Prunus salicina 'Shazikongxinli' is one of the most economically valuable and reputable Prunus salicina varieties in China. Understanding the genetic diversity and population structure of 'Shazikongxinli' is crucial for excellent germplasm breeding and conservation of genetic resources. In the present study, the genetic variation status of 50 'Shazikongxinli' was assessed using morphological traits, IRAP and ISSR markers, while 18 other plum varieties were selected as outgroups. The results show that the average Shannon-Weaver diversity index (H') of 32 qualitative traits in 50 test 'Shazikongxinli' is 0.557, the average coefficient of variation of 11 quantitative traits is 15.57%, and a total of 232 and 105 polymorphic loci are obtained from 22 IRAP and 15 ISSR primers, respectively. All three marker systems show relatively rich polymorphism, especially the IRAP markers. This may be related to the nature of the retrotransposons in the IRAP markers, which may be more suitable for intraspecific variability detection than ISSR. In addition, all three markers cluster the 68-test germplasm into two groups, with all of 'Shazikongxinli' clustered into one group and most of the other plum varieties as outgroups clustered into another group. This suggests a relatively narrow genetic base within the current 'Shazikongxinli'. These results will be useful in understanding the genetic diversity of the germplasm resources of 'Shazikongxinli' and provide comprehensive information for the breeding of superior germplasm.

Rhododendron is well‐known for its beauty and colourful corolla. Although some high‐quality whole‐genome sequencing of it has been completed, there are few studies on long terminal repeat (LTR) retrotransposons in Rhododendron, which limits our ability to elucidate the causes of genetic variations in Rhododendron species. Properties of the intact Rhododendron LTR retrotransposons were investigated at a genome‐wide level. Based on available data, the high‐quality genomes from five species, i.e. R. griersonianum, R. simsii, R. henanense subsp. lingbaoense, R. mucronatum var. ripense and R. ovatum, were selected as targets with good assembly continuity. A total of 17,936 intact LTR retrotransposons were identified; these belong to superfamilies Copia and Gypsy, with 17 clades. The insertion time of these transposons was later than 120 million years ago (Mya), and the outbreak period was concentrated more recently than 30 Mya. Phylogenetic analysis revealed that many LTR retrotransposons might originate from intraspecific duplication. Current evidence also suggests that most LTR retrotransposons were inserted in the interstitial part of genes in R. griersonianum, R. simsii, R. henanense, and R. ovatum, and the functions of the inserted genes mainly involve starch metabolism, proteolysis, etc. The effect of the LTR retrotransposon on gene expression depends on its insertion site and activation. Highly expressed LTR retrotransposons tend to be younger. The results herein improve our knowledge of LTR retrotransposons in Rhododendron genomes and facilitate further study of genetic variation and trait evolution in Rhododendron.

Prunus salicina 'Shazikongxinli' is one of the most economically valuable and reputable Prunus salicina varieties in China. Understanding the genetic diversity and population structure of 'Shazikongxinli' is crucial for excellent germplasm breeding and conservation of genetic resources. In the present study, the genetic variation status of 50 'Shazikongxinli' was assessed using morphological traits, IRAP and ISSR markers, while 18 other plum varieties were selected as outgroups. The results show that the average Shannon-Weaver diversity index (H') of 32 qualitative traits in 50 test 'Shazikongxinli' is 0.557, the average coe cient of variation of 11 quantitative traits is 15.57%, and a total of 232 and 105 polymorphic loci are obtained from 22 IRAP and 15 ISSR primers, respectively. All three marker systems show relatively rich polymorphism, especially the IRAP markers.This may be related to the nature of the retrotransposons in the IRAP markers, which may be more suitable for intraspeci c variability detection than ISSR. In addition, all three markers cluster the 68-test germplasm into two groups, with all of 'Shazikongxinli' clustered into one group and most of the other plum varieties as outgroups clustered into another group. This suggests a relatively narrow genetic base within the current 'Shazikongxinli'. These results will be useful in understanding the genetic diversity of the germplasm resources of 'Shazikongxinli' and provide comprehensive information for the breeding of superior germplasm.

Background Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter conditions, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter conditions.Results To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3,584 differentially expressed genes were identified with the combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins ( Lhca and Lhcb ) and photosynthetic electron transporters (PsbP , PsbR , PsbY , and PetF ), were upregulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS , were clearly increased in comparison to those under shelter-free conditions, giving rise to improved CO 2 utilization. Furthermore, the transcription levels of genes involved in chlorophyll ( hemA , hemN , and chlH ) and carotenoid synthesis ( crtB , PDS , crtISO , and lcyB ) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid ( PAL , C4H , and 4CL ) and flavonoid ( CHS , CHI , F3’H , DFR , and ANS ) in the sheltered fruits were also upregulated earlier than those in the shelter-free fruits, conducive to an increase in anthocyanin content in the fruits.Conclusions According to the physiological indicators and transcriptional expression levels of related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.

Background: Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter covering, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter covering. Results: To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3,584 differentially expressed genes were identified with a combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins (Lhca and Lhcb) and photosynthetic electron transporters (PsbP, PsbR, PsbY, and PetF), were up-regulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS, were clearly increased compared with those under shelter-free conditions, resulting in improved CO2 utilization. Furthermore, the transcription levels of genes involved in chlorophyll (hemA, hemN, and chlH) and carotenoid synthesis (crtB, PDS, crtISO, and lcyB) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid (PAL, C4H, and 4CL) and flavonoid (CHS, CHI, F3’H, DFR, and ANS) in the sheltered fruits were also up-regulated earlier than of those in the unsheltered fruits, conducive to an increase in anthocyanin content in the fruits. Conclusions: According to the physiological indicators and transcriptional expression levels of the related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.