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.
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 F2 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 plant-related traits in the 40 individuals of the F2 population, we identified 12 and 11 SSR markers associated with leaf-related 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 marker-assisted selection (MAS) breeding programs.
In this study, genetic analysis was conducted on the inheritance of qualitative traits, such as leaf color, flower color, seed size, and seed hardness, in the F2 population derived from the cross between var. frutescens and var. crispa. As determined by the separation pattern of each trait in the F2 population, F2 plants with a green color were more common than those with a purple color on the leaf surface, whereas F2 plants with a purple color were more common than those with a green color on the reverse side of the leaf. For flower color, more F2 plants were observed to have a white color. For seed size, more F2 plants were observed to have a seed size of above 2 mm, and for seed hardness, more F2 plants were observed to have characteristics of seed hardness. Our examination of the genetic separation ratios with respect to Mendel's law of genetics revealed that three traits, leaf color (surface and reverse side) and flower color, did not follow the separation ratio of 1:2:1, and the seed size did not follow the segregation ratio of 3:1, but seed hardness was found to follow the separation ratio of 3:1. The results of this study are expected to provide basic information to help understand the genetic segregation of leaf and seed characteristics in the F2 population derived from the cross between var. frutescens and var. crispa, and also to provide useful information for breeding studies to assist the development of varieties of Perilla crop.
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