Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Abstract

Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.

Application of Multi-Perspectives in Tea Breeding and the Main Directions

“…A genetic linkage map based on amplified fragment-length polymorphism (AFLP), simple sequence repeat (SSR) and RAPD markers was constructed to design the molecular markers related to tea plants resistance and quality, as well as to promote the localization and mining of quantitative trait loci (QTLs) for essential traits in tea plants [ 110 ]. In addition, intron length polymorphic (ILP), sequence-related amplified polymorphism (SRAP), start codon targeted polymorphism (SCoT), cleaved amplified polymorphic sequence (CAPS) and other markers have also been developed and applied in tea plants, which laid the foundation for subsequent marker-assisted breeding and genetic diversity analysis [ 23 , 111 , 112 ].…”

Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels

“…As a crucial and abundant part of plant genomes, TEs have been used as genetic markers in plant research and breeding. Molecular marker systems based on TEs have been effectively employed in crop breeding, notably in rice and tea, enabling precise identification of desirable traits and the development of superior crops [11,12]. The use of TE-derived markers in genome-wide association studies (GWAS) may recover a large portion of single-nucleotide polymorphism (SNP)-based GWAS peaks and, in the meantime, reduce false positives associated with linkage disequilibrium among SNP markers [13].…”