Prunus genetics and applications after de novo genome sequencing: achievements and prospects

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

Published: April 5, 2019

Prior to the availability of whole-genome sequences, our understanding structural and functional aspects Prunus tree genomes was limited mostly molecular genetic mapping important traits development EST resources. With public release peach genome others that followed, significant advances in knowledge underpinnings ensued. In this review, we highlight key achievements genetics breeding driven by these sequences. Within evolutionary contexts, summarize: (1) current status sequences; (2) preliminary ongoing work on sequence structure diversity genomes; (3) analyses evolution natural man-made selection; (4) provide insight into haploblocking as a means define genome-scale patterns can be leveraged for trait selection pedigree-based programs worldwide. Functionally, summarize recent leverages sequences identify characterize genes controlling 22 agronomically traits. These include phenology, fruit quality, allergens, disease resistance, architecture, self-incompatibility. Translationally, explore application sequence-based marker-assisted technologies other sequence-guided biotechnological approaches crop improvement. Finally, present publically available genomics data housed mainly Genome Database Rosaceae (GDR) its updated functionalities future bioinformatics-based inquiry.

Language: Английский

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High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

GigaScience, Journal Year: 2020, Volume and Issue: 9(5)

Published: May 1, 2020

Abstract Background The release of the first reference genome walnut (Juglans regia L.) enabled many achievements in characterization genetic and functional variation. However, it is highly fragmented, preventing integration genetic, transcriptomic, proteomic information to fully elucidate biological processes. Findings Here, we report new chromosome-scale assembly (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative previous genome, features an 84.4-fold increase N50 size, 16 chromosomal pseudomolecules assembled representing 95% its total length. Using full-length transcripts from single-molecule real-time sequencing, predicted 37,554 gene models, a mean length higher than annotations. Most protein-coding genes (90%) present both start stop codons, which represents significant improvement compared Chandler v1.0 (only 48%). We then tested potential impact chromosome-level on different areas research. By studying proteome changes occurring during male flower development, observed that virtual v2.0 presents fewer artifacts enabling identification pollen allergen walnut. Also, facilitates in-depth studies intraspecies diversity revealing previously undetected autozygous regions Chandler, likely resulting inbreeding, 195 genomic differentiated between Western Eastern cultivars. Conclusion Overall, will serve as valuable resource better understand explore biology.

Language: Английский

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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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The apple REFPOP—a reference population for genomics-assisted breeding in apple

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

Published: Nov. 1, 2020

Abstract Breeding of apple is a long-term and costly process due to the time space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic phenotypic information increase efficiency in programs, measurements phenotypes different environments can facilitate application approach under various climatic conditions. Here we present an reference population: REFPOP, large collection formed 534 genotypes planted six European countries, as unique tool accelerate breeding. The population consisted 269 accessions 265 progeny from 27 parental combinations, representing diversity cultivated current material, respectively. A high-density genome-wide dataset 303,239 SNPs was produced combined output two SNP arrays densities using marker imputation with accuracy 0.95. Based on genotypic data, linkage disequilibrium low structure weak. Two well-studied phenological traits horticultural importance were measured. We found marker–trait associations several previously identified regions maximum predictive abilities 0.57 0.75 floral emergence harvest date, With decreasing density, detection significant varied depending trait architecture. Regardless trait, 10,000 sufficed maximize prediction ability. confirm suitability REFPOP design genomics-assisted breeding, especially programs related germplasm, emphasize advantages coordinated multinational effort customizing methods genomics era.

Language: Английский

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Genome-wide analysis of the apple family 1 glycosyltransferases identified a flavonoid-modifying UGT, MdUGT83L3, which is targeted by MdMYB88 and contributes to stress adaptation

Plant Science, Journal Year: 2022, Volume and Issue: 321, P. 111314 - 111314

Published: May 13, 2022

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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Prospects for achieving durable disease resistance with elite fruit quality in apple breeding

Tree Genetics & Genomes, Journal Year: 2020, Volume and Issue: 16(1)

Published: Jan. 17, 2020

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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Genetic origin and climate determine fruit quality and antioxidant traits on apple (Malus x domestica Borkh)

Scientia Horticulturae, Journal Year: 2021, Volume and Issue: 285, P. 110142 - 110142

Published: April 10, 2021

Apples are highly appreciated in terms of flavor, nutritional and health-promoting compounds associated with a reduced risk to develop age-related chronic diseases. In this study, 155 accessions Malus x domestica Borkh from the apple germplasm collection, located at Experimental Station Aula Dei NE Spain, were analyzed during five consecutive years (2014–2018). Basic fruit quality traits including soluble solids content (SSC), titratable acidity (TA) ratio SSC/TA (ripening index - RI) obtained. addition, biochemical such as total phenolics (TPC), flavonoids (TFC), vitamin C (Ascorbic acid AsA) relative antioxidant capacity (RAC) determined. Statistical analysis was used determine differences trait values among years. The well adapted local showed, general, higher average antioxidants RAC compared foreign commercial ones. A multivariate model fitted climate features each year independent variables. cluster then performed on coefficients space classify within groups. showed that cultivars (those not originating Spain) concentrated two groups while could be segregated had very different profiles. Furthermore, they increased concentration bioactive tended decrease temperatures, solar radiation. analyses emphasized between highlighted main factors affecting metabolite profiles characteristics.

Language: Английский

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Ppe.XapF: High throughput KASP assays to identify fruit response to Xanthomonas arboricola pv. pruni (Xap) in peach

PLoS ONE, Journal Year: 2022, Volume and Issue: 17(2), P. e0264543 - e0264543

Published: Feb. 25, 2022

Bacterial spot, caused by Xanthomonas arboricola pv. pruni ( Xap ), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on fruit global economic impacts. A management option for control meeting consumer demand chemical-free, environmentally friendly production the development of resistant tolerant cultivars. We developed simple, accurate, efficient DNA assays (Ppe.XapF) based SNP genotyping KASP technology to quickly test bacterial spot resistance alleles in allows breeders cull seedlings at greenhouse stage. The objective this research was validate newly tests target two major QTLs diagnostic utility predicting response infection. Our study confirms only Ppe.XapF tests, Ppe.XapF1-1 Ppe.XapF6-2, individuals carrying susceptible can be identified. Use these accurate resulted 44% reduction seedling planting rate Clemson University breeding program.

Language: Английский

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