Comparative transcriptome analyses provide novel insights into etiolated shoot development of walnut (Juglans regia L.).

MAIN CONCLUSION: In general, genes promoting IAA, CTK GA and ethylene biosynthesis were upregulated, while genes participating in ABA, chlorophyll and starch biosynthesis pathways performed opposite tendency during etiolation. Etiolation as a method for rejuvenation plays an important role in the vegetative propagation of woody plants. However, the molecular mechanism of etiolated shoot development remains unclear. In this study, we investigated changes at different etiolation stages of Juglans regia. The histology and transcriptome of J. regia were analysed using etiolated stems, which were treated in darkness for 30, 60, 90 days. The results showed that the ratios of pith (Pi) diameter/stem diameter (D), cortex (Co) width/D, and phloem (Ph) width/D increased, while the ratio of xylem (Xy) width/D decreased after etiolation, and the difference in these ratios between etiolated stems and the control was more significant at 60 days than 90 days. Differentially expressed genes (DEGs) were significantly enriched in pathways such as plant hormone biosynthesis and signal transduction, chlorophyll biosynthesis and degradation, and starch and sucrose metabolism. The difference in the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), sugar and chlorophyll between etiolated stems and the control increased with increasing treatment duration; in contrast, the concentrations of gibberellin (GA), zeatin (ZT), and starch, as well as the difference between the etiolated stems and control were lowest at 60 days among the three stages. On the whole, the positive effect of etiolation on the rejuvenation of walnut stems changed as the treatment period increased. The present investigation lays a foundation for future studies on the effect of etiolation on rejuvenation and for promoting the efficiency of vegetative propagation.

Integrative Analysis of Metabolome and Transcriptome Reveals Molecular Insight into Metabolomic Variations during Hawthorn Fruit Development.

Hawthorn (Crataegus pinnatifida var. major), a cultivated fruit tree, is native and unique to China. Its fruits have high nutritional, health, and medicinal values. However, the development and ripening process of hawthorns is accompanied by dramatic changes in flavor, aroma, and bioactive phytochemicals, which are the fundamental factors that contribute to the potential health benefits and establishment of fruit quality. Therefore, an exploration of the dynamic changes in metabolites and their regulatory networks during the development of hawthorn fruits can elucidate the formation mechanisms of active substances in hawthorn fruits. In this study, we used a broad targeted metabolomics approach to identify and analyze the dynamics of metabolites in hawthorn fruits at five developmental stages. The results revealed 998 primary and secondary metabolites that were classified into 15 categories. The accumulation levels of most sugars increased during fruit development and then accelerated at the fruit ripening stage. The accumulation levels of a few organic acids (e.g., citric acid, isocitric acid, and quinic acid) continuously increased. Many organic acids exhibited significant decreasing trends. Among the 561 secondary metabolites detected, 189 were phenolic acids and 199 were flavonoids. The levels of many flavonoids were significantly reduced at later stages of fruit development; in contrast, the levels of two anthocyanins significantly increased during fruit ripening. Correlation analysis revealed that there is a certain correlation within and between primary as well as secondary metabolites during fruit development. Furthermore, the integration of metabolomic and transcriptomic data in this study revealed that changes in the expression of some differentially expressed genes (DEGs) were associated with the accumulation of metabolites such as sugars, organic acids, and flavonoids, e.g., the upregulated expression levels of CS (citrate synthase) genes were consistent with the continued accumulation of citric acid. Overall, this study demonstrates the metabolic changes that occur during the development of hawthorn fruit, explores the molecular mechanisms that underlie metabolite changes during fruit development, and lays a strong theoretical foundation for the improvement of hawthorn fruit quality and the development of functional components.

Corrigendum: Haplotype analysis of chloroplast genomes for jujube breeding.

[This corrects the article DOI: 10.3389/fpls.2022.841767.].

Haplotype Analysis of Chloroplast Genomes for Jujube Breeding.

Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.

The complete chloroplast genome of Crataegus bretschneideri Schneid. (Rosaceae).

Crataegus bretschneideri Schneid., with an unclear phylogenic position, is mainly distributed in northeast and inner mongolia area of China. In this study, the complete chloroplast genome sequence of C. bretschneideri was determined by using Illumina high-throughput sequencing method. The chloroplast genome was 159,607 bp in length and consisted of a large single-copy (LSC) region (87,601 bp), a small single-copy (SSC) region (19,312 bp), separated by a pair of inverted repeat (IRs: 26,347 bp, each) regions. It comprised a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on complete chloroplast genomes indicated that C. bretschneideri was closely related to C. marshallii Eggl in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.

The complete chloroplast genome of Crataegus hupehensis Sarg. (Rosaceae), a medicinal and edible plant in China.

Crataegus hupehensis Sarg. is well-known for its medicinal and nutritive value. In this study, the complete chloroplast genome sequence of C. hupehensis was determined by using Illumina high-throughput sequencing approach. The complete chloroplast genome is 159,766 bp with 36.6% GC content. It contained a pair of inverted repeat regions of 26,385 bp, a large single-copy region of 87,852 bp, and a small single-copy region of 19,144 bp. It contained 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicated that C. hupehensisis was closely related to C. kansuensis and C. marshallii in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.

Effects of green-manure and tillage management on soil microbial community composition, nutrients and tree growth in a walnut orchard.

This study characterized the effect of green manures (February orchid, hairy vetch, rattail fescue and a no-green-manure control) and the termination method (flail or disk) on nutrient contents, enzyme activities, microbial biomass, microbial community structure of rhizosphere soil and vegetative growth of walnut tree. All three selected green manures significantly enhanced the water content, organic C, total N and available P. The rattail fescue significantly decreased the mineral N. Total organic C, total N, mineral N and available P were significantly greater under flail than under disk. Hairy vetch and February orchid significantly improved levels of soil ß-glucosidase, N-acetyl-glucosaminidase and acid phosphatase activity, whereas rattail fescue improved only ß-glucosidase activity. All of the green manures significantly decreased phenoloxidase activity. ß-glucosidase, N-acetyl-glucosaminidase and acid phosphatase activities were significantly greater under flail relative to disk. The termination method had no significant effect on phenoloxidase activity. The different types of green manures and termination methods significantly altered the soil microbial biomass and microbial community structure. The green-manure treatments were characterized by a significantly greater abundance of Gram-positive (Gram +) bacteria, total bacteria and saprophytic fungi compared to the control. Hairy vetch significantly decreased the abundance of arbuscular mycorrhizal fungi (AMF) while February orchid and rattail fescue increased their abundance compared to the no-green-manure treatment. The abundance rates of Gram+ bacteria, actinomycetes, saprophytic fungi and AMF were significantly greater in soils under flail than under disk. In terms of vegetative growth of walnut tree, hairy vetch showed the greatest positive effects. The growth of walnut tree was significantly greater under flail relative to disk. Our results indicate that green-manure application benefits the rhizosphere soil micro-ecology, rhizosphere soil nutrient contents and tree growth. Overall, the hairy vetch and flail combined treatment is recommended for walnut orchards in northern China.

Chloroplast genome sequence of the wild Ziziphus jujuba Mill. var. spinosa from North China.

In this study, the complete chloroplast (cp) genome sequence of Ziziphus jujuba Mill. var. spinosa was mapped and determined based on Illumina sequencing data. The complete cp genome is 161,606 bp and contains a pair of inverted repeat regions of 26,479 bp each, a large single-copy region of 89,292 bp, and a small single-copy region of 19,356 bp. It harbors 112 unique genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on cp genomes indicates that the cp genome of wild Z. jujuba Mill. var. spinosa is similar to that of cultivated Z. jujuba and closely related to that of Z. incurva of the family Rhamnaceae.