Development and Application of SNP-KASP Markers Based on Genes Related to Nitrogen Uptake, Assimilation and Allocation in Tea Plant (Camellia sinensis L.)

Abstract

Nitrogen is essential for the growth and quality formation of tea plants. Excessive and inefficient use of nitrogen fertilizer leads to cost increases and ecosystem pollution. It is important to improve the nitrogen use efficiency (NUE) for tea plantation. Breeding high-NUE varieties by marker-assisted selection using NUE-associated genes is a viable approach. However, few molecular markers related to nitrogen uptake and utilization have been identified in tea plants. In this study, a total of 2554 SNP loci within NUE-related genes were identified in a database. Of the non-synonymous SNPs, 46 were successfully converted to KASP markers. These markers were deployed on 35 tea germplasms to assess their suitability and accuracy in genetic analysis. The results show that 42 markers exhibited polymorphisms and the PIC values ranged from 0.05 to 0.38. The clustering results of the phylogenetic tree was basically consistent with the phenotype, showing that tea germplasms with high nitrogen accumulation and large biomass were grouped into one cluster. Using these markers, the fingerprints of these germplasms were constructed. The preliminary association analysis showed that there were two SNPs (CsSNP07 and CsSNP11) within CsNRT2.4 (CSS0001304) that were significantly associated with nitrogen accumulation (F = 4.631, P = 0.039 and F = 3.054, p = 0.047) and one SNP (CsSNP40) within CsAAP6 (CSS0035405) that was significantly associated with biomass (F = 3.842, p = 0.032). These functional SNP-KASP markers will be valuable for the early evaluation of tea germplasms and could accelerate the breeding of high-NUE varieties.