Apple whole genome sequences:recent advances and new prospects

In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for apple.Over the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.

Control of ovule development in Vitis vinifera by VvMADS28 and interacting genes

Seedless grapes are increasingly popular throughout the world,and the development of seedless varieties is a major breeding goal.In this study,we demonstrate an essential role for the grapevine MADS-box gene VvMADS28 in morphogenesis of the ovule.We found that VvMADS28 mRNA accumulated in the ovules of a seeded cultivar,‘Red Globe’,throughout the course of ovule and seed development,especially within the integument/seed coat.In contrast,in the seedless cultivar‘Thompson Seedless’,VvMADS28 was expressed only weakly in ovules,and this was associated with increased levels of histone H3 lysine 27 trimethylation(H3K27me3)within the VvMADS28 promoter region.RNAi-mediated transient suppression of VvMADS28 expression in‘Red Globe’led to reduced seed size associated with inhibition of episperm and endosperm cell development.Heterologous overexpression of VvMADS28 in transgenic tomatoes interfered with sepal development and resulted in smaller fruit but did not obviously affect seed size.Assays in yeast cells showed that VvMADS28 is subject to regulation by the transcription factor VvERF98,and that VvMADS28 could interact with the Type I/MβMADS-domain protein VvMADS5.Moreover,through DNA-affinity purification-sequencing(DAP-seq),we found that VvMADS28 protein specifically binds to the promoter of the grapevine WUSCHEL(VvWUS)gene,suggesting that maintenance of the VvMADS28–VvMADS5 dimer and VvWUS expression homeostasis influences seed development.Taken together,our results provide insight into regulatory mechanisms of ovule and seed development associated with VvMADS28.

Breeding better cultivars,faster:applications of new technologies for the rapid deployment of superior horticultural tree crops

Woody perennial plants,including trees that produce fruits and nuts of horticultural value,typically have long breeding cycles,and development and introduction of improved cultivars by plant breeders may require many breeding cycles and dozens of years.However,recent advances in biotechnologies and genomics have the potential to accelerate cultivar development greatly in all crops.This mini-review summarizes approaches to reduce the number and the duration of breeding cycles for horticultural tree crops,and outlines the challenges that remain to implement these into efficient breeding pipelines.

Physiological evaluation of nitrogen use efficiency of different apple cultivars under various nitrogen and water supply conditions

Nitrogen(N) deficiency is a common problem for apple(Malus×domestica) production in arid regions of China.However,N utilization efficiency(NUE) of different apple cultivars grown under low N conditions in arid regions has not been evaluated.In this study,NUE was assessed for one-year-old seedlings of six apple cultivars,Golden Delicious,Qinguan,Jonagold,Honeycrisp,Fuji and Pink Lady,grafted onto Malus hupehensis Rehd.rootstocks.Four treatments were used,including control water with control N(CWCN),limited water with control N(LWCN),control water with low N(CWLN) and limited water with low N(LWLN).Our results showed that growth indices such as biomass,plant height and stem diameter,and photosynthetic rate of all cultivars decreased in the order CWCN>CWLN>LWCN>LWLN.When subjected to LWLN treatment,Qinguan showed better growth and photosynthetic characters than other tested cultivars.Additionally,Qinguan and Pink Lady had higher NUE,while Honeycrisp and Jonagold had lower NUE,based on the determination of biomass,photosynthetic parameters,chlorophyll content,the maximal photochemical efficiency of PSII(Fv/Fm),15 N and N contents.

Gene cloning and expression analyses of WBC genes in the developing grapevine seeds

White-brown complex （WBC） transporters, also called half-size ATP binding cassette G （ABCG） transporters, are involved in many biological processes, including seed development; however, the WBC transporters in grapevines received less attention to date. To reveal the molecular characteristics of WBCs and the connection between WBCs and agronomic traits of stenospermocarpic （seedless） grapevine, we carried out a genomic census and analysis of ovule-associated expression for VvWBC genes in grapevine. We identified 30 VvWBC genes and cloned full-length complementary DNAs （cDNAs） for 20 of these. The tissue or organ-specific expression analysis showed that several VvWBCs exhibited distinct expression patterns with some showing tissue specificity. Twelve VvWBC genes were found to be expressed in the developing ovules. Moreover, the results of quantitative real-time PCR （qRT-PCR） suggested that four of twelve ovule-expressed VvWBCs have distinct expression profiles during the development of ovules between seeded and stenospermocarpic grapevines. These four genes might be involved in ovule abortion. Meanwhile, chromosome mapping, multiple sequence alignments, exon/intron structure analyses and synteny analyses were preformed on VvWBC genes. Our experiments provide a new perspective on the mechanism of stenospermocarpic seedlessness and put forward a framework for further study of WBC transporters.

Hybrids withouthybridization-can it revolutionize horticulture?

The often-cited idiom“The apple doesn’t fall far from the tree”refers to the occasional striking similarity in appearance or behavior between a human parent and child.However,in heterozygous organisms—be it human or apple—strong similarity in multiple traits across generations tends to be the exception.Rather,the phenomenon of genetic segregation ensures that off-spring show variation.While this can be advantageous in nature,it poses numerous problems for horticulture and plant agriculture in general,as the perpetual need to reproduce high-performing hybrids through crossing of parental genotypes,as well as the clonal vegetative propagation of elite hybrid cultivars,involves expensive and time consuming procedures.A recent study by Khanday and colleagues,published 12 December in the journal Nature 1,combined the characterization of a mechanism that triggers embryogenesis in the absence of fertilization。

Identification of potential key genes in resveratrol biosynthesis via transcriptional analyses of berry development in grapevine(Vitis spp.)genotypes varying in trans-resveratrol content

Resveratrol is an important secondary metabolite not only owing to its function as a phytoalexin,but also its potential benefits to human health.In this study,the content of trans-resveratrol was documented in seven accessions of grapevine,in the seed,pulp and skin of berries,and at three developmental stages.The highest amount(2.99μg g^(−1) FW)was found in the skin of berries at the ripe stage from V.amurensis‘Tonghua-3'.Resveratrol was not detected in several samples,including skin of berries at the green hard or véraison stage from V.davidii‘Tangwei'.We carried out transcriptional profiling of developing‘Tonghua-3'and‘Tangwei'berries to identify gene expression patterns that may be linked with the difference in resveratrol content between these accessions.The expression levels of several differentially expressed genes(DEGs)with presumed function in resveratrol biosynthesis,including STILBENE SYNTHASEs(STSs),CINNAMATE 4-HYDROXYLASEs(C4Hs)and 4-COUMARATE-COA LIGASEs(4CLs),were significantly higher in‘Tonghua-3',than in'Tangwei'during the véraison and ripe stages.Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggested that these DEGs were enriched for multiple biological processes at the three stages of fruit development.Additionally,we identified a total of 36 transcription factors,including MYBs,WRKYs,ERFs,bHLHs and bZIPs,that were coexpressed with 17 STSs via a weighted gene co-expression network analysis,suggesting roles as regulators of resveratrol biosynthesis.Overall,these findings provide insight into genotypic differences in resveratrol biosynthesis in grapevine,as well as the molecular genetics of its regulation.