First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

Abstract

Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

“…In this study, a total of 54526 SSRs were discovered from the cashew genome, with a mean density of 153 SSRs/Mb. The density of markers found in this study was higher than that reported in apple (40.8 SSRs/Mb, 485 Mb) ( Zhang et al., 2021b ), Chinese spring wheat (36.68 SSRs/Mb, 9.93 Gb) ( Han et al., 2015 ), and Matthiola incana (23.25 SSRs/Mb, 1977.48 Mb) ( Tan et al., 2023 ), while it was less than mango (418.17 SSRs/Mb, 253.6 Mb) ( Ravishankar et al., 2015 ), Prunus mume (794 SSRs/Mb, 237 Mb) ( Sun et al., 2013 ), and Pomegranate (527.97 SSRs/Mb, 296 Mb) ( Patil et al., 2020 ), suggesting that generally, the density of SSRs decrease with an increase in the genome size. Further, the frequency of perfect SSRs (87.39%) was much higher than the frequency of imperfect SSRs (12.61%) in the discovered genome-wide SSRs and is consistent with similar results in eggplant ( Portis et al., 2018 ), Anemone coronaria ( Martina et al., 2022 ), and Aristotelia chilensis ( Bastías et al., 2016 ).…”

Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea

“…AT/TA repeat motifs (62.44%) were most frequently distributed in di-nucleotides. It has also been observed in Matthiola incana [43], rice [44], Fagopyrum tataricum [45], and other species. This may be the reason for the higher number of slips in shorter repetitions [46].…”

The Relationship Between the Genetic Marker DIK20 and A Range of Physiological and Productive Traits in Holstein Cattle

“…Genetic markers, which encompass any observable or testable phenotype, as well as the genetic basis for assessing the observed phenotypic variability, are collectively known as. There are three categories for genetic markers: morphological and productive features, which are visually determined; biochemical markers, which are based on gene products; and molecular markers, which are based on DNA analysis (Sudan et al, 2016;Tan et al, 2023). The study samples revealed two genetic polymorphisms, 270/260 and 280/271, with significantly different percentages of 63.79 (2010) pointed out the high productivity potential of using techniques for estimating and preserving genetic material, as well as emphasizing that genetic markers have a role in preserving animal breeds.…”