The genomic route to tomato breeding: Past, present, and future

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 195(4), С. 2500 - 2514

Опубликована: Апрель 30, 2024

Over the past 10,000 years, tomato species have undergone both unintentional and intentional selection to enhance their favorable traits for human consumption manufacturing. These processes significantly influenced genomes of played a critical role in improving varieties. In this review, we summarize recent advances genome sequencing, explore impact human-driven selection, recapitulate key genes associated with important agronomic breeding. We provide several examples genomics-guided breeding highlight potential resources facilitating improvement. Furthermore, elaborate progress strategies through design present how such efforts can help future enhancements align demands sustainability evolving societies.

Язык: Английский

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Application of CRISPR/Cas9 in the Improvement of Industrially Important Crops

Опубликована: Янв. 1, 2025

Язык: Английский

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Genome-wide association mapping and genomic prediction analyses reveal the genetic architecture of grain yield and agronomic traits under drought and optimum conditions in maize

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Фев. 1, 2025

Drought is a major abiotic stress in sub-Saharan Africa, impacting maize growth and development leading to severe yield loss. tolerance complex trait regulated by multiple genes, making direct grain selection ineffective. To dissect the genetic architecture of flowering traits under drought stress, genome-wide association study (GWAS) was conducted on panel 236 lines testcrossed evaluated managed optimal growing conditions environments using seven multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO, FARMCPU) from mrMLM GAPIT R packages. Genomic prediction with RR-BLUP model applied BLUEs across locations optimum conditions. A total 172 stable reliable quantitative nucleotides (QTNs) were identified, which 77 are associated GY, AD, SD, ASI, PH, EH, EPO EPP 95 linked Among these QTNs, 17 QTNs explained over 10% phenotypic variation (R2 ≥ 10%). Furthermore, 43 candidate genes discovered annotated. Two Zm00001eb041070 closely near peak QTN, qGY_DS1.1 (S1_216149215) Zm00001eb364110 related anthesis-silking interval qASI_DS8.2 (S8_167256316) encoding AP2-EREBP transcription factor 60 TCP-transcription 20, respectively stress. Haplo-pheno analysis identified superior haplotypes for higher revealed moderate high accuracies The carrying can be used as potential donors improving Integration genomic results leads not only an increase accuracy but also validate function well accumulation favorable alleles minor effects elite breeding lines. This provides valuable insight into secondary

Язык: Английский

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Two decades of association mapping: Insights on disease resistance in major crops

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Дек. 6, 2022

Climate change across the globe has an impact on occurrence, prevalence, and severity of plant diseases. About 30% yield losses in major crops are due to diseases; emerging diseases likely worsen sustainable production coming years. Plant have led increased hunger mass migration human populations past, thus a serious threat global food security. Equipping modern varieties/hybrids with enhanced genetic resistance is most economic, environmentally friendly solution. geneticists done tremendous work identifying stable primary genepools many times other than breed resistant varieties different crops. Over last two decades, availability crop pathogen genomes advances next generation sequencing technologies improved our understanding trait genetics using approaches. Genome-wide association studies been effectively used identify candidate genes map loci associated plants. In this review, we highlight successful examples for discovery important addition, developments studies, statistical models bioinformatic tools that improve power, resolution efficiency marker-trait associations. Overall review provides comprehensive insights into decades GWAS discusses challenges opportunities research area breeding varieties.

Язык: Английский

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Genome-wide association mapping for component traits of drought and heat tolerance in wheat

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Авг. 16, 2022

Identification of marker trait association is a prerequisite for marker-assisted breeding. To find markers linked with traits under heat and drought stress in bread wheat (Triticum aestivum L.), we performed genome-wide study (GWAS). GWAS mapping panel used this consists advanced breeding lines from the IARI programme produced by pairwise complex crosses. Phenotyping was done at multi locations namely New Delhi, Karnal, Indore, Jharkhand Pune augmented-RCBD design different moisture regimes, timely sown irrigated (IR), restricted (RI) late (LS) conditions. Yield its component traits, viz., Days to Heading (DH), Maturity (DM), Normalized Difference Vegetation Index (NDVI), Chlorophyll Content (SPAD), Canopy temperature (CT), Plant Height (PH), Thousand grain weight (TGW), Grain per spike (GWPS), Plot (PLTY) Biomass (BMS) were phenotyped. Analysis variance descriptive statistics revealed significant differences among studied traits. Genotyping using 35k SNP Wheat Breeder's Array. Population structure diversity analysis filtered 10,546 two subpopulations sufficient diversity. A large whole genome LD block size 7.15 MB obtained half decay value. Genome-wide search identified 57 unique associated various across locations. Twenty-three be stable, them nine pleiotropic also identified. In silico against IWGSC ref presence majority SNPs or near gene coding region. These can transfer genes/QTLs after validation develop climate-resilient cultivars.

Язык: Английский

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A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin

The Plant Journal, Год журнала: 2023, Номер 116(4), С. 1152 - 1171

Опубликована: Июнь 7, 2023

Legumes represent an important component of human and livestock diets; they are rich in macro- micronutrients such as proteins, dietary fibers polyunsaturated fatty acids. Whilst several health-promoting anti-nutritional properties have been associated with grain content, in-depth metabolomics characterization major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) liquid (LC-MS) to assess the metabolic diversity five commonly grown Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) pearl mutabilis), at tissue level. We were able detect quantify over 3400 metabolites covering nutritional compounds. Specifically, atlas includes 224 derivatized metabolites, 2283 specialized 923 lipids. The data generated here will serve community a basis for future integration metabolomics-assisted crop breeding facilitate metabolite-based genome-wide association studies dissect genetic biochemical bases metabolism species.

Язык: Английский

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Adapting crops for climate change: regaining lost abiotic stress tolerance in crops

Frontiers in Science, Год журнала: 2024, Номер 2

Опубликована: Дек. 5, 2024

It is often stated that agricultural outputs need to increase substantially meet the demands for more food posed by a growing population. However, when accounting climate change, we argue current projected increases are unrealistic and realistic goal would be maintain yields per area of production. This will require breeding crops with increased tolerance abiotic stresses such as drought, salinity, waterlogging, high temperatures. can accomplished in one two ways: introducing stress genes into present high-yielding or increasing already tolerant orphan and/or wild plants. We first strategy easing restrictions on use gene editing technologies making substantial improvements cell-based phenotyping identify available pool crop its relatives. The success second depend number domestication selected order obtain comparable present-day cultivars. still too early conclude which strategies, rewilding (bringing lost from ancestors back domesticated crops) de novo (domesticating resilient plants underutilized directly), most effective future sustainable agriculture. given importance issue, some rapid action needs taken.

Язык: Английский

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Unveiling the genetic basis of Fusarium wilt resistance in chickpea using GWAS analysis and characterization of candidate genes

Frontiers in Genetics, Год журнала: 2024, Номер 14

Опубликована: Янв. 19, 2024

Introduction: Chickpea is a legume crop that thrives in regions with semi-arid or temperate climates. Its seeds are an excellent source of proteins, carbohydrates, and minerals, especially high-quality proteins. cultivation faces several challenges including Fusarium wilt (FW), major fungal disease significantly reduces productivity. Methods: In this study, Genome-wide Association Analysis (GWAS) was conducted to identify multiple genomic loci associated FW resistance chickpea. We comprehensive evaluation 180 chickpea genotypes for across three distinct locations (Ethiopia, Tunisia, Lebanon) during the 2-year span from 2015 2016. Disease infection measurements were recorded, incidence each genotype calculated. employed set 11,979 single nucleotide polymorphisms (SNPs) markers distributed entire genome SNP genotyping. Population structure analysis determine genetic genotypes. Results Discussion: The population unveiled analyzed germplasm could be categorized into four sub-populations. Notably, these sub-populations displayed diverse geographic origins. GWAS identified 11 SNPs resistance, dispersed genome. Certain consistent trials, while others specific particular environments. Chromosome CA2 harbored five markers, CA5 featured two, CA4, CA6, CA7, CA8 had one representative marker. Four demonstrated association consistently observed minimum These included SNP5826041, SNP5825086, SNP11063413, SNP5825195, which located CaFeSOD, CaS13like, CaNTAQ1, CaAARS genes, respectively. Further investigations gain insights functions genes their role resistance. This progress holds promise reducing negative impact on production.

Язык: Английский

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Salinity tolerance mechanisms and their breeding implications

Journal of Genetic Engineering and Biotechnology, Год журнала: 2021, Номер 19(1), С. 173 - 173

Опубликована: Ноя. 9, 2021

The era of first green revolution brought about by the application chemical fertilizers surely led to explosion food grains, but left behind notable problem salinity. Continuous these coupled with fertilizer-responsive crops make country self-reliant, continuous deposition altered water potential and thus negatively affecting proper plant functioning from germination seed setting.

Язык: Английский

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Pathways to de novo domestication of crop wild relatives

PLANT PHYSIOLOGY, Год журнала: 2021, Номер 188(4), С. 1746 - 1756

Опубликована: Ноя. 24, 2021

Growing knowledge about crop domestication, combined with increasingly powerful gene-editing toolkits, sets the stage for continual domestication of wild relatives and other lesser-known plant species.

Язык: Английский

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