Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

Abstract

High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.

Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China

“…DNA fingerprinting has the advantages of being fast and accurate. In addition, DNA fingerprinting is a powerful tool for identifying varieties and strains, and it is also well suited for the identification of plant germplasm resources (Sorkheh et al, 2007 ; Gramazio et al, 2017 ; He et al, 2020 ; Wu et al, 2020 ). SNP marker-based high-throughput detection technology and data analysis is mainly based on the genetic characteristics of its “binary variation”—using two different fluorophores to label two different allelic variants—and a fluorescence detection system that can effectively distinguish two homozygous and one heterozygous genotypes.…”

MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry (Morella rubra)

“…It is rich in anthocyanins, proanthocyanidins, vitamin C, and volatile organic compounds (VOCs), and is known as the "treasure fruit of Jiangnan, " highly appreciated by the vast number of consumers. There are over 100 cultivars or varieties in this species (Wu et al, 2020). Normally, the cultivar is identified by the color and size of the fruit.…”

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

“…DNA ngerprinting is a powerful approach based on molecular markers or special sequences to identify genetic diversity and distinguish different cultivars in plants [29,30]. So far, DNA ngerprinting databases have been established in a series of plants such as maize [29,31], grapevine [32], cigar tobacco [33], and red bayberry [34], demonstrating their technical signi cance for variety identi cation and germplasm innovation. In cabbage, 50 core SNPs were selected from 59 varieties and used in e cient identi cation of seed authenticity and purity [35].…”