC-QTL was able detect important viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , qGW6.1 can be used rice genomics assisted breeding. A major (qZn5.2 ) grain Zn has been on chromosome 5 that accounted 13% R2. In all, 26 clusters identified different chromosomes. qPH6.1 epistatically interacted qZn5.1 qGY6.2 . Most co-located functionally related candidate genes indicating the accuracy mapping. genomic region qZn5.2 putative such as OsZIP5, OsZIP9, LOC_OS05G40490 are involved uptake. These included polymorphic functional SNPs, their promoter regions enriched cis-regulatory elements plant growth development, biotic abiotic stress tolerance. Major effect utilized breeding biofortified varieties.

Язык: Английский

---