Identification of an Aux/IAA regulator for flesh firmness using combined GWAS and bulked segregant RNA-Seq analysis in watermelon

Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh.Among various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial value.The auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric fruits.However,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains unknown.In this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in watermelon.Transcriptome analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh firmness.The sequence alignment revealed a single base mutation in the coding region of Aux/IAA.Furthermore,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh firmness.Aux/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh firmness.We determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard flesh.Moreover,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell sizes.Additionally,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated trait.These findings significantly enhanced our understanding of watermelon fruit flesh firmness and consequently the watermelon fruit quality.

Genomic analysis provides insights into the westward expansion of domesticated peaches in China

Peach, an economically important model plant of the Rosaceae family, has been domesticated and cultivated in China for approximately5 000 years. The Hexi Corridor, an important corridor connecting east-central China and the Tarim Basin, is the starting point of the Silk Road that links China and the Eurasian region. As a globally distributed fruit tree, the spread of peach was accomplished through historical trade routes in the Hexi Corridor and the Tarim Basin. However, knowledge of peach genetic diversity in these regions remains limited. In this study,we examined the relationships and the spread history of domesticated peaches through sequencing and genomic analysis of 161 peach accessions collected from Northwest China, including 43 from the Hexi Corridor and 104 from the Tarim Basin. The results indicate that peach landraces in the Hexi Corridor and the Tarim Basin are derivatives of peaches from the east and south of China (ESC). Notably, the genetic diversity of accessions from both the Hexi Corridor and the Tarim Basin was lower than that of ESC accessions. Reduction of diversity (ROD) and linkage disequilibrium (LD) analyses detected a genetic bottleneck in peaches from these regions. Additionally, these peaches have undergone varying degrees of selection from natural environment. Moreover, genes responsive to biotic and abiotic stresses were under selection, which could be the result of the climate change of Northwest China after the Last Glacial Maximum (LGM). Our findings provide a better understanding of the genetic basis of peach migration in Northwest China. Furthermore, this study expands the available genomic data for peaches and provides critical information for future peach breeding programs.

Peculiarity of transcriptional and H3K27me3 dynamics during peach bud dormancy

Bud dormancy facilitates the survival of meristems under harsh environmental conditions.To elucidate how molecular responses to chilling accumulation controlling dormancy in peach buds,chromatin immunoprecipitation sequencing to identify the H3K27me3 modifications and RNA sequencing of two peach cultivars with pronounced differences in chilling requirement were carried out,the results showed that genes associated with abscisic acid and gibberellic acid signal pathways play key roles in dormancy regulation.The results demonstrated that peach flower bud differentiation occurred continuously in both cultivars during chilling accumulation,which was correlated with the transcript abundance of key genes involved in phytohormone metabolism and flower bud development under adverse conditions.The more increased strength in high chillingrequirement cultivar along with the chilling accumulation at the genome-wide level.The function of the dormancy-associated MADS-box gene PpDAM6 was identified,which is involved in leaf bud break in peach and flower development in transgenic Nicotiana tabacum(NC89).In addition,PpDAM6 was positively regulated by PpCBF,and the genes of putative dormancy-related and associated with metabolic pathways were proposed.Taken together,these results constituted a theoretical basis for elucidating the regulation of peach bud dormancy transition.

Genetic Resources,Breeding Programs in China,and Gene Mining of Peach:A Review

Research on peach genetic resources and breeding has achieved remarkable progress in recent decades,especially in China.In this review,we first described the geographic distribution,ecology,phenotypes,and genetic diversity of peach landraces and wild relatives in China.We also discussed the almond.Subsequently,breeding programs of peaches in China are summarized,including breeding history,breeding targets,breeding institutes,elite breeding materials,breeding solutions,and domestically bred representative cultivars.Furthermore,we reviewed the genes or loci that have been mined using both linkage mapping and genome wide association study(GWAS)as well as the evolutionary genetics and domestication history of the peach.Finally,we gave our perspectives and suggestions for future breeding in terms of breeding material selection and breeding technology innovation.

Growth and physiological responses of four kiwifruit genotypes to salt stress and resistance evaluation

In this study,four genotypes(Acva-1,Acva-2,Acva-3 and ZM-2) of Actinidia germplasm resources were grown in different NaCl concentrations(0,0.4,0.8 and 1.2 g L–1).The growth,physiological and biochemical indicators were measured,and a graded scale was developed as the salt damage index(SDI) according to different damage symptoms in leaves.The results showed SDI increased gradually,and average number and length of new shoot decreased significantly.Three antioxidant enzymes(superoxide dismutase,peroxidase and catalase) and two osmotic adjustment substances(soluble sugar and proline) showed different changes in old and new leaves of four genotypes.SPAD values exhibited a decreased trend in the whole except in the new leaves of Acva-2.Malonaldehyde contents increased and root activity decreased with the increasing salt concentrations.Principal component analysis was used to assess the salt tolerance,and the results showed Acva-3,from Actinidia valvata Dunn.,had the strongest tolerance to salt,and could be a potential resistant resource to the salt-tolerance dedicated rootstock breeding of kiwifruit.

Accumulated chilling hours during endodormancy impact blooming and fruit shape development in peach(Prunus persica L.)

Winter chill is essential for the growth and development of deciduous species. To understand the relationship between accumulated chilling hours during endodormancy and blooming and fruit shape development, we controlled chilling hours and investigated their effects on blooming date and fruit shape of peaches. The results showed that the number of days to full bloom date and the heat requirement for blooming were negatively correlated with accumulated chilling hours. Accumulated chilling hours were significantly negatively correlated with fruit shape index and fruit tip lengths, suggesting that the number of chilling hours affect the fruit shape development. Fewer accumulated chilling hours may be the major reason for longer fruit shape and protruding fruit tips. In conclusion, our results indicate specifically that decreased winter chilling hours can delay the bloom date and may lead to aberrant fruit shape development in peaches. Our study provides preliminary insights into the response of temperate fruit species to global climate change.

Anatomical berry characteristics during the development of grape berries with different shapes

The aim of this study was to characterize the changes in berry anatomy during the development of grape(Vitis vinifera L.,and Vitis vinifera×Vitis labrusca)with different shapes.Paraffin sectioning was used to examine the structural parameters of the cells.The results revealed that,with the development of berries,the transverse and longitudinal diameters of the flesh cells gradually increased,revealing certain regularity.However,the transverse and longitudinal diameters of the epidermal and sub-epidermal cells were different between varieties,reflecting the specificity of the varieties.The growth of the transverse and longitudinal diameters of the berries was found to be completed in the early stage of development.A combination of correlation analysis and size analysis for each cell layer revealed that,due to the small crosssectional area of the epidermal and sub-epidermal cells,the influence of these cells on the transverse and the longitudinal diameters of the berries would be small.In conclusion,the longitudinal and transverse diameters of the grape berries were mainly determined by the longitudinal and transverse diameters of the flesh cells.The different shapes of the grape berries could mainly be attributed to the different growth rates of the flesh cells in the longitudinal and transverse directions.These different rates of growth led to different lengths and widths of the berry.

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents,which undergo considerable variations during development and maturation.The molecular mechanisms underlying these variations remain unclear.In this study,we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism.We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids.Within these modules,based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction(RT-qPCR),we identified 7 genes involved in the metabolism of sugars and organic acids.Among these genes,Cla97C01G000640,Cla97C05G087120 and Cla97C01G018840(r^(2)=0.83 with glucose content)were identified as sugar transporters(SWEET,EDR6 and STP)and Cla97C03G064990(r^(2)=0.92 with sucrose content)was identified as a sucrose synthase from information available for other crops.Similarly,Cla97C07G128420,Cla97C03G068240 and Cla97C01G008870,having strong correlations with malic(r^(2)=0.75)and citric acid(r^(2)=0.85),were annotated as malate and citrate transporters(ALMT7,CS,and ICDH).The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon.These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.

Genome-wide association study of berryrelated traits in grape[Vitis vinifera L.]based on genotyping-by-sequencing markers

Deciphering the genetic control of grape berry traits is crucial for optimizing yield,fruit quality,and consumer acceptability.In this study,an association panel of 179 grape genotypes comprising a mixture of ancient cultivars,landraces,and modern varieties collected worldwide were genotyped with genotyping-by-sequencing using a genome-wide association approach based on 32,311 single-nucleotide polymorphism(SNP)markers.Genome-wide efficient mixed-model association was selected as the optimal statistical model based on the results of known control loci of grape berry color traits.Many of the associated SNPs identified in this study were in accordance with the previous QTL analyses using biparental mapping.The grape skin color locus was found to be associated with a mybA transcription factor on chromosome 2.Two strong and distinct association signals associated with berry development periods were found on chromosome 16.Most candidate genes of the interval were highlighted as receptor-like protein kinase.For berry weight,significant association loci were identified on chromosome 18,as previously known,and on chromosome 19 and chromosome 17,as newly mapped.Berry flesh texture was newly located on chromosome 16;candidate genes in the interval were related to calcium.Berry flavor was determined on chromosome 5.Genomic regions were further investigated to reveal candidate genes.In this work,we identified interesting genetic determinants of grape berry-related traits.The identification of the markers closely associated with these berry traits may be useful for grape molecular breeding.

PpERF3 positively regulates ABA biosynthesis by activating PpNCED2/3 transcription during fruit ripening in peach

The plant hormone ethylene regulates ripening in climacteric fruits.The phytohormone abscisic acid(ABA)affects ethylene biosynthesis,but whether ethylene influences ABA biosynthesis is unknown.To explore this possibility,we investigated the interactions between the ABA biosynthesis genes PpNCED2/3 and the ethylene response transcription factor PpERF3 in peach fruit.The ABA content increased during fruit maturation and reached a peak at stage S4 III.The increase was greatly inhibited by the ethylene inhibitor 1-MCP,which also suppressed PpERF3 expression.PpERF3 shared a similar expression profile with PpNCED2/3,encoding a rate-limiting enzyme involved in ABA biosynthesis,during fruit ripening.A yeast one-hybrid assay suggested that the nuclear-localized PpERF3 might bind to the promoters of PpNCED2/3.PpERF3 increased the expression of PpNCED2/3 as shown by dual-luciferase reporters,promoter-GUS assays and transient expression analyses in peach fruit.Collectively,these results suggest that ethylene promotes ABA biosynthesis through PpERF3’s regulation of the expression of ABA biosynthesis genes PpNCED2/3.

Molecular and biological characterization of melon-infecting squash leaf curl China virus in China

It has been reported that squash leaf curl China virus(SLCCNV)infects some Cucurbitaceae crops except for melon(Cucumis melo L.).A new disease of melon exhibiting severe leaf curl and dwarfing was observed in Hainan Province of China.In this study,the pathogen was identified as SLCCNV through biological and molecular characterization.The isolate(SLCCNV-HN)possess a bipartite genome,DNA-A(HM566112.1)with the highest nucleotide identity(99%)to SLCCNV-Hn(MF062251.1)pumpkin and SLCCNV-Hn61(AM260205.1)squash isolates from China,whereas DNA-B(HM566113.1)with the highest nucleotide identity(99%)to SLCCNV-Hn(MF062252.1).Phylogenetic analyses based on the full-length SLCCNV-HN DNA-A and-B sequences indicated that SLCCNV-HN melon isolate is clustered with SLCCNV-Hn pumpkin,SLCCNV-Hn61 and SLCCNV-SY squash isolates from southern China,forming an independent cluster.Infectious clone of SLCCNV-HN was constructed and the melon plants were inoculated and the infection rate is 100%,the systemic symptoms in melon showed identical to those of melon plants infected in fields.Additionally,melon plants transmission of this virus by Bemisia tabaci with a transmission rate of 95%(19/20)showed leaf curl and dwarf symptoms 15 days post transmission,thereby fulfilling Koch’s postulates.Analysis of genomic organization and phylogenetic trees indicated that SLCCNV-HN melon isolate belongs to the Begomovirus genus.To the best of our knowledge,this is the first characterization of meloninfecting SLCCNV through its genome,infectious clone and transmission.

Establishment and application of an SNP molecular identification system for grape cultivars

We aimed to develop a set of single nucleotide polymorphism(SNP) markers that can be used to distinguish the main cultivated grape(Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection. A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions using specific locus amplified fragment sequencing, of which 442 were successfully designed as Kompetitive Allele Specific PCR(KASP) markers. A set of 27 markers that completely distinguishes 304 sequenced grape accessions was determined by using the program, and 26 effective markers were screened based on 23 representative grape cultivars. Finally, a total of 46 out of 48 KASP markers, including 22 markers selected by the research group in the early stage, were re-screened based on 348 grape accessions. Population structure, principal component, and cluster analyses all showed that the 348 grape accessions were best divided into two populations. In addition, cluster analysis subdivided them into six subpopulations. According to genetic distance, V. labrusca, V. davidii, V. heyneana, and V. amurensis were far from V. vinifera, while V. vinifera×V. labrusca and V. amurensis×V. vinifera were somewhere in between these two groups. Furthermore, a core set of 25 KASP markers could distinguish 95.69% of the 348 grape accessions, and the other 21 markers were used as extended markers. Therefore, SNP molecular markers based on KASP typing technology provide a new way for mapping DNA fingerprints in grape cultivars. With high efficiency and accuracy and low cost, this technology is more competitive than other current identification methods. It also has excellent application prospects in the grape distinctness, uniformity, and stability(DUS) test, as well as in promoting market rights protection in the near future.

Morphological and ISSR molecular markers reveal genetic diversity of wild hawthorns (Crataegus songorica K. Koch.) in Xinjiang, China

The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in five populations from Daxigou, Xinjiang, China were evaluated based on phenotypic traits and ISSR molecular markers to provide basic infor- mation on resource protection, rational utilization and genetic improvement. The F-value for the phenotypic differentiation coefficient of the 33 traits measured ranged from 0.266 to 15.128, and mean value was 13.85%. The variation among populations was found to be lower than that within population. A total of 303 loci were detected within the five populations by 12 primers. Within 298,polymorphic loci, the polymorphism was 98.35%, showing a high genetic diversity in C. songorica K. Koch. The gene diversity within population, total population genetic diversity, genetic differentiation coefficient and gene flow were 0.2779, 0.3235, 0.1408, and 3.0511, respectively. Our results showed that C. songorica K. Koch. from Xinjiang has a high level of genetic diversity at both the phenotypic and molecular levels. Significant genetic differentiation existed within population and the differentiation trend showed a regional association. And in this study, in situ and ex situ conser- vation approaches were raised for wild hawthorn protection utilization.

ABI5 promotes heat stress-induced chlorophyll degradation by modulating the stability of MYB44 in cucumber

The yellowing of leaves caused by the decomposition of chlorophyll(Chl)is a characteristic event during senescence,which can be induced by various environmental stresses.However,the molecular mechanisms of high temperature-induced Chl degradation in horticultural plants remain poorly understood.Here,we found that heat stress induced Chl degradation and the expression of ABI5 and MYB44 in cucumber.Silencing of ABI5 compromised heat stress-induced Chl degradation,and the transcription of pheophytinase(PPH)and pheophorbide a oxygenase(PAO),two key genes in Chl catabolic pathway,but silencing of MYB44 exhibited the opposite results.Furthermore,ABI5 interacted with MYB44 in vitro and in vivo.ABI5 positively regulated heat stress-induced Chl degradation through two pathways.ABI5 directly bound to PPH and PAO promoters to promote their expression,leading to accelerating Chl degradation.On the other hand,the interaction between ABI5 and MYB44 reduced the binding of MYB44 to PPH and PAO promoters and led to the ubiquitination-depended protein degradation of MYB44,thereby alleviating the transcription inhibitory effect of MYB44 on PPH and PAO.Taken together,our findings propose a new regulatory network for ABI5 in regulating heat stress-induced Chl degradation.

Dot-Blot Hybridization for Detection of Five Cucurbit Viruses by Digoxigenin-Labelled cDNA Probes

Dot-blot hybridization was applied in this paper to detect five viruses infecting cucurbitaceous crops, Zuccini yellow mosaic virus （ZYMV）, Watermelon mosaic virus （WMV）, Cucumber mosaic virus （CMV）, Papaya ringspot viruswatermelon strain （PRSV-W） and Squash mosaic virus （SqMV）, as a good alternative assay in seed health test and epidemiological and transgenic research. Digoxigenin-labelled cDNA probes of the five viruses were synthesized by PCR with the specific primers and applied in dot-blot hybridization to detect five viruses in crude extraction of the infected leaves. And three SqMV probes of different lengths （0.55, 1.6, and 2.7 kb, respectively） were designed to investigate the effect of hybridization. The results showed that the sensitivity for detecting the crude extraction of infected leaves by ZYMV, WMV, CMV, PRSV-W, and SqMV was down to 1：160, 1：160, 1：320, 1：160, and 1：320, respectively. Three SqMV probes of different length showed no differences on the sensitivity and specificity. The digoxigenin-labelled probes prepared by PCR could be used for accurate and rapid identification of 5 viruses infecting cucurbitaceous crops with good stabilities, sensitivities, specificity, and reproducibilifies.

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

Pears with red skin are attractive to consumers and provide additional health benefits.Identification of the gene(s)responsible for skin coloration can benefit cultivar selection and breeding.The use of QTL-seq,a bulked segregant analysis method,can be problematic when heterozygous parents are involved.The present study modified the QTL-seq method by introducing a|Δ(SNP-index)|parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears.The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the‘Mantianhong’and‘Hongxiangsu’red-skinned cultivars.The‘Dangshansuli’cultivar genome was used as reference for sequence alignment.An average single-nucleotide polymorphism(SNP)index was calculated using a sliding window approach(200-kb windows,20-kb increments).Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM.There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin(R/G)locus,which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome.The ZFRI 130-16,In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations.This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

Genome-wide identification and expression analysis of NIN-like Protein(NLP)genes reveals their potential roles in the response to nitrate signaling in watermelon

To balance the relationship between high yield and low nitrogen supply,the nitrogen utilization efficiency of watermelon needs to be improved urgently.Nodule inception-like Protein(NLP)transcription factors play a key node role in nitrate response and growth and development of plant,however,comprehensive analysis of the NLP gene family in watermelon is unclear.This study explored the functional classification,evolutionary characteristics,and expression profile of the ClNLP gene family.Three ClNLPs were categorized into three groups according to their gene structure and phylogeny.All of them contained the conserved RWP-RK and PB1 domains.Evolutionary analysis of ClNLPs revealed that ClNLP1 and ClNLP3 underwent strong purified selection.In addition,cis-acting elements related to plant hormones and abiotic stresses were present in the ClNLP promoter.According to tissue-specific analysis ClNLP was widely expressed in roots,stems,leaves,flowers and fruits,and ClNLP1 was significantly induced in the roots of different nitrogen utilization varieties under different nitrate nitrogen supply.The SRTING functional protein association network suggested that ClNLP1 is associated with most genes,such as NRT1.1,NRT2.1,NIA1,and NIR1,and the dual-luciferase reporter assay found that ClNLP1 positively regulates the expression of ClNRT2.1.We speculated that ClNLP1 might play a central role in regulating the response of watermelon to nitrate nitrogen.

Transcriptomic profiling of watermelon(Citrullus lanatus) provides insights into male flowers development

Watermelon(Citrullus lanatus(Thunb.) Matsum. & Nakai) is an important cucurbit crop grown worldwide. Watermelon fruit quality, fertility, and seed-setting rate are closely related to male flower development. In this study, the different developmental stages of flower buds of the watermelon cultivar ’Xinteda Zhengkang 9’ were distinguished by cytological observation, and transcriptome sequencing analysis was performed subsequently. Acetocarmine staining of anthers was performed and the longitudinal and transverse diameters of the unopened male flower buds were measured. Cytological observations of anthers at different developmental stages showed that the anther grew from the tetrad to the mature stage, and the longitudinal and transverse diameters of the flower buds increased. The length of the male flower buds also changed significantly during development. Transcriptome sequencing analysis at four periods, the tetrad(A group), mononuclear(B group), dikaryophase(C group), and mature stages(D group). A total of 16 288 differentially expressed genes(DEGs) were detected in the four stages, with the prolongation of developmental stages, the number of DEGs increased gradually in the comparison groups, there was 2 014, 3 259, 4 628, 1 490, 3 495 and 1 132 DEGs revealed in six comparison groups(A-vs.-B, A-vs.-C, A-vs.-D, B-vs.-C, B-vs.-D, and C-vs.-D), respectively. Gene Ontology(GO) and KEGG enrichment analysis showed that the DEGs were mainly enriched in cellular component and starch and sucrose metabolism, phenylpropanoid biosynthesis and pentose sugar, etc. Finally, we completely screened 59 DEGs in the six comparison groups, interestingly, we found one pollen-specific protein(Cla001608) that was significantly down-regulated(the value of log2 Fold Change up to 17.32), which indicated that it may play an important role in the development of male flowers. This work provides insight into the molecular basis of the developmental stages of male flowers in watermelon and may aid in dominant cross breeding.

Comparative transcriptome analysis of the effect of different heat shock periods on the unfertilized ovule in watermelon(Citrullus lanatus)

In vitro gynogenesis is an important tool used in haploid or homozygous double-haploid plant breeding.However,because of low repeatability,embryoid induction rate and quality,the molecular mechanisms remain poorly understood.Heat shock treatment can promote the transformation of the gametophytic pathway into the sporophyte pathway,which induces the occurrence of haploid.In this study,unfertilized ovaries were heat shocked for 0 h(A0)before flowering and for 0 h(A1),4 h(A3),8 h(A5),12 h(A7),and 24 h(A8),respectively,at 37℃at the first day of the flowering stage.The ovule enlargement rate was increased from 0%at 25℃to 96.8%at 37℃(24 h treatment).Thus,we aimed to investigate the gene expression patterns in unfertilized ovules of watermelon after different periods of heat shock by using RNA-Seq technology.The results showed that compared with A3,A5,A7,and A8,the biosynthesis of amino acid,glycine,serine and threonine metabolic pathways in A1 has changed significantly.This indicated that heat shock treatment affected the synthesis and transformation of amino acids during ovule expansion.The transcriptome data suggested gene expressions of ovule growth were significantly changed by heat-specific influences.The results provide new information on the complex relationship between in vitro gynogenesis and temperature.This provides a basis for further study of the mechanism of heat shock affecting the expansion of watermelon ovule.

QTL mapping for berry shape based on a high-density genetic map constructed by whole-genome resequencing in grape

Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved in-depth results.Here,a high-density map was constructed to identify quantitative trait loci(QTLs)for berry shape.A total of 358709 polymorphic SNPs were obtained using whole-genome resequencing(WGS)based on 208 F2 individuals derived from round grape‘E42-6’and oblong grape‘Rizamat’.The 1635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM.Using this map,three significant QTLs for fruit shape index(ShI:ratio of berry length to berry width)identified over three years were mapped onto LG4 and LG5,including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb.Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry(their average ShI was 1.89 and 1.10,respectively)at four developmental stages,four candidate genes were selected from the above QTLs.They were mainly involved in DNA replication,cell wall modification,and phytohormone biosynthesis.Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes(DEGs),which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population.Furthermore,a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages.Our findings provide molecular insights into the genetic variation in grape berry shape.Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.