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

Horticulture Research, Год журнала: 2019, Номер 6(1)

Опубликована: Апрель 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.

Язык: Английский

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

GigaScience, Год журнала: 2020, Номер 9(5)

Опубликована: Май 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.

Язык: Английский

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Apple whole genome sequences: recent advances and new prospects

Horticulture Research, Год журнала: 2019, Номер 6(1)

Опубликована: Апрель 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

Язык: Английский

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

Horticulture Research, Год журнала: 2020, Номер 7(1)

Опубликована: Ноя. 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.

Язык: 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, Год журнала: 2022, Номер 321, С. 111314 - 111314

Опубликована: Май 13, 2022

Язык: Английский

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

Horticulture Research, Год журнала: 2020, Номер 7(1)

Опубликована: Ноя. 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.

Язык: Английский

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

Tree Genetics & Genomes, Год журнала: 2020, Номер 16(1)

Опубликована: Янв. 17, 2020

Язык: Английский

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

BMC Genomics, Год журнала: 2020, Номер 21(1)

Опубликована: Июль 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.

Язык: Английский

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

Scientia Horticulturae, Год журнала: 2021, Номер 285, С. 110142 - 110142

Опубликована: Апрель 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.

Язык: Английский

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Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome

Frontiers in Plant Science, Год журнала: 2021, Номер 12

Опубликована: Фев. 25, 2021

Peach is one of the most important fruit crops in world, with global annual production about 24.6 million tons. The United States fourth-largest producer after China, Spain, and Italy. consumption has decreased over last decade, likely due to inconsistent quality on market. Thus, marker-assisted selection for traits highly desired fresh market peach breeding programs major goals RosBREED project. ability use DNA information select desirable would enable breeders efficiently plan crosses seedlings early process before fruiting. Therefore, we assembled a multi-locus genome wide association study (GWAS) 620 individuals from three public (Arkansas, Texas, South Carolina). material was genotyped using 9K SNP array were phenotyped phenological (bloom date, ripening days bloom) 11 quality-related (blush, diameter, weight, adherence, firmness, redness around pit, texture, pit soluble solid concentration, titratable acidity, pH) seasons (2010, 2011, 2012). Multi-locus analyses, carried out mrMLM 4.0 FarmCPU R packages, revealed total 967 180 quantitative trait nucleotides (QTNs), respectively. Among 88 consistently reliable QTNs detected multiple GWAS methods and/or at least two seasons, 44 first time. Fruit hotspots identified chromosomes 1, 3, 4, 5, 6, 8. Out 566 candidate genes genomic regions harboring QTN clusters, 435 functionally annotated. Gene enrichment analyses 68 different gene ontology (GO) terms associated traits. Data reported here advance our understanding genetic mechanisms underlying further support development tools breeding.

Язык: Английский

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