Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

Abstract

<jats:p>Chinese bayberry (<jats:italic>Morella rubra</jats:italic>) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (<jats:italic>N</jats:italic><jats:sub><jats:italic>a</jats:italic></jats:sub>) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.</jats:p>

Development of High Quality EST-SSR Markers Without Stutter Bands in Peach and Their Application in Cultivar Discrimination and Hybrid Authentication

“…However, for some SSR markers, accurate size identification and allele designation can be difficult due to the presence of stutter bands, or stutter peaks. This problem was encountered in our preliminary study in peach as well as extensively reported in other plants (Caruso et al, 2008;Goulão and Oliveira, 2001;Huang et al, 2000;Jones et al, 1997;Song et al, 2002;Teulat et al, 2000;Wang et al, 2016;W€ unsch and Hormaza, 2002). The stutter bands occur as a result of enzyme slippage during amplification and was most common for SSR markers with dinucleotide motifs and the problem is amplified as the repeat number of the alleles increases (Guichoux et al, 2011;Hite et al, 1996).…”

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

“…Red bayberry has been domesticated by humans for more than 2000a, and thus it is difficult to infer the founder wild populations of the modern red bayberry cultivars. Previous clustering analysis of M. rubra accessions using data of AFLP (Zhang et al, 2009) and SSRs (Jia et al, 2014;Jia et al, 2015;Wang et al, 2016) yielded significantly inconsistent results, with clustered groups ranging from 2 to 6 groups. Although large groups were not well supported by all studies for supporting rates were either very low (< 50%) (Jia et al, 2014;Jia et al, 2015) or not provided (Zhang et al, 2009;Wang et al, 2016), several small groups were nevertheless well supported by SSR based clustering.…”

“…Research on the population structure of wild red bayberry in Guangxi province identified two main groups (He et al, 2010). More studies on the genetic diversity and putative clusters of red bayberry accessions yielded quite different results (Zhang et al, 2009;Jia et al, 2014;Jia et al, 2015;Wang et al, 2016). Moreover, the large clusters identified in these studies either had low (< 50%) bootstrap support or had no support rate given.…”

“…In this respect, much effort has been made to identify molecular markers associated with its important traits such as sex determination ( Jia et al, 2019 ; Wang et al, 2020 ). Different types of molecular markers have been mined and applied, including amplified fragment length polymorphism (AFLP) ( Zhang et al, 2009 ), inter-simple sequence repeat (ISSR) ( He et al, 2010 ), simple sequence repeat (SSR) ( Jiao et al, 2012 ; Jia et al, 2015 ; Wang et al, 2016 ; Wang et al, 2020 ), inter primer binding site (iPBS), and start codon targeted polymorphism (SCoT) ( Chen and Liu, 2014 ). Liu et al (2015) applied restriction site-associated DNA sequencing (RAD-seq) on pooled DNA of 18 individuals from 6 species (including M. rubra ) of Morella and detected 8,360 single nucleotide polymorphisms (SNPs).…”