Apple whole genome sequences: recent advances and new prospects

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: April 5, 2019

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) apple (Malus domestica). This WGS, v1.0, valuable as initial reference information, fine mapping, gene discovery, variant and tool development. A new, high quality GDDH13 v1.1, released in 2017 now serves apple. Over past decade, these WGSs have had an enormous impact on our understanding biological functioning, trait physiology inheritance, leading to practical applications improving this highly valued crop. Causal identities phenotypes fundamental interest can today be discovered much more rapidly. Genome-wide polymorphisms at genetic resolution are screened efficiently over hundreds thousands individuals with new insights into relationships pedigrees. High-density maps constructed quantitative loci traits readily associated positional candidate genes and/or converted diagnostic tests breeders. We understand species, geographical, genomic origins domesticated precisely, well its relationship wild relatives. The WGS has turbo-charged application classical research steps crop improvement drives innovative methods achieve durable, environmentally sound, productive, consumer-desirable production. review includes examples basic breakthroughs challenges using WGSs. Recommendations "what's next" focus necessary upgrades data pool, use data, reach frontiers genomics-based

Language: Английский

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High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(6), P. e0210928 - e0210928

Published: June 27, 2019

High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation ploidy levels can lead to spurious marker-locus-trait associations incorrect origin assignment alleles individuals. High-throughput genotyping requires automated scoring, as manual inspection thousands scored loci too time-consuming. However, SNP scoring result that should be corrected ensure recorded are accurate thereby confidence downstream To enable quick identification large set, we have developed comprehensive workflow. This multiple-step workflow based on inheritance principles removal markers individuals do not follow these principles, demonstrated here apple, peach, sweet cherry. Genotypic was obtained pedigreed germplasm using 6-9K arrays each crop subset well-performing SNPs created ASSIsT. Use correct (and corrected) records readily identified violations simple the data, streamlined with FlexQTL software. Retained were grouped into haploblocks increase information content single reduce computational power needed Haploblock borders defined by recombination locations detected ancestral generations cultivars selections. Another round inheritance-checking conducted, haploblock (i.e., haplotypes). sets this collections representing U.S. breeding cherry evaluated within RosBREED project. These contain 3855, 4005, 1617 spread over 932, 103, 196 cherry, respectively. The highly curated phased haplotype sets, well raw iScan Crop Reference Sets available through Genome Database Rosaceae.

Language: Английский

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Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

PLANT PHYSIOLOGY, Journal Year: 2019, Volume and Issue: 182(2), P. 992 - 1006

Published: Nov. 26, 2019

Malate accumulation in the vacuole largely determines apple (Malus domestica) fruit acidity, and low acidity is strongly associated with truncation of Ma1, an ortholog ALUMINUM-ACTIVATED MALATE TRANSPORTER9 (ALMT9) Arabidopsis (Arabidopsis thaliana). A mutation at base 1,455 open reading frame Ma1 leads to a premature stop codon that truncates protein by 84 amino acids its C-terminal end. Here, we report both full-length protein, naturally occurring truncated ma1, localize tonoplast; when expressed Xenopus laevis oocytes Nicotiana benthamiana cells, mediates malate-dependent inward-rectifying current, whereas ma1-mediated transmembrane current much weaker, indicating ma1 has significantly lower malate transport activity than Ma1. RNA interference suppression expression 'McIntosh' leaves, 'Empire' fruit, 'Orin' calli results significant decrease level. Genotyping phenotyping 186 accessions from diverse genetic background 17 Malus species combined functional analyses described above indicate plays key role determining genetically responsible for apple. Furthermore, identified domain conserved all tonoplast-localized ALMTs essential function; truncations into this activity. We conclude reduces function removing domain, leading

Language: Английский

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Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus × domestica Borkh.) using the OpenArray® platform

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: Jan. 14, 2019

Genome mapping has promised much to tree fruit breeding during the last 10 years. Nevertheless, one of greatest challenges remaining geneticists is translation trait loci and whole genome sequences into diagnostic genetic markers that are efficient cost-effective for use by breeders, who must select genetically optimal parents subsequently superior individuals among their progeny. To take this translational step, we designed apple International RosBREED SNP Consortium OpenArray v1.0 (IRSCOA v1.0) assay using a set 128 single nucleotide polymorphisms (SNPs) linked quality pest disease resistance loci. The Thermo Fisher Scientific OpenArray® technology enables multiplexed screening real-time PCR instrument with fluorescent probe-based Taqman® assays. We validated IRSCOA multi-trait 240 phenotyped from Plant & Food Research cultivar programme. This comprised commercial heritage cultivars, elite selections, families segregating traits importance breeders. In total, 33 were in marker-assisted selection (MAS) scab resistances Rvi2/Vh2, Rvi4/Vh4, Rvi6/Vf, fire blight MR5/RLP1, powdery mildew Pl2, firmness, skin colour, flavour intensity, acidity. availability trait-associated markers, which can be used individually on multiple genotyping platforms available various programmes or re-designed flanking sequences, represents large genetics step genomics crop improvement apple.

Language: Английский

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Genetic architecture and genomic predictive ability of apple quantitative traits across environments

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Abstract Implementation of genomic tools is desirable to increase the efficiency apple breeding. Recently, multi-environment reference population (apple REFPOP) proved useful for rediscovering loci, estimating predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using REFPOP, although may be valuable when dissecting genetic architecture reporting abilities additional key in Here we show contrasting 30 quantitative across up six European locations REFPOP. A total 59 stable 277 location-specific associations found GWAS, 69.2% which are novel compared with 41 reviewed publications. Average 0.18–0.88 estimated main-effect univariate, multivariate, multivariate models. The G E accounted 24% phenotypic variability. This most comprehensive study terms trait-environment combinations provided knowledge trait biology prediction models that can readily applied marker-assisted or selection, thus facilitating increased breeding efficiency.

Language: Английский

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Effect of Genetics and Climate on Apple Sugars and Organic Acids Profiles

Agronomy, Journal Year: 2022, Volume and Issue: 12(4), P. 827 - 827

Published: March 29, 2022

Apple is widely cultivated in temperate regions. The beneficial properties of apple for preventing several illnesses are known. Nevertheless, qualitative variables such as sweetness or sourness may influence consumer satisfaction; they critical factors fruit consumption and essential plant breeding. In the present work, 155 accessions were assessed during five consecutive years (2014–2018). Four individual sugars seven organic acids analysed by HPLC. A mixed-effects model was fitted with years’ climatic features independent variables. cluster analysis applied on coefficients. groups considered optimum. Genetics seemed to have strongest effect showed clear differences between accession groups, while climate effects strong only certain compounds had a more horizontal behaviour equally affecting different groups. fact, non-Spanish cultivars tended concentrate, autochthone much wider spread. Individual concentrations correlated negatively precipitation positively temperature range solar radiation all geographic region where orchard grown thus very important resulting metabolites profiles. Moreover, genetics would also play decisive role highlighted analysis.

Language: Английский

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Comparative analysis of antioxidant activity and capacity in apple varieties: Insights from stopped flow DPPH• kinetics, mass spectrometry and electrochemistry

Food Bioscience, Journal Year: 2024, Volume and Issue: 58, P. 103729 - 103729

Published: Feb. 7, 2024

The aim of this research was to investigate the antioxidant kinetics different apple varieties, a red-flesh variety ('R201'), non-browning ('Majda'), and 'Golden Delicious'. Kinetic approaches for activity provide more detailed information than conventional assays by examining both quantity velocity active molecules in their reaction with radicals. In study, DPPH• stopped flow method applied study capacity three apples allowing determination rates. results show that 'R201' not significantly from Instead, 20 times higher others according kinetic approach, despite having lowest phenolic content. To further understand reactivity, were identified using HPLC-HRMS/MS coupled coulometric array detector, which validated kinetics. This analysis also found differences profile attributed enhanced 'Majda' its high content ascorbic acid. Overall, highlights behavior primarily depends on antioxidants rather amount compounds.

Language: Английский

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An insertion in the promoter of a malate dehydrogenase gene regulates malic acid content in apple fruit

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(1), P. 432 - 445

Published: May 24, 2024

Abstract Malic acid is an important flavor determinant in apple (Malus × domestica Borkh.) fruit. One known variation controlling malic the A/G single nucleotide polymorphism aluminum-activated malate transporter gene (MdMa1). Nevertheless, there are still differences content varieties with same Ma1 genotype (Ma1/Ma1 homozygous), such as ‘Honeycrisp’ (high content) and ‘Qinguan’ (low content), indicating that other loci may influence fruit acidity. Here, F1 (Filial 1) hybrid generation of was used to analyze quantitative trait for content. A major locus (Ma7) identified on chromosome 13. Within this locus, a dehydrogenase gene, MDH1 (MdMa7), best candidate further study. Subcellular localization suggested MdMa7 encodes cytosolic protein. Overexpression RNA interference increased decreased content, respectively. An insertion/deletion (indel) promoter found affect expression both hybrids cultivated varieties. The insertion deletion genotypes were designated MA7 ma7, transcription factor MdbHLH74 stimulate but not ma7 genotype. Transient transformation showed affected ‘Gala’ (MA7/MA7) ‘Fuji’ (ma7/ma7). Our results indicated genetic (MDH1) alters binding ability MdbHLH74, which fruit, especially Ma1/Ma1 homozygous accessions.

Language: Английский

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RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

Horticulture Research, Journal Year: 2020, Volume and Issue: 7(1)

Published: Nov. 1, 2020

Abstract The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized utilization of genomics, genetics, breeding develop new cultivars exhibiting both disease resistance superior horticultural quality. However, rosaceous breeders lacked certain knowledge tools fully implement DNA-informed breeding—a “chasm” existed between existing genomics genetic information application this in breeding. RosBREED project (“Ros” signifying a community initiative, “BREED”, indicating core focus on programs), addressed challenge through comprehensive coordinated 10-year effort funded by USDA-NIFA Specialty Crop Research Initiative. was designed enable routine modern genetics technologies programs, thereby enhancing their efficiency effectiveness delivering with producer-required resistances market-essential This review presents synopsis approach, deliverables, impacts RosBREED, highlighting synergistic global collaborations future needs. Enabling developed are described, including genome-wide scanning platforms DNA diagnostic tests. Examples use participants presented for all stages, pre-breeding resistance, parental seedling selection, elite selection advancement. chasm now bridged, accelerating improvement.

Language: Английский

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Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

BMC Genomics, Journal Year: 2020, Volume and Issue: 21(1)

Published: July 29, 2020

Fruit quality traits have a significant effect on consumer acceptance and subsequently peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit is essential for industry to improve increase Pedigree-based analysis across multiple pedigrees can identify genomic basis complex direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions improves selection efficiency and, subsequently, saves resources time.

Language: Английский

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