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Extreme-phenotype GWAS unravels a complex nexus between apple(Malus domestica)red-flesh colour and internal flesh browning

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Fruit Research 2022年第1期2卷 110-123页

作者： Satish Kumar Cecilia H.Deng Claire Molloy Chris Kirk Blue Plunkett Kui Lin-Wang Andrew Allan richard espley The New Zealand Institute for Plant and Food Research Limited Hawke's Bay Research CentreHavelock North 4130New Zealand The New Zealand Institute for Plant and Food Research Limited Mount Albert Research CentreAuckland 1025New Zealand The New Zealand Institute for Plant and Food Research Limited Palmerston North Research CentrePalmerston North 4410New Zealand

The genetic link between apple red flesh(RF)coloration and the internal flesh browning disorder(FBD)is a major challenge when breeding high fruit quality RF apple cultivars.A genome-wide association study(GWAS)was conducted in a population of about 900 red-leaved seedlings to identify genomic regions and putative candidate genes using whole genome sequencing of the pools of extreme phenotypes(XP)for the RF colour coverage(using the weighted cortex index(WCI))and *** study identified novel genomic regions contributing to WCI and FBD variation in the red-leaved *** FBD-associated regions were enriched for genes regulating senescence,heat shock proteins,cytochrome P450,ascorbate metabolism and pectin methyl *** there were no significant regions in common for WCI and FBD,there were several genes(***85,MYB66,ethylene insensitive 3,DNAJ heat shock protein,WRKY7,and NAC42)enriched commonly between the genomic regions associated with these traits,potentially underpinning the genetic connection between WCI and *** of the differentially expressed genes between the R6:MdMYB10 and white-fleshed‘control’apples resided within the GWAS hotspot for WCI(*** synthase,UDP-Glycosyl transferase)and FBD(*** GTPase activating protein,lipoxygenase 1,phytoene synthase)–validating the XP-GWAS *** of several genes resided in the trait-associated genomic regions,suggesting that whole genome duplication plays an important role in the regulation of these *** genetic correlations between WCI and sensory traits were observed,and strategies to develop FBD-free high fruit quality RF cultivars are discussed.

关键词： cultivar breeding GWAS

Genomic analysis uncovers functional variation in the C-terminus of anthocyanin-activating MYB transcription factors

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Horticulture Research 2021年第1期8卷 885-898页

作者： Jessica A.Rodrigues richard V.espley Andrew C.Allan The New Zealand Institute for Plant and Food Research Limited 120 Mount Albert RoadSandringhamAuckland 1025New Zealand School of Biological Sciences University of Auckland3A Symonds StAuckland 1010New Zealand

MYB transcription factors regulate diverse aspects of plant development and secondary metabolism,often by partnering in transcriptional regulatory ***,we harness genomic resources to identify novel MYBs,thereby producing an updated eudicot MYB phylogeny with revised relationships among subgroups as well as new information on sequence variation in the disordered C-terminus of anthocyanin-activating ***®and hidden Markov model scans of gene annotations identified a total of 714 MYB transcription factors across the genomes of four crops that span the eudicots:apple,grape,kiwifruit and *** model-based phylogenetic inference identified novel members of previously defined subgroups,and the function of specific anthocyanin-activating subgroup 6 members was assayed transiently in tobacco *** conservation within subgroup 6 highlighted one previously described and two novel short linear motifs in the disordered C-terminal *** novel motifs have a mix of hydrophobic and acidic residues and are predicted to be relatively ordered compared with flanking protein *** of motifs with the Eukaryotic Linear Motif database suggests roles in protein–protein *** of motifs and their flanking regions from strong anthocyanin activators into weak activators,and vice versa,affected *** conclude that,although the MYB C-terminal sequence diverges greatly even within MYB clades,variation within the C-terminus at and near relatively ordered regions offers opportunities for exploring MYB function and developing superior alleles for plant breeding.

关键词： phylogeny metabolism thereby

Fine-mapping and validation of the genomic region underpinning pear red skin colour

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Horticulture Research 2019年第1期6卷 1607-1613页

作者： Satish Kumar Chris Kirk Cecilia Hong Deng Claudia Wiedow Mengfan Qin richard espley Jun Wu Lester Brewer The New Zealand Institute for Plant and Food Research Limited Hawkes Bay Research CentreHavelock NorthNew Zealand The New Zealand Institute for Plant and Food Research Limited Palmerston North Research CentrePalmerston NorthNew Zealand The New Zealand Institute for Plant and Food Research Limited Mount Albert Research CentreAucklandNew Zealand Centre of Pear Engineering Technology Research Nanjing Agricultural University210095 NanjingChina The New Zealand Institute for Plant and Food Research Limited Motueka Research CentreMotuekaNew Zealand

Red skin colour is an important target trait in various pear breeding *** this study,the genetic control of red skin colour was investigated in an interspecific population derived using the descendants of the red sport European pear cultivar‘Max Red Bartlett’(MRB)and the red-blushed Chinese pear cultivar‘Huobali’.Approximately 550 seedlings from nine families were phenotyped for red skin over-colour coverage(Ocolcov)and the intensity of red over-colour(Ocolint)on a 0–9 scale,and genotyped using ***-wide association analyses were conducted using 7500 high-quality single nucleotide polymorphisms(SNPs).Genomic regions on linkage groups(LG)4 and 5 were found to be associated,and the best SNP(S578_25116)on LG4 accounted for~15%of phenotypic variation in Ocolcov and *** association of S578_25116 with Ocolcov and Ocolint was successfully validated in a sample of~200 European and Asian pear *** association with red skin at locus S578_25116 was not present in Asian pear accessions,suggesting its close proximity to the MRB’s Cardinal *** putative candidate genes,including MYB transcription factors(PCP027962 and PCP027967),were identified in the quantitative trait locus region on LG4 and await functional validation.

关键词： cultivar breeding colour

Competition between anthocyanin and kaempferol glycosides biosynthesis affects pollen tube growth and seed set of Malus

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Horticulture Research 2021年第1期8卷 2439-2455页

作者： Weifeng Chen Zhengcao Xiao Yule Wang Jinxiao Wang Rui Zhai Kui Lin-Wang richard espley Fengwang Ma Pengmin Li State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple College of HorticultureNorthwest A&F UniversityYanglingShaanxi 712100China College of Food Science and Technology Northwest UniversityXi'anShaanxi 710069China The New Zealand Institute for Plant and Food Research Ltd Private Bag92169 AucklandNew Zealand

Flavonoids play important roles in regulating plant growth and *** this study,three kaempferol 3-O-glycosides were identi fi ed and mainly accumulated in fl owers but not in leaves or fruits of *** Malus,fl ower petal color is normally white,but some genotypes have red fl owers containing *** biosynthesis appears to be in competition with kaempferol 3-O-glycosides production and controlled by the biosynthetic *** white fl ower Malus genotypes had better-developed seeds than the red fl ower *** fl owers,the overexpression of MYB10 in Malus domestica enhanced the accumulation of anthocyanin,but decreased that of kaempferol *** pollination the transgenic plants showed slower pollen tube growth and fewer developed *** application ofdifferent fl avonoid compounds suggested that kaempferol 3-O-glycosides,especially kaempferol 3-O-rhamnoside,regulated pollen tube growth and seed set rather than cyanidin or quercetin *** was found that kaempferol 3-O-rhamnoside might regulate pollen tube growth through effects on auxin,the Rho of plants(ROP)GTPases,calcium and the phosphoinositides signaling *** the inhibition of auxin transport,the transcription levels of Heat Shock Proteins(HSPs)and ROP GTPases were downregulated while the levels were not changed or even enhanced when blocking calcium signaling,suggesting that HSPs and ROP GTPases were downstream of auxin signaling,but upstream of calcium *** summary,kaempferol glycoside concentrations in pistils correlated with auxin transport,the transcription of HSPs and ROP GTPases,and calcium signaling in pollen tubes,culminating in changes to pollen tube growth and seed set.

关键词： kaempferol slower upstream

Differential regulation of the anthocyanin profile in purple kiwifruit(Actinidia species)

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Horticulture Research 2019年第1期6卷 1746-1761页

作者： Yongyan Peng Kui Lin-Wang Janine M.Cooney Tianchi Wang richard V.espley Andrew C.Allan School of Biological Sciences University of AucklandAucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited Mt AlbertAucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited East Street3214 HamiltonNew Zealand

Anthocyanins are a group of secondary metabolites that colour fruit and flowers orange,red,purple or blue depending on a number of factors,such as the basic structure,co-pigmentation,metal ion complexation and vacuolar *** biosynthesis of anthocyanin is regulated at the transcriptional level by a group of transcription factors,the MYB–bHLH–WD40(MBW)*** this study,the purple colouration in several kiwifruit(Actinidia)species was identified and characterised as red cyanidin-based and blue delphinidin-based *** differential pigmentation in the skin and flesh can be attributed to the differential ratio of cyanidin and delphinidin derivatives accumulated in the total anthocyanin *** expression of anthocyanin biosynthetic genes chalcone synthase(CHS),flavonoid 3-O-glucosyltransferase(F3GT),flavonoid 3′-hydroxylase(F3′H)and flavonoid 3′5′-hydroxylase(F3′5′H)is crucial for anthocyanin ***,the balance of expression of the F3′H and F3′5′H genes appears responsible for the ratio of cyanidin and delphinidin derivatives,while a lack of CHS,F3GT and MYB110 expression is responsible for a lack of total *** transcriptional regulation of the F3′H and F3′5′H promoters by the R2R3 MYB transcription factor MYB110 is markedly different in tobacco transient *** kiwifruit MYB10 or MYB110 are over-expressed in Actinidia chinensis both cyanidin-based and delphinidin-based anthocyanins are elevated,but F3′H and F3′5′H genes are not strongly correlated with MYB *** results suggest that the core kiwifruit anthocyanin pathway genes are dependent on characterised MYB transcription factors,while other regulatory proteins are more directly responsible for the expression of the F3′H and F3′5′H genes.

关键词： Actinidia orange flowers

PbGA2ox8 induces vascular-related anthocyanin accumulation and contributes to red stripe formation on pear fruit

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Horticulture Research 2019年第1期6卷 18-30页

作者： Rui Zhai Zhigang Wang Chengquan Yang Kui Lin-Wang richard espley Jianlong Liu Xieyu Li Zhongying Wu Pengmin Li Qingmei Guan Fengwang Ma Lingfei Xu College of Horticulture Northwest A&F UniversityTaicheng Road No.3YanglingShaanxi ProvinceChina The New Zealand Institute for Plant&Food Research Ltd.(Plant and Food Research)Mt.Albert Research CentrePrivate Bag92169 AucklandNew Zealand Horticultural Research Institute Henan Academy of Agricultural SciencesHuayuan Road No.116ZhengzhouHenan ProvinceChina State Key Laboratory of Crop Stress Biology for Arid Areas Northwest A&F UniversityTaicheng Road No.3YanglingShaanxi ProvinceChina

Fruit with stripes,which are generally longitudinal,can occur naturally,but the bioprocesses underlying this phenomenon are ***,we observed an atypical anthocyanin distribution that caused red-striped fruit on the spontaneous pear bud sport“Red Zaosu”(Pyrus bretschneideri Rehd.).In this study,comparative transcriptome analysis of the sport and wild-type“Zaosu”revealed that this atypical anthocyanin accumulation was tightly correlated with abnormal overexpression of the gene-encoding gibberellin(GA)2-beta-dioxygenase 8,***,decreased methylation was also observed in the promoter region of PbGA2ox8 from“Red Zaosu”compared with“Zaosu”.Moreover,the GA levels in“Red Zaosu”seedlings were lower than those in“Zaosu”seedlings,and the application of exogenous GA4 reduced abnormal anthocyanin accumulation in“Red Zaosu”.Transient overexpression of PbGA2ox8 reduced the GA4 level and caused anthocyanin accumulation in pear fruit ***,the presence of red stripes indicated anthocyanin accumulation in the hypanthial epidermal layer near vascular branches(VBs)in“Red Zaosu”.Transient overexpression of PbGA2ox8 resulting from vacuum infiltration induced anthocyanin accumulation preferentially in calcium-enriched areas near the vascular bundles in pear *** propose a fruit-striping mechanism,in which the abnormal overexpression of PbGA2ox8 in“Red Zaosu”induces the formation of a longitudinal array of anthocyanin stripes near vascular bundles in fruit.

关键词： anthocyanin fruit abnormal

Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple

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Horticulture Research 2021年第1期8卷 911-925页

作者： Luigi Falginella Christelle M.Andre Sylvain Legay Kui Lin-Wang Andrew P.Dare Cecilia Deng Ria Rebstock Blue J.Plunkett Lindy Guo Guido Cipriani richard V.espley Dipartimento di Scienze Agroalimentari Ambientali e AnimaliUniversity of UdineUdineItaly Research Center Vivai Cooperativi RauscedoRauscedoItaly The New Zealand Institute for Plant and Food Research AucklandNew Zealand The Luxembourg Institute of Science and Technology Esch-sur-AlzetteLuxembourg

Waxy apple cuticles predominantly accumulate ursane-type triterpenes,but the profile shifts with the induction of skin russeting towards lupane-type *** previously characterised several key enzymes in the ursane-type and lupane-type triterpene pathways,but this switch in triterpene metabolism associated with loss of cuticle integrity is not fully *** analyse the relationship between triterpene biosynthesis and russeting,we used microscopy,RNA-sequencing and metabolite profiling during apple fruit *** compared the skin of three genetically-close clones of‘Golden Delicious’(with waxy,partially russeted and fully russeted skin).We identified a unique molecular profile for the russet clone,including low transcript abundance of multiple cuticle-specific metabolic pathways in the early stages of fruit *** correlation analyses between gene transcription and metabolite concentration we found MYB transcription factors strongly associated with lupane-type triterpene *** showed how their transcription changed with the onset of cuticle cracking followed by russeting and that one factor,MYB66,was able to bind the promoter of the oxidosqualene cyclase OSC5,to drive the production of lupeol *** results provide insights into the breakdown of cuticle integrity leading to russet and how this drives MYB-regulated changes to triterpene biosynthesis.

关键词： metabolism Golden cracking

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

Unraveling a genetic roadmap for improved taste in the domesticated apple

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Molecular Plant 2021年第9期14卷 1454-1471页

作者： Liao Liao Weihan Zhang Bo Zhang Ting Fang Xiao-Fei Wang Yarning Cai Collins Ogutu Lei Gao Gang Chen Xiaoqing Nie Jinsheng Xu Quanyan Zhang Yiran Ren Jianqiang Yu Chukun Wang Cecilia H.Deng Baiquan Ma Beibei Zheng Chun-Xiang You Da-Gang Hu richard espley Kui Lin-Wang Jia-Long Yao Andrew C.Allan Awais Khan Schuyler S.Korban Zhangjun Fei Ray Ming Yu-Jin Hao Li Li Yuepeng Han CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Hubei Hongshan LaboratoryWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhan 430074China Agricultural Bioinformatics Key Laboratory of Hubei Province College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhan 430074China University of Chinese Academy of Sciences 19A YuquanluBeijing 100049China College of Horticulture Science and Engineering Shandong Agricultural UniversityTai-An 271018China Sino-African Joint Research Center Chinese Academy of SciencesWuhan 430074China The New Zealand Institute for Plant&Food Research Limited AucklandNew Zealand School of Biological Sciences University of AucklandPrivate Bag 92019Auckland 1142New Zealand Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Department of Natural Resources and Environmental Sciences University of Illinois at Urbana-ChampaignUrbanaIL 61801USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

关键词： apple fruit taste organic acids soluble sugars fruit size domestication