The genome of low-chill Chinese plum "Sanyueli" (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds.

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum "Sanyueli", which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46 Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in "Sanyueli" revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of "Sanyueli" was significantly lower than that in the dormant flower buds of the high chill requiring "Furongli" plum. In addition, PsDAM6 expression was repressed by chilling treatment. The genome sequence of "Sanyueli" plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Activation of PsMYB10.2 Transcription Causes Anthocyanin Accumulation in Flesh of the Red-Fleshed Mutant of 'Sanyueli' (Prunus salicina Lindl.).

Plum is one of the most important stone fruits in the world and anthocyanin-rich plums are increasingly popular due to their health-promoting potential. In this study, we investigated the mechanisms of anthocyanin accumulation in the flesh of the red-fleshed mutant of the yellow-fleshed plum 'Sanyueli'. RNA-Seq and qRT-PCR showed that anthocyanin biosynthetic genes and the transcription factor PsMYB10.2 were upregulated in the flesh of the mutant. Functional testing in tobacco leaves indicated that PsMYB10.2 was an anthocyanin pathway activator and can activate the promoter of the anthocyanin biosynthetic genes PsUFGT and PsGST. The role of PsMYB10.2 in anthocyanin accumulation in the flesh of plum was further confirmed by virus-induced gene silencing. These results provide information for further elucidating the underlying mechanisms of anthocyanin accumulation in the flesh of plum and for the breeding of new red-fleshed plum cultivars.

Changes in secondary metabolites, organic acids and soluble sugars during the development of plum fruit cv. 'Furongli' (Prunus salicina Lindl).

BACKGROUND: Organic acids, sugars and pigments are key components that determine the taste and flavor of plum fruit. However, metabolism of organic acid and sugar is not fully understood during the development of plum fruit cv. 'Furongli'. RESULTS: Mature fruit of 'Furongli' has the highest content of anthocyanins and the lowest content of total phenol compounds and flavonoids. Malate is the predominant organic acid anion in 'Furongli' fruit, followed by citrate and isocitrate. Glucose was the predominant sugar form, followed by fructose and sucrose. Correlation analysis indicated that malate content increased with increasing phosphoenolpyruvate carboxylase (PEPC) activity and decreasing nicotinamide adenine dinucleotide-malate dehydrogenase (NAD-MDH) activity. Citrate and isocitrate content increased with increasing PEPC and aconitase (ACO) activities, respectively. Both acid invertase and neutral invertase had higher activities at the early stage than later stage of fruit development. Fructose content decreased with increasing phosphoglucoisomerase (PGI) activity, whereas glucose content increased with decreasing hexokinase (HK) activity. CONCLUSION: Dynamics in organic acid anions were not solely controlled by a single enzyme but regulated by the integrated activity of enzymes such as nicotinamide adenine dinucleotide phosphate-malic enzyme (NADP-ME), NAD-ME, PEPC, ACO and NADP-isocitrate dehydrogenase. Sugar metabolism enzymes such as PGI, invertase and HK may play vital roles in the regulation of individual sugar metabolic processes. © 2018 Society of Chemical Industry.

[Mapping and cloning of GAD1-2 for long awn using CSSLs in rice (Oryza sativa L.)].

Rice is an important food crop in the world. The awn may protect rice seeds from being cut by birds, which is important in rice domestication, survival and diffusion. However, the characteristic of awn is gradually washed out during rice domestication and artificial selection. Mapping and cloning of rice awn genes is the basis of studying the genetic mechanism of awn domestication. In this study, 146 chromosome segment substitution lines (CSSLs) derived from DongNanHui 810/ZhangPu wild rice with DongNanHui 810 as the recurrent parent were used to analyze the quantitative trait loci (QTL) controlling the long awn of rice. The results showed that four CSSLs contained one QTL for the long awn. Using substitution mapping, the GAD1-2 gene was mapped between two markers (Ind8-10 and RM4936) on chromosome 8, with a genetic distance of about 4.75 Mb. Using the dominant individuals of segregating populations, the GAD1-2 gene was eventually located between two Indel markers, with a physical distance of about 27 kb, which contained only two candidate genes Os08g0485500 and Os08g0485400. Sequencing analysis showed that Os08g0485500 was the candidate gene of GAD1-2. Further analysis showed that there were six bases missing in the conservative ORF region, resulting in the absence of serine and cysteine that led to the long awn of the four CSSLs. The GAD1 gene was also cloned in this position, suggesting that GAD1-2 and GAD1 were allelic. This study laid a foundation for further understanding of the genetic regulation mechanism and genetic evolution of the awn gene in rice.

Identification of candidate genes involved in anthocyanin accumulation in the peel of jaboticaba (Myrciaria cauliflora) fruits by transcriptomic analysis.

Jaboticaba is a grape-like fruit that accumulates high levels of anthocyanins in the peel and is proposed as a good source of functional pigments. However, the molecular mechanisms underlying anthocyanin accumulation in jaboticaba peel remains to be elucidated. In this study, we employed RNA-seq technique to compare the transcriptomic differences between green-colored and black-colored jaboticaba peels. Over 5 million high-quality reads were assembled into 62,190 unigenes with an average length of 737 bp, 29,320 (47.15%) of them were annotated by public databases. 2152 unigenes were found to be differentially expressed (830 upregulated and 1322 downregulated). Gene ontology analysis and pathway enrichment annotation revealed that 18 differentially expressed genes encode phenylalanine ammonialyase, 4-coumaroyl:CoA-ligase, chalcone synthase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, anthocyanidin synthase, UDP-glucose: flavonoid 3-O-glucosyltransferase, glutathione S-transferase, Cytochrome b5 were associated with anthocyanin biosynthesis. Additionally, 54 differentially expressed transcription factors were identified. Furthermore, the expression of genes involved in biosynthesis and signal transduction of ethylene and abscisic acid were negatively and positively correlated with that of anthocyanin pathway genes and anthocyanin accumulation, respectively. Quantitative reverse transcription PCR analysis of candidate genes showed trends similar to those in the RNA-seq analysis. McMYB, a homolog of AtMYB113, induced anthocyanin accumulation in tobacco leaves when co-infiltrated PsbHLH3. These results will contribute to further understanding of the molecular mechanisms regulating anthocyanin accumulation in jaboticaba peel.

Identification of Candidate Anthocyanin-Related Genes by Transcriptomic Analysis of 'Furongli' Plum (Prunus salicina Lindl.) during Fruit Ripening Using RNA-Seq.

Anthocyanins are important pigments and are responsible for red coloration in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits. In this study, the RNA-seq technique was used to analyze the transcriptomic changes during fruit ripening in the red-fleshed plum (Prunus salicina Lindl.) cultivar 'Furongli'. Over 161 million high-quality reads were assembled into 52,093 unigenes and 49.4% of these were annotated using public databases. Of these, 25,681 unigenes had significant hits to the sequences in the NCBI Nr database, 17,203 unigenes showed significant similarity to known proteins in the Swiss-Prot database and 5816 and 8585 unigenes had significant similarity to existing sequences in the Kyoto Encyclopedia of Genes and Genomes and the Cluster of Orthologous Groups databases, respectively. A total of 3548 unigenes were differentially expressed during fruit ripening and 119 of these were annotated as involved in "biosynthesis of other secondary metabolites." Biological pathway analysis and gene ontology term enrichment analysis revealed that 13 differentially expressed genes are involved in anthocyanin biosynthesis. Furthermore, transcription factors such as MYB and bHLH, which may control anthocyanin biosynthesis, were identified through coexpression analysis of transcription factors, and structural genes. Real-time qPCR analysis of candidate genes showed good correlation with the transcriptome data. These results contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in plum flesh. The transcriptomic data generated in this study provide a basis for further studies of fruit ripening in plum.

[Morphological characteristics and gene mapping of a palea degradation(pd2) mutant in rice].

The yield and quality of rice are directly impacted by floral organ development in rice. Understanding of the floral development mechanism will be useful in genetic improvement of yield and quality. In this study, a rice mutant palea degradation 2 (pd2) in an indica cultivar '8PW33' was obtained after 60Co γ-ray treatment. Analysis of the mutant showed that, compared to the wild type, plant height, total grain number per panicle, and sword leaf width were significantly increased, but the seed setting rate were significantly decreased. The florets of the mutant exhibited degraded palea and sickle-shaped tortuous lemma. Detail examination using scanning electron microscopy revealed that when epidermis of the vane and lemma were normal, epidermis of the palea were arranged tightly, which might result from degraded palea. Genetic analysis supported that this mutation phenotype was controlled by a single recessive gene. Polymorphic analysis of simple sequence repeat markers demonstrated that PD2 gene is located on chromosome 9. With a larger mapping population and more indel markers, we further mapped PD2 gene between 2 indel markers with a physical region of about 82 kb. Within this region, there is a cloned gene REP1 known to control rice palea development. By comparing the DNA sequences of REP1 from pd2 and 8PW33, in combination with the results of phenotypic analysis, we concluded that PD2 is an allele of REP1.