Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze)

Background Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-assimilation in the collection of tea plant Camellia sinensis (L.) Kuntze. In addition, the objective of this study was to reveal efficient vegetation indices for phenotyping of nitrogen deficiency response in tea collection. Methods The study was conducted on the tea plant collection of Camellia sinensis (L.) Kuntze of Western Caucasus grown without nitrogen fertilizers. Phenotypic data was collected by measuring the spectral reflectance of leaves in the 350–1100 nm range calculated as vegetation indices by the portable hyperspectral spectrometer Ci710s. Single nucleotide polymorphisms were identified in 30 key genes related to nitrogen assimilation and tea quality. For this, pooled amplicon sequencing, SNPs annotation and effect prediction with SnpEFF tool were used. Further, a linear regression model was applied to reveal associations between the functional SNPs and the efficient vegetation indices. Results PCA and regression analysis revealed significant vegetation indices with high R2 values (more than 0.5) and the most reliable indices to select ND-tolerant genotypes were established: ZMI, CNDVI, RENDVI, VREI1, GM2, GM1, PRI, and Ctr2, VREI3, VREI2. The largest SNPs frequency was observed in several genes, namely F3’5’Hb, UFGTa, UFGTb, 4Cl, and AMT1.2. SNPs in NRT2.4, PIP, AlaDC, DFRa, and GS1.2 were inherent in ND-susceptible genotypes. Additionally, SNPs in AlaAT1, MYB4, and WRKY57, were led to alterations in protein structure and were observed in ND-susceptible tea genotypes. Associations were revealed between flavanol reflectance index (FRI) and SNPs in ASNb and PIP, that change the amino acids. In addition, two SNPs in 4Cl were associated with water band index (WBI). Conclusions The results will be useful to identify tolerant and susceptible tea genotypes under nitrogen deficiency. Revealed missense SNPs and associations with vegetation indices improve our understanding of nitrogen effect on tea quality. The findings in our study would provide new insights into the genetic basis of tea quality variation under the N-deficiency and facilitate the identification of elite genes to enhance tea quality

Circular Mining Wastes Management for Sustainable Production of Camellia sinensis (L.) O. Kuntze

Mining operations have a significant negative impact on the surrounding ecosystems. The operation of mines and quarries creates a large amount of waste that accumulate and are practically unrecyclable in the environment. The involvement of these wastes in economic activity is an extremely urgent task. This can make the economy more sustainable and reduce its influence on ecosystems. This work presents the attempts of using quarry wastes as a fertilizer applied for growing tea crops. The novelty of this research involves revealing the quarry wastes as a fertilizer when growing Camellia sinensis (L.) O. Kuntze and assessing changes in the productivity of this plant when applying these calcium wastes. The waste of a quarry intended for extracting crushed stone was studied in this article. The composition of the waste was analyzed. Fertilizers used for manuring the soil were prepared based on the waste. Two experimental sites were selected. One of them was a control, where Camellia sinensis (L.) O. Kuntze was grown without using fertilizers. Fertilizers obtained from the waste were applied on the second site. The experimental work proceeded for 10 years. When discussing the results, special attention was paid to climatic conditions. This was caused by the need to show that it was the use of the fertilizer that influenced the change in the yield, not the climatic conditions. As a result of using calcium fertilizers based on the waste, the productivity of Camellia sinensis (L.) O. Kuntze was increased. The application of the fertilizers based on the quarry wastes was shown to provide an increase in the yield. The possibility of using calcium fertilizers to overcome unfavorable agroclimatic conditions during the tea cultivation was also demonstrated. To assess the climatic impact of applying new fertilizers, three-dimensional modeling in the “gnuplot v.5.4” software was used. As a result, an increase in the average annual precipitation, from 1000 to 1980 mm/year, in the range of the average annual air temperature, from 14 to 16 °C, was found to lead to an increase (when using a new fertilizer) in the yield of Camellia sinensis (L.) O. Kuntze up to 4.8 times (from 20 to 95 centner/ha). The results have shown that applying fertilizers based on the quarry wastes is also possible in unfavorable climatic conditions