Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Abstract

Camellia chekiangoleosa is a popular variety of Oil-camellia that has high oil production and ornamental value. Microsatellite (SSR) markers are the preferred tool for the molecular marker-assisted breeding of C. chekiangoleosa. By focusing on the problems of the low development efficiency of polymorphic SSR markers and the lack of available functional markers in Oil-camellia, we identified 97,510 SSR loci based on the full-length transcriptome sequence of C. chekiangoleosa. An analysis of SSR characteristics showed that mononucleotide (51.29%) and dinucleotide (34.36%) SSRs were the main repeat types. The main SSR distribution areas based on proportion covered were ordered as follows: 5'UTR > 3'UTR > CDS. By comparing our data with those in databases such as GO and KEGG, we obtained functional annotations of unigene sequences containing SSR sites. The data showed that the amplification efficiency of the SSR primers was 51.72%, and the development efficiency of polymorphic SSR primers was 26.72%. Experiments verified that dinucleotide and pentanucleotide SSRs located in UTR regions could produce more polymorphic markers. An investigation into the genetic diversity of several C. chekiangoleosa populations also suggested that the developed SSR markers had higher levels of polymorphism. This study will provide a reference and high-quality markers for the large-scale development of functional SSR markers and genetic research in Oil-camellia.

Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu) in Indonesia

“…The dominant SSR motifs in other palmae families are dinucleotides in coconut (Cocos nucifera) (Hatta et al 2022) A B and oil palm (Elaeis guineensis) (Xiao et al 2014;Zhou et al 2020). SSR dinucleotide motifs are dominant in other plants such as Oil-Camellia (Camellia oleifera) (Tian et al 2022) and Himalayan Canary (Juglans regia) (Itoo et al 2023). The abundance of dinucleotides increases the chance of amplification, because there are many dinucleotides compared to the others.…”