The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.
Yu Bai, Ying Zhou, Xiaoqing Tang, Yu Wang, Fangquan Wang and Jie Yang
Shuang Jiang, Haishan An, Xiaoqing Wang, Chunhui Shi, Jun Luo and Yuanwen Teng
Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.
Chun-hui Shi, Xiao-qing Wang, Xue-ying Zhang, Lian-ying Shen, Jun Luo and Yu-xing Zhang
This study explored the effects of different colored bags (blue, green, white, yellow, orange, and red) on russet deposition on the peel of semi-russet ‘Cuiguan’ pears 10 days after full bloom (DAFB). The process of russeting of the peel and structure of the cork layer were characterized by microscopy and scanning electron microscopy (SEM), followed by the detection of lignin and the activity of enzymes involved in lignin synthesis. The expression of cinnamate-4-hydroxylase, 4-coumarate:coenzyme A ligase, cinnamyl alcohol dehydrogenase, cinnamoyl-CoA reductase, and peroxidase, which were related to phenylalanine ammonia-lyase, was determined via real-time quantitative polymerase chain reaction. Russeting of the outer peel of ‘Cuiguan’ pear accumulated rapidly at 80 DAFB, and a positive relationship between the russet index and lignin content was observed. Red and infrared (IR) ray, partial far-IR light (600–800 nm), and ultraviolet-A light (350–400 nm) promoted russeting in ‘Cuiguan’ pear peel, whereas green light decreased russeting, the russet index, enzymatic activities, and the expression levels of enzymes involved in lignin synthesis. Values of all these factors were higher for ‘Cuiguan’ pears in red bags than for those in bags of other colors. These findings suggested that spectral components affected the synthesis of lignin and the formation of fruit russet. Storage in green bags reduced russeting and improved fruit appearance.
Haishan An, Jiajia Meng, Fangjie Xu, Shuang Jiang, Xiaoqing Wang, Chunhui Shi, Boqiang Zhou, Jun Luo and Xueying Zhang
Vegetative propagation by cuttings is a very popular method. However, blueberry propagation using cuttings is still a main factor limiting its expansion because its results can vary according to the blueberry cultivar and environmental factors. This study aimed to evaluate the rooting abilities of hardwood cuttings for six blueberry cultivars (O’Neal, Misty, Diana, Biloxi, Bluebeauty, and Coville) using three different exogenous indole-butyric acid (IBA) concentrations (1000, 2000, and 3000 ppm), and to determine if the cutting position (basal, central, apical) affects rooting performance. A control treatment (0 ppm IBA) was also performed. After 90 days of each treatment, rooting percentage, average root length, and average root number per cutting were assessed and used to calculate rooting index, which is a measure of rooting ability. The rooting percentages of hardwood cuttings differed largely among cultivars and were highest for ‘Bluebeauty’ (68.55%), followed by ‘Biloxi’ (68.01%). The rooting index values of these two cultivars (33.59 and 35.18, respectively) were significantly higher than those of the other four cultivars. The rooting response of blueberry hardwood cuttings to IBA concentrations was quadratic, and 1000 and 2000 ppm IBA were sufficient to express the maximum rooting percentage in most cultivars. The rooting abilities of basal, central, and apical cuttings were similar with treatments with high IBA concentrations. The effects of the cultivar, IBA concentration, and interaction between them on rooting percentage, average root length, and average root number were significant; however, the effects of the cutting position on the rooting percentage and average root length were not. This suggested that the rooting abilities of blueberry hardwood cuttings were significantly influenced by the cultivar and IBA concentration rather than by the cutting position.