Identification of yield-related genes through genome-wide association: case study of weeping forsythia, an emerging medicinal crop.

KEY MESSAGE: This study identified candidate genes related to fruit yield for an emerging medicinal crop, weeping forsythia. BACKGROUND: The genetic basis of crop yield is an agricultural research hotspot. Identifying the genes related to yield traits is the key to increase the yield. Weeping forsythia is an emerging medicinal crop that currently lacks excellent varieties. The genes related to fruit yield in weeping forsythia have not been identified. OBJECTIVE: Thus, we aimed to screen the candidate genes related to fruit yield of weeping forsythia by using genome-wide association analysis. METHODS: Here, 60 samples from the same field and source of weeping forsythia were collected to identify its yield-related candidate genes. Association analysis was performed on the variant loci and the traits related to yield, i.e., fruit length, width, thickness, and weight. RESULTS: Results from admixture, neighbor-joining, and kinship matrix analyses supported the non-significant genetic differentiation of these samples. Significant association was found between 2 variant loci and fruit length, 8 loci and fruit width, 24 loci and fruit thickness, and 13 loci and fruit weight. Further search on the 20 kb up/downstream of these variant loci revealed 1 gene related to fruit length, 16 genes related to fruit width, 12 genes related to fruit thickness, and 13 genes related to fruit weight. Among which, 4 genes, namely, WRKY transcription factor 35, salicylic acid-binding protein, auxin response factor 6, and alpha-mannosidase were highly related to the fruit development of weeping forsythia. CONCLUSION: This study identify four candidate genes related to fruit development, which will provide useful information for the subsequent molecular-assisted and genetic breeding of weeping forsythia.

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia.

BACKGROUND: Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. RESULTS: Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. CONCLUSIONS: Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

[Community structure and leaf trait diversity in a vulnerable species, Phoebe chekiangensis (Lauraceae).] / æ¸å±æ¤ç‰©æµ™æ±Ÿæ¥ ç¾¤è½ç»“æž„åŠå¶ç‰‡æ€§çŠ¶å¤šæ ·æ€§.

Phoebe chekiangensis, as one original species of 'Nanmu with golden tint', harbors limited natural distribution regions, which is recognized as a vulnerable species in China under nationwide protection. Under the background of global climate change, it is of scientific significance to study the community structure and diversity of the natural populations of P. chekiangensis. In this study, community structure, species diversity and the phenotypic variation leaf traits in the communities of thirteen residue natural populations were analyzed. A total of 235 vascular species from 162 genera and 87 families were found in 16 plots within 13 natural populations, including 221 seed plants from 151 genera and 79 families. The species diversity in tree layer of community in Kaihua, Zhejiang and Linan, Zhejiang was significantly lower than that of other communities due to severe disturbance, while intermediate disturbance promoted the species diversity of shrub layer in community in Jianning, Fujian, and slight disturbance was beneficial to natural regeneration of P. chekiangensis. Foliage phenotype was important for species identification within Phoebe genus. There existed substantial variation in foliage phenotypic diversity among and within populations. The mean coefficient of variation was 17.2%, ranging from 10.4% to 27.5%. The variation was greater among populations (53.6%) than within populations (17.0%). Mean phenotypic differentiation coefficient was 75.1% among populations, indicating that the variance among populations was the main source for the phenotypic variation of the species. Results from the cluster analysis indicated that the 13 natural populations were divided into two distinct groups based on the Euclidean distance (10 cm), with stochastic variation.

[Characteristics of rain season atmospheric PM2.5 concentration and its water-soluble ions contents in forest parks along an urban-rural gradient in Guangzhou City of South China].

During the rainy season (April-September) of 2012, the atmospheric particulate matter with a diameter less than 2.5 mm (PM2.5) were sampled from the forest parks in the urban area, suburban area, and rural area of Guangzhou City. The mass concentration of PM2.5 and its water-soluble ions (SO4(2-), NO3-, NO2-, Cl-, F-, Na+, NH4+, Ca2+, K+, and Mg2+) contents were also measured. In the forest parks in the urban area, suburban area, and rural area, the diurnal variation of PM2.5 mass concentration was 21.8-161.7, 19.4-156.3, and 17.2-66.5 microg x m(-3), with an arithmetic average being 55.9, 49.8, and 44.4 microg x m(-3), respectively. SO4(2-), Na+, and NH4+ were the main components of water-soluble ions in the PM2.5, and the SO4(2-) had the highest content and decreased gradually from urban to rural forest parks. The contribution of the SO2 and NOx in the PM2.5 from coal combustion to the forest parks was larger than that from vehicle exhaust, but presented a decreasing trend from urban to rural forest parks, indicating that vehicle exhaust had a greater contribution to the atmospheric SO2 and NOx in the urban forest park. In the sampling period, the contribution of sea salt to the water soluble fractions (especially K+) of the PM2.5 was greater for the suburban forest park than for the other two parks. The equivalent concentration of the NH4+ in the PM2.5 was far less than those of the SO4(2-) and NO3-, with a neutralization ratio being much lower than 1.0, which suggested that the PM2.5 had a higher acidity. The PM2.5 acidity had an increasing trend from rural to urban forest parks.

[Identification of plant species based on DNA barcode technology].

It is crucial for the studies of taxonomy and biodiversity by using DNA barcode technology to fast and accurately make species identification in the forests across tropics and temperate zones. In this study, the 183 plant species in a 20 hm2 subtropical forest plot in Dinghushan (DHS) National Nature Reserve of South China were sampled and sequenced, and the matK, rbcL, and psbA-trnH were employed to generate multi-locus barcodes. For the plot, the psbA-trnH possessed the highest integral success rate, i. e., the product of sequencing recovery and correct species identification (75%), followed by matK (70%), and rbcL (56%). A combination of three-locus barcode (matK, rbcL and psbA-trnH) could identify greater than 87% of the total species, followed by two-locus barcode (85% for matK+psbA-trnH, 83% for rbcL+psbA-trnH, and 81% for matK+rbcL). A comparison was made with the previously published results from one subtropical forest plot (LFDP in Puerto Rico, 143 species) and two tropical forest plots (BCI in Panama, 296 species; and NRS in French Guiana, 254 species) to evaluate the universality and species identification correctness of the proposed DNA barcodes for these four forest plots. For the plots in tropics and subtropics, the sequencing success rate of rbcL, psbA-trnH and matK were 93% and 95.1%, 91.5% and 94.6%, and 68.5% and 79.7%, respectively. The combination of matK + rbcL showed a high identification capacity in geographically restricted regions in taxonomic groups, whereas the three-locus barcode had a high rate of correct species identification both in tropics (84%) and in subtropics (90%).