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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Malus sieversii: the origin, flavonoid synthesis mechanism, and breeding of red-skinned and red-fleshed apples

Horticulture Research, Journal Year: 2018, Volume and Issue: 5(1)

Published: Oct. 8, 2018

Flavonoids play essential roles in human health. Apple (Malus domestica Borkh.), one of the most widely produced and economically important fruit crops temperate regions, is a significant source flavonoids diet among top nutritionally rated consumed fruits worldwide. Epidemiological studies have shown that consumption apples, which are rich variety free easily absorbable flavonoids, associated with decreased risk various diseases. However, apple production challenged by serious inbreeding problems. The narrowing hereditary base has resulted apples poor nutritional quality low flavonoid contents. Recently, there been advances our understanding Malus sieversii (Ledeb.) M.Roem played process domestication breeding. In this study, we review origin cultivated red-fleshed discuss genetic diversity construction core collections M. sieversii. We also current research progress breeding programs on red-skinned summarize exploitation utilization high-flavonoid, apples. This study highlights valuable pattern horticultural crop using wild germplasm resources. future challenges directions molecular mechanisms accumulation high-flavonoid discussed.

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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Latent postharvest pathogens of pome fruit and their management: from single measures to a systems intervention approach

European Journal of Plant Pathology, Journal Year: 2020, Volume and Issue: 156(3), P. 663 - 681

Published: Jan. 21, 2020

Abstract Postharvest diseases of pome fruit are typically caused by a wide diversity fungal pathogens, and the list confirmed causal agents is still growing. There considerable knowledge on epidemiology wound such as Botrytis cinerea Penicillium expansum. In contrast, occurrence different postharvest after latent (quiescent) infections during long-term storage their limited. Well-known pathogens causing losses Neofabraea spp. Colletotrichum spp., but in many cases that occur specific region remain unknown control relies routine use fungicide applications. However, due to growing concern over synthetic fungicides, alternative measures highly desired. Over past years physical treatments, natural compounds, biocontrol have been investigated alternatives. no single method has emerged can robustly reliably practice. this review it argued approach complex problems require multiple interventions at stages disease process systems intervention for control. Such requires deep understanding orchard, defence mechanisms against molecular biology host-pathogen interactions order develop novel methods which deployment resistant cultivars be cornerstone.

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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The role of conventional plant breeding in ensuring safe levels of naturally occurring toxins in food crops

Trends in Food Science & Technology, Journal Year: 2020, Volume and Issue: 100, P. 51 - 66

Published: April 3, 2020

The process of selecting superior performing plants for food, feed and fiber products dates back more than 10,000 years has been substantially refined in the last century. While perceived risks posed by genetically engineered crop extensively addressed, extant levels naturally occurring plant toxins food crops received far less attention. This review discusses how conventional breeding practices are used breeders to develop safe new varieties. Crops grouped into two categories: 1) with no significant plant-produced toxins; 2) known natural toxins. Examples case studies from each category illustrate safety considerations these economically important adjusted prior commercialization, depending on whether produces toxin(s). Conventional practices, such as cross- or self-pollinating, shuffle genetic allelic combinations produce progeny varieties without giving rise novel uncharacterized biosynthetic pathways. Therefore, can fine tune their specific inherent that species, thereby ensuring a supply consumers. Breeders often select different single use disparate markets, unique selection desirable characteristics portion is consumed nature particular processing industry.

Language: Английский

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Genomic consequences of apple improvement

Horticulture Research, Journal Year: 2021, Volume and Issue: 8(1)

Published: Jan. 1, 2021

Abstract The apple ( Malus domestica ) is one of the world’s most commercially important perennial crops and its improvement has been focus human effort for thousands years. Here, we genetically characterise over 1000 accessions from United States Department Agriculture (USDA) germplasm collection using 30,000 single-nucleotide polymorphisms (SNPs). We confirm close genetic relationship between modern cultivars their primary progenitor species, sieversii Central Asia, find that cider apples derive more ancestry European crabapple, sylvestris , than do dessert apples. determine USDA a large complex pedigree: half interconnected by series first-degree relationships. In addition, 15% have with top 8 produced in USA. With exception ‘Honeycrisp’, are to each other via pedigree ‘Golden Delicious’ ‘Red were found 60 relatives, consistent repeated use breeders. detected signature intense selection red skin provide evidence breeders also selected increased firmness. Our results suggest Americans eating largely single family tree apple’s future will benefit exploitation tremendous natural diversity.

Language: Английский

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Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Theoretical and Applied Genetics, Journal Year: 2022, Volume and Issue: 135(11), P. 3961 - 3985

Published: April 20, 2022

Language: Английский

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In the name of the rose: a roadmap for rose research in the genome era

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

Published: May 3, 2019

The recent completion of the rose genome sequence is not end a process, but rather starting point that opens up whole set new and exciting activities. Next to high-quality other genomic tools have also become available for rose, including transcriptomics data, high-density single-nucleotide polymorphism array software perform linkage quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous diverse. This vast diversity cultivated roses can be explained through genetic potential genus, introgressions from wild species into commercial tetraploid germplasm inimitable efforts historical breeders. We now investigate how this best exploited refined future breeding work, given rich molecular toolbox community. paper presents possible lines research has entered genomics era, attempts partially answer question arises after any draft sequence: 'Now we "the" genome, what's next?'. Having access will allow both (fundamental) scientific (applied) breeding-orientated questions addressed. outline approaches number these questions.

Language: Английский

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Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

Tree Genetics & Genomes, Journal Year: 2019, Volume and Issue: 15(2)

Published: Feb. 12, 2019

Acidity is a critical component of the apple fruit consumption experience. In previous biparental family studies, two large-effect acidity QTLs were reported using freshly harvested fruit. Objectives this study to determine number and location for variation in large breeding program ascertain quantitative effects relevance QTL allelic combinations at harvest after commercially relevant periods cold storage. Pedigree-connected germplasm 16 full-sib families representing nine important parents, genotyped 8K SNP array, was assessed titratable 10- 20-week storage treatments, three successive seasons. Using pedigree-based mapping software, FlexQTL™, evidence found only QTLs, on linkage groups (the Ma locus) LG 8 (here called Ma3) that jointly explained 66 ± 5% phenotypic variation. An additive allele dosage model effectively most variation, with an average + 1.8 mg/L per high-acidity allele. The more alleles, faster depletion storage, all appearing eventually converge common baseline. All parent cultivars selections had one or four possible alleles. Each rare second stronger reduced effect. Diagnostic markers identified alleles derived from distinct sources. Combined highlighted utility DNA-based information new cultivar development targeting desired levels before

Language: Английский

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