Genome-Wide Association Study of Brown Rot (Monilinia spp.) Tolerance in Peach

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

Опубликована: Март 9, 2021

Brown rot, caused by Monilinia spp., is one of the most important diseases on stone fruit worldwide. Severe yield loss can be pre- and post-harvest decay. Although some degree tolerance has been reported in peach almond, genetic resistance cultivars still lacking. To date, only few genomic regions associated with brown rot response skin flesh have detected peach. Previous studies suggested being a polygenic quantitative trait. More information needed to uncover genetics behind identify this trait, 26 progeny from 9 crosses 'Bolinha' sources tolerance, were phenotyped across two seasons (2015 2016) for disease severity index wounded non-wounded fruits genotyped using newly developed 9+9K SNP array. Genome wide association study single- multi-locus methods GAPIT version 3, mrMLM 4.0, G Model, revealed 14 reliable SNPs significantly infection responses (10) (4) whole genome except chromosome 3. Candidate gene analysis within haplotype markers identified 25 predicted genes pathogen response/resistance. Results presented here facilitate further understanding provide an foundation DNA-assisted breeding.

Язык: Английский

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Construction of a high density linkage map in Oil Palm using SPET markers

Scientific Reports, Год журнала: 2020, Номер 10(1)

Опубликована: Июнь 19, 2020

Abstract A high-density genetic linkage map from a controlled cross of two oil palm ( Elaeis guineensis ) genotypes was constructed based on Single Primer Enrichment Technology (SPET) markers. 5K panel hybridization probes were used for this purpose which derived previously developed SNP primers in palm. Initially, 13,384 SNPs detected reduced to 13,073 after filtering only bi-allelic SNP. Around 75% the markers found be monomorphic progeny, reducing left mapping 3,501. Using Lep-MAP3 software, contained initially 2,388 and had total length 1,370 cM. In many cases several adjacent located same locus, due missing recombination events between them, leading 1,054 loci 16 LG. Nevertheless, marker density 1.74 per cM (0.57 cM/marker) should allow detection QTLs future. This study shows that cost efficient SPET are suitable construction probably, also other species.

Язык: Английский

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Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’

Horticulture Research, Год журнала: 2021, Номер 8(1)

Опубликована: Фев. 1, 2021

Abstract Breeding apple cultivars with resistance offers a potential solution to fire blight, damaging bacterial disease caused by Erwinia amylovora . Most alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm poor fruit quality, which reduces breeding utility. This study utilized pedigree-based QTL analysis approach elucidate the genetic basis of resistance/susceptibility blight from multiple sources relevant U.S. programs. Twenty-seven important parents (IBPs) represented 314 offspring 32 full-sib families, ‘Honeycrisp’ being most highly IBP. Analyzing data two-year replicated field inoculation and curated genome-wide single nucleotide polymorphism data, QTLs consistently mapped on chromosomes (Chrs.) 6, 7, 15. These together explained ~28% phenotypic variation. The Chr. 6 15 colocalized reported QTLs, while 7 is possibly novel. inherited rare reduced-susceptibility allele its grandparent ‘Frostbite’. resistant IBP ‘Enterprise’ had least one putative all three QTLs. In general, lower susceptibility was observed for individuals higher numbers across highlighted mapping characterization complex pedigree-connected germplasm. Knowledge gained will enable more informed parental selection development trait-predictive DNA tests pyramiding favorable superior blight.

Язык: Английский

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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Plants, Год журнала: 2021, Номер 10(2), С. 415 - 415

Опубликована: Фев. 23, 2021

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit berries, potatoes woody ornamentals. The primary goal is usually to identify true-to-type material, detect possible synonyms, investigate diversity relatedness among accessions. A secondary may be create sustainable databases that can utilized research breeding for several years ahead. Commonly applied DNA markers (like microsatellite SNPs) next-generation sequencing each their pros cons these purposes. Methods phenotyping lagged behind, which unfortunate since many commercially important traits (yield, growth habit, storability, disease resistance) are difficult score. Nevertheless, the analysis gene action development robust depends environmentally controlled screening very large sets material. Although more time-consuming, co-operative with broad-scale data collection likely produce reliable results. In this review, we will describe some approaches taken and/or concerning a wide variety crops.

Язык: Английский

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Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

BMC Genomics, Год журнала: 2021, Номер 22(1)

Опубликована: Апрель 7, 2021

Abstract Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed take advantage and improved probe design using genome sequence panel data, a need integrate from different platforms arisen. This study was undertaken view our an integrated high-quality dataset Illumina Infinium® 20 K Affymetrix Axiom® 480 apple ( Malus × domestica ). In this study, we qualify quantify the compatibility calling, defined as calls that both accurate concordant, across by two approaches. First, concordance evaluated set 417 duplicate individuals genotyped on starting 10,295 robust SNPs Infinium array. Next, accuracy additional germplasm n = 3141) Mendelian inconsistent consistent errors thousands pedigree links. While performing work, took opportunity evaluate reasons failure observed discordant calls. Results Concordance among average 97.1% SNPs. Of these SNPs, 35% had call(s) were further curated, leading final 8412 (81.7%) deemed compatible. Compatibility highly influenced presence alternate binding locations secondary polymorphisms. The impact latter their number proximity 3′ end probe. Conclusions Axiom mostly However, integration required intense filtering curation. work resulted workflow information may be other efforts. Such in-depth analysis ours not previously described literature will useful future interpretation, probe/platform development.

Язык: Английский

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The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Horticulture Research, Год журнала: 2021, Номер 8(1)

Опубликована: Сен. 1, 2021

Abstract Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify confirm direct parent–offspring relationships are routine, those for other types close yet be effectively widely implemented with plants, due complications such as asexual propagation extensive inbreeding. The objective this study was develop demonstrate that support complex pedigree reconstruction via the total length identical by state haplotypes (referred “summed potential lengths shared haplotypes”, SPLoSH). A custom Python script, HapShared, developed generate SPLoSH data apple sweet cherry. HapShared used establish empirical distributions known these crops. These were then estimate previously relationships. Case studies each crop demonstrated various scenarios using data. For cherry, a full-sib relationship deduced ‘Emperor Francis, ‘Schmidt’, half-sib ‘Van’ ‘Windsor’, paternal grandparents ‘Stella’ confirmed. apple, 29 cultivars found share an parent, parent ‘Cox’s Pomona’ reconstructed, ‘Fameuse’ likely grandparent ‘McIntosh’. Key genetic resources enabled large genome-wide SNP array datasets, integrated maps, identified Crops similar also expected benefit from empowering reconstruction.

Язык: 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, Год журнала: 2022, Номер 17(2), С. e0264543 - e0264543

Опубликована: Фев. 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.

Язык: Английский

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Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 17, 2024

Abstract Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F 1 2 families from the Clemson University peach breeding program (CUPBP). RPT SSC QTLs consistently identified in two seasons (2011 2012) average datasets (average of seasons). A target region spanning 10,981,971–11,298,736 bp on chromosome 4 reference genome used for haplotype analysis revealed four haplotypes significant differences trait values among different diplotype combinations. Favorable alleles at both determined DNA test predicting was developed. Two Kompetitive Allele Specific PCR (KASP) assays validated 84 cultivars 163 seedlings CUPBP, only one assay ( Ppe.RPT/SSC-1 ) needed to predict between early late-season low high SSC. These results advance our understanding genetic basis facilitate selection new desired

Язык: Английский

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Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Malus domestica)

Horticulture Research, Год журнала: 2024, Номер 11(8)

Опубликована: Июнь 27, 2024

Abstract Red-flesh color development in apple fruit is known to depend upon a particular allele of the MdMYB10 gene. While anthocyanin metabolic pathway well characterized, current genetic models do not explain observed variations red-flesh pigmentation intensity. Previous studies focused on total content as phenotypic trait characterize overall flesh color. this approach led global understanding mechanisms involved expression, it essential adopt more quantitative approach, by analyzing other phenolic compound classes, order better understand molecular subtle variation and distribution. In study, we performed pedigree-based loci (QTL) mapping, using FlexQTL™ software, decipher determinism five F1 inter-connected families segregating for trait. A 452 genotypes were evaluated profiles during 3 years (2021–2023). We identified 24 QTLs intensity profiles. Six detected LG1, LG2, LG8, LG9, LG11, LG16. Several genes QTL confidence intervals related metabolism. Further analyses allowed us propose model which competition between anthocyanins flavan-3-ols (monomer oligomer) end-products decisive development. model, alleles favorable high can be inherited from both white-flesh parents.

Язык: Английский

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Genetic Status of the Swedish Central collection of heirloom apple cultivars

Scientia Horticulturae, Год журнала: 2020, Номер 272, С. 109599 - 109599

Опубликована: Июль 17, 2020

Cultivated apple is one of the most widely grown fruit crops worldwide.With introduction modern cultivars, from foreign and national breeding programs, use local cultivars decreased during 20th century.In order to minimize genetic erosion avoid loss special genotypes, a number clonal archives were established across Sweden, with goal retaining old cultivars.About 220 appointed for preservation, obtained status mandate cultivars.Initially, they identified based on pomological traits, but prior establishment Swedish Central Collection genotyped simple sequence repeat (SSR) markers.SSR markers helped evaluate preserved material, as well find best possible true-to-type source propagation, thus guiding Collection.Recently, 215 accessions this collection using 20 K Infinium® single nucleotide polymorphism (SNP) array, in gain insight into its structure.The initial SSR analysis confirmed identity multiple samples same cultivar name different locations several mislabeled samples.In subsequent SNP we 30 relationships parent-offspring relationships, including 18 trios.We also five inconsistent ploidy levels between data, some cases indicating problematic either or archives.These need further investigation ensure their true-to-typeness.Furthermore, has continued grow since onset work now contains additional which should be included future studies.The results indicate that holds high potential value programs.

Язык: Английский

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