Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers

Abstract

The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of SSR markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that dinucleotide repeats were the most abundant (62.0%) type, followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. A total of 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, a total of 40 individuals from the F 2 population of Perilla were selected for association analysis based on their leaf-and plant-related characteristics. In an association analysis of 37 SSR markers and 9 leaf-and plantrelated traits in the 40 individuals of the F 2 population, we identi ed 12 and 11 SSR markers associated with leafrelated traits and plant-related traits, respectively. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through markerassisted selection (MAS) breeding programs.

Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea

“…The accessions of the CWTPC have the same number of chromosomes, 2n = 40 [ 13 ]. Additionally, cross experiments have been carried out by securing mating between accessions of the CWTPC using artificial pollination [ 14 , 15 , 16 , 17 , 18 , 19 ]. Therefore, it is important to understand the genetic variation and phylogenetic relationships between accessions of the CWTPC, and this will provide a rich source of information for making full use of germplasm resources in Perilla crop breeding programs.…”

“…In the Perilla crop, molecular marker technology has recently provided more comprehensive information on the genetic variation and phylogenetic relationships between and within accessions of the CWTPC. Molecular markers such as randomly amplified polymorphic DNA (RAPD) [ 3 , 12 ], amplified fragment length polymorphism (AFLP) [ 2 , 6 ], and simple sequence repeat (SSR) or microsatellite [ 5 , 7 , 19 , 20 , 21 , 22 ] have been successfully applied to accessions of the CWTPC, providing rich genetic diversity and genetic relationship information for genetic research of the Perilla crop. Among them, SSR markers are considered to be the preferred choices of markers for genetic studies because of their codominance, polymorphism, high repeatability, and rich genetic information [ 20 , 23 ].…”

Association analysis for agronomic traits in wheat under terminal heat stress

“…Simple sequence repeats markers distinguish the closely related genotypes due to existence of hyper variable regions in genome ( Pidigam et al, 2021 , Kim et al, 2021a , Kim et al, 2021b ). In current study, 165 SSR markers were utilized to observe genetic diversity among 158 wheat genotypes.…”

“…Quantitative trait loci (QTLs) are the nucleotides sequence on the genome controlling the trait of interest. It requires the progenies/population developed from crosses between desirable parents which includes RILs (recombinant inbred lines), backcross progenies, F 2 population, double haploid and near isogenic lines ( Kim et al, 2021a , Kim et al, 2021b , Bányai et al, 2021 ). QTL mapping have advantages viz., rare allele identification, few genetic markers requirement and no population structure effects.…”

“…QTL mapping have advantages viz., rare allele identification, few genetic markers requirement and no population structure effects. Whereas, disadvantages includes long period to develop populations, costly, laborious, limited detection of QTLs and few events of recombination consequently coarse mapping ( Kim et al, 2021a , Kim et al, 2021b , Bányai et al, 2021 ).…”