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Genetic and genomic resources for Rubus breeding:a roadmap for the future

Horticulture Research 2019年第1期6卷 260-268页

作者： Toshi M.Foster nahla v.bassil Michael Dossett Margaret Leigh Worthington Julie Graham The New Zealand Institute for Plant and Food Research(PFR)Ltd 55 Old Mill RoadMotuekaNew Zealand USDA ARS National Clonal Germplasm Repository(NCGR) 33447 Peoria Rd.CorvallisORUSA Blueberry Council(in Partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre ColumbiaBC V0M 1A0Canada Department of Horticulture University of Arkansas316 Plant Science BuildingFayettevilleAR 72701USA The James Hutton Institute Errol RoadInvergowrieDundee DD25DAScotland

Rubus fruits are high-value crops that are sought after by consumers for their flavor,visual appeal,and health *** meet this demand,production of red and black raspberries(*** *** *** L.),blackberries(*** Rubus),and hybrids,such as Boysenberry and marionberry,is growing *** breeding programmes are continually striving to improve flavor,texture,machine harvestability,and yield,provide pest and disease resistance,improve storage and processing properties,and optimize fruits and plants for different production and harvest *** face numerous challenges,such as polyploidy,the lack of genetic diversity in many of the elite cultivars,and until recently,the relative shortage of genetic and genomic resources available for *** review will highlight the development of continually improving genetic maps,the identification of Quantitative Trait Loci(QTL)s controlling key traits,draft genomes for red and black raspberry,and efforts to improve gene *** development of genetic maps and markers,the molecular characterization of wild species and germplasm,and highthroughput genotyping platforms will expedite breeding of improved *** sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.

关键词： breeding cultivar crops

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A roadmap for research in octoploid strawberry

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Horticulture Research 2020年第1期7卷 2300-2316页

作者： vance M.Whitaker Steven J.Knapp Michael A.Hardigan Patrick P.Edger Janet P.Slovin nahla v.bassil Timo Hytönen Kathryn K.Mackenzie Seonghee Lee Sook Jung Dorrie Main Christopher R.Barbey Sujeet verma University of Florida Institute of Food and Agricultural SciencesGulf Coast Research and Education CenterWimaumaFlorida 33598USA Department of Plant Sciences University of CaliforniaDavisCA 95616USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA USDAARS Genetic Improvement of Fruits and vegetables Laboratory BeltsvilleMA 20705USA USDA-ARS National Clonal Germplasm Repository CorvallisOR 97333USA Department of Agricultural Sciences Viikki Plant Science CentreUniversity of HelsinkiHelsinki 00790Finland Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental SciencesViikki Plant Science CentreUniversity of HelsinkiHelsinki 00790Finland NIAB EMR Kent ME196BJUK Department of Horticulture Washington State UniversityPullmanWA 99164USA

The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the *** that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health *** recent publication of the first highquality chromosome-scale octoploid strawberry genome(***)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research *** this forward-looking review we propose avenues of research toward new biological insights and applications to *** these are the origins of the genome,characterization of genetic variants,and big data approaches to *** areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen *** order to realize this potential as a global community,investments in genome resources must be continually augmented.

关键词： straw cultivated looking

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

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Horticulture Research 2019年第1期6卷 1348-1363页

作者： David Chagné Stijn vanderzande Chris Kirk Natalie Profitt Rosemary Weskett Susan E.Gardiner Cameron P.Peace Richard K.volz nahla v.bassil The New Zealand Institute for Plant&Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston NorthNew Zealand Department of Horticulture Washington State UniversityPullmanWAUSA Plant&Food Research Hawke’s Bay Research CentreHavelock NorthNew Zealand USDA-ARS National Clonal Germplasm RepositoryCorvallisORUSA

Genome mapping has promised much to tree fruit breeding during the last 10 ***,one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders,who must select genetically optimal parents and subsequently select genetically superior individuals among their *** take this translational step,we designed the apple International RosBREED SNP Consortium OpenArray v1.0(IRSCOA v1.0)assay using a set of 128 apple single nucleotide polymorphisms(SNPs)linked to fruit quality and pest and disease resistance trait *** Thermo Fisher Scientific OpenArray®technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman®*** validated the apple IRSCOA v1.0 multitrait assay by screening 240 phenotyped individuals from the Plant&Food Research apple cultivar breeding *** set of individuals comprised commercial and heritage cultivars,elite selections,and families segregating for traits of importance to *** total,33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection(MAS)for the scab resistances Rvi2/vh2,Rvi4/vh4,Rvi6/vf,fire blight resistance MR5/RLP1,powdery mildew resistance Pl2,fruit firmness,skin colour,flavour intensity,and *** availability of this set of validated trait-associated SNP markers,which can be used individually on multiple genotyping platforms available to various apple breeding programmes or re-designed using the flanking sequences,represents a large translational genetics step from genomics to crop improvement of apple.

关键词： Open resistance breeding

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Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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Horticulture Research 2023年第11期10卷 96-105页

作者： Alan E.Yocca Adrian Platts Elizabeth Alger Scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe v.Ferrão MacKenzie Jacobs Michal Babinski Maria Magallanes-Lundback Philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard v.Espley David Chagné Nick W.Albert Sara Montanari Nicholi vorsa James Polashock Luis Díaz-Garcia Juan Zalapa nahla v.bassil Patricio R.Munoz Massimo Iorizzo Patrick P.Edger Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of Plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States Plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of Western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for Plant and Food Research Limited(PFR) AucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) PalmerstonNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed *** industry continues to face a wide variety of production challenges(*** pressures),as well as a demand for higher-yielding cultivars with improved fruit quality ***,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value ***,we describe the construction and analysis of the first pangenome for both blueberry and *** analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in *** genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality *** discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding *** pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for vaccinium-a curated and integrated web-based relational ***,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

关键词： breeding cultivar crops

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Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis

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Horticulture Research 2017年第1期4卷 85-93页

作者： Sujeet verma Jason D Zurn Natalia Salinas Megan M Mathey Beatrice Denoyes James F Hancock Chad E Finn nahla v.bassil vance M Whitaker IFAS/Department of Horticulture University of FloridaGulf Coast Research and Education Center14625 CR 672Wimauma33598FLUSA USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallis97333ORUSA Department of Horticulture Oregon State University4017 Agriculture and Life Sciences BuildingCorvallis97331ORUSA Department of Horticulture UMR 1332 Biologie du Fruit et PathologieINRAUniv.BordeauxVillenave d’OrnonF-33140France Michigan State University East Lansing48824MIUSA USDA-ARS HCRU3420 NW Orchard AvenueCorvallis97330ORUSA

The cultivated strawberry(Fragaria×ananassa)is consumed worldwide for its flavor and nutritional *** analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this *** several quantitative trait loci(QTL)have been previously detected for fruit quality and flowering traits using low-density genetic maps,clarity on the sub-genomic locations of these QTLs was *** discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism(SNP)array,enabling high-density genetic maps and finer resolution QTL *** this study,breeder-specified traits were evaluated in the Eastern(Michigan)and Western(Oregon)United States for a common set of breeding populations during 2 *** QTLs were validated for soluble solids content(SSC),fruit weight(FWT),pH and titratable acidity(TA)using a pedigree-based QTL analysis *** fruit quality,a QTL for SSC on linkage group(LG)6A,a QTL for FWT on LG 2BII,a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were *** addition,a large-effect QTL for flowering was detected at the distal end of LG 4A,coinciding with the FaPFRU *** haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal *** probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.

关键词： breeding straw Fragaria

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

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Horticulture Research 2020年第1期7卷 527-549页

作者： Amy F.Iezzoni Jim McFerson James Luby Ksenija Gasic vance Whitaker nahla bassil Chengyan Yue Karina Gallardo vicki McCracken Michael Coe Craig Hardner Jason D.Zurn Stan Hokanson Eric van de Weg Sook Jung Dorrie Main Cassia da Silva Linge Stijn vanderzande Thomas M.Davis Lise L.Mahoney Chad Finn Cameron Peace Michigan State University East LansingMI 48824USA Washington State University WenatcheeWA 98801USA University of Minnesota St.PaulMN 55108USA Clemson University ClemsonSC 29634USA University of Florida WimaumaFL 33598USA USDA-ARS CorvallisOR 97333USA Washington State University PuyallupWA 98371USA Washington State University PullmanWA 99164USA Cedar Lake Research Group PortlandOR 97215USA University Queensland BrisbaneQLDAustralia Wageningen University and Research 6700 AA WageningenThe Netherlands University of New Hampshire DurhamNH 03824USA

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 and is economically significant across the *** 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural ***,rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a“chasm”existed between existing genomics and genetic information and the application of this knowledge in *** RosBREED project(“Ros”signifying a Rosaceae genomics,genetics,and breeding community initiative,and“BREED”,indicating the core focus on breeding programs),addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research *** was designed to enable the routine application of modern genomics and genetics technologies in *** crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural *** review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future *** technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic *** of DNA-informed breeding use by project participants are presented for all breeding stages,including pre-breeding for disease resistance,parental and seedling selection,and elite selection *** chasm is now bridged,accelerating rosaceous crop genetic improvement.

关键词： breeding cultivar crops

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Effects of exogenous enzymes, Lactobacillus acidophilus or their combination on feed performance response and carcass characteristics of rabbits fed sugarcane bagasse

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Journal of Integrative Agriculture 2015年第3期14卷 544-549页

作者： nahla A Abdel-Aziz Mounir El-Adawy Maria A Mariezcurrena-Berasain Abdelfattah Z M Salem Jaime Olivares-Pérez Ahmed E Kholif Borhami E Borhami Department of Animal and Fish Production Faculty of Agriculture Alexandria University Faculty of veterinary Medicine and Animal Science Autonomous University of the State of Mexico Faculty of veterinary Medicine and Animal Science Autonomous University of Guerrero Dairy Science Department National Research Centre

The aim of this study was to evaluate the effect of Lactobacillus acidophilus（LAC）, exogenous enzymes of ZAD（exogenous enzyme preparation） or their combination on feed conversion, and dressing of rabbits fed different treatments of sugarcane bagasse（SCB）. Five rations were allotted randomly to five groups of New-Zealand White（NZW） rabbits（n=10） with initial live body weight of（838±42.4） g and 5 weeks of age. Rabbits were fed on diets with different sources of fiber as follows,（i） a control diet composed of 100% berseem hay and 0% SCB,（ii） 50% berseem hay and 50% untreated SCB（USCB）,（iii） 50% berseem hay and 50% SCB treated with L. acidophilus（LAC）,（iv） 50% berseem hay and 50% SCB treated with ZAD（ZAD）, and（v） 50% berseem hay and 50% SCB treated with a combination of LAC＋ZAD（LZ）. Treatments of SCB with L. acidophilus, ZAD and LAC＋ZAD had the highest feed conversion ratio than both USCB and control. The dressing percentage of rabbits that fed the LAC and LZ diets was higher（P〈0.05） compared with that in the other groups. Performance index（PI） for LAC group was improved（P〈0.05） compared to that for the other groups; however, PI for USCB group was the lowest（P〈0.05）. It could be concluded that treating SCB with L. acidophilus, exogenous enzymes of ZAD or their combination improved feed conversion and performance with more positive effects with L. acidophilus than the other treatments.

关键词： exogenous enzymes feed conversion Lactobacillus acidophilus rabbit sugarcane bagasse

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Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

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Horticulture Research 2018年第1期5卷 868-878页

作者： Rubina Jibran Helge Dzierzon nahla bassil Jill M.Bushakra Patrick P.Edger Shawn Sullivan Chad E.Finn Michael Dossett Kelly J.vining Robert vanBuren Todd C.Mockler Ivan Liachko Kevin M.Davies Toshi M.Foster David Chagné The New Zealand Institute for Plant&Food Research Limited Private Bag 11600Palmerston North4474New Zealand USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallisOR97333USA Department of Horticulture Michigan State UniversityEast LansingMI48824-2604USA Phase Genomics SeattleWA98195USA USDA-ARS Horticultural Crops Research Unit CorvallisOR97330USA B.C.Blueberry Council(in Partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre AgassizBCV0M 1A0Canada The Donald Danforth Plant Science Center St.LouisMO63132USA Department of Genome Sciences University of Washington School of MedicineSeattleWA98195USA

Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health *** improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference *** recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome *** used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven *** seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic *** regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire *** demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only PacBio long-read *** conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

关键词： breeding black interaction

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Using General and Specific Combining Ability to Further Advance Strawberry（Fragaria sp.）Breeding

Using General and Specific Combining Ability to Further Adva...

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第七届世界草莓大会

作者： M.M.Mathey S.Mookerjee L.Mahoney C.E.Finn J.F.Hancock S.Serce T.Davis P.Stewart v.M.Whitaker A.R.Jamieson N.v.bassil I.Amaya B.Denoyes K.E.Hummer D.Sargent E.van de Weg A.Iezzoni Oregon State University Michigan State University University of New Hampshire USDA-ARS HCRL Mustafa Kemal University

Strawberry is one of the five fruit crops included in the USDA-funded multiinstitutional and trans-disciplinary project, "RosBREED:Enabling MarkerAssisted Breeding in Rosaceae".A Crop Reference Set（CRS） was developed of 900 genotypes and seedlings from 40 crosses representing the breadth of relevant diversity and encompassing founders used in breeding the domesticated *** native species and cultivar genotypes were included along with 10 progeny from 36 of the crosses of genotypes representing eastern and western North American and European short day and remontant *** CRS has been phenotyped in five *** 14 fruit quality traits have been studied,as well as remontancy,truss size,peduncle length,crop estimate,plant architecture,and disease *** phenotyping conducted in the first growing season showed considerable variability amongst the genotypes and the locations for all of the *** and specific combining ability variance components were determined from the populations in order to provide breeders with guidance on the most effective breeding strategies for incorporating the superior traits from this germplasm into their programs.

关键词： RosBREED Rosaceae marker assisted breeding remontancy

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