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The comparative gene expression concern to the seed pigmentation in maize (Zea mays L.)
Sa, Kyu Jin,Choi, Ik-Young,Lee, Ju Kyong Korea Genome Organization 2020 Genomics & informatics Vol.18 No.3
Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. In differentially expressed gene analysis, it was revealed that 7,044 genes were differentially expressed by at least two-fold, with 4,067 upregulated in colored maize inbred lines and 2,977 upregulated in colorless maize inbred lines. Of them,18 genes were included to the anthocyanin biosynthesis pathways, while 15 genes were upregulated in both CM22/5 and CM22/19. Additionally, 37 genes were detected in the metabolic pathway concern to the seed pigmentation by BINs analysis using MAPMAN software. Finally, these differently expressed genes may aid in the research on seed pigmentation in maize breeding programs.
Characterization of volatile compounds of Perilla crop (Perilla frutescens L.) in South Korea
Sa Kyu Jin,Jang So Jung,Lee Sookyeong,Park Hyun,Cho Jungeun,Sung Jungsook,Lee Ju Kyong 한국응용생명화학회 2023 Applied Biological Chemistry (Appl Biol Chem) Vol.66 No.-
This study was performed to identify and profile the volatile compounds present in three different types of Perilla leaves collected from South Korea. Volatile compounds were analyzed by gas-chromatograph-mass spectrometry. In total, 41 volatile compounds were identified belonging to nine chemical classes (six alcohols, seven aldehydes, two benzodioxoles, two esters, three ethers, four ketones, five monoterpenes, one phenylpropanoid, and eleven sesquiterpenes). In cultivated type of var. frutescens (CF), weedy type of var. frutescens (WF), and weedy type of var. crispa (WC), a total of 34, 39, and 41 volatile compounds, respectively, were identified. The predominant compound in CF and WF was perilla ketone (PK; 87.2% and 64.5%, respectively) and in WC was perilla aldehyde (PA; 26.4%). There were 29 and 27 volatile compounds that showed significant differences of content between WC and CF or WF, respectively. In terms of chemotype based on the volatile compounds, CF and WC were PK type and PA or phenylpropanoid (PP) types, respectively. WF accessions, which were PK and PP types in chemical composition, showed intermediate characteristics in the composition of volatile compounds compared with CF and WC. The results obtained in this study identified successfully the composition and content of volatile compounds in Perilla crop in South Korea. These results will provide useful information for industries and research related to Perilla crop.
Jin-Ah Kim,Kyu Jin Sa,Ju Kyong Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
In this study, 18 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, genetic relationships, and population structure among 96 accessions of the two cultivated types of Perilla crop and their weedy types in East and Southeast Asia. A total of 168 alleles were identified at all the loci with an average of 9.3 and a range between 3 and 18 alleles per locus. Of the 168 alleles, 21 alleles (12.5%) were private, 67 alleles (39.9%) were rare (frequency < 0.05), 96 alleles (57.1%) were detected at an intermediate frequency (range, 0.05 - 0.50), and five alleles (3.0%) were abundant (frequency > 0.50), respectively. The gene diversity values varied from 0.443 to 0.898 with an average of 0.749. The PIC values varied from 0.397 to 0.890 with an average of 0.721. The gene diversity of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were respectively showed 0.662, 0.744, 0.540, and 0.584. On the analysis of population structure using software program STRUCTURE 2.2, the 96 Perilla accessions were divided into Groups I, II, and admixed group. The phylogenetic tree revealed that the 96 accessions cluster into three major groups. No clear geographic structure and also between two cultivated types of Perilla crop and their weedy types were detected. The present study has demonstrated the utility of SSR analysis for the study of genetic diversity, genetic relationships and population structure among 96 accessions of the two cultivated types of Perilla crop and their weedy types in East and Southeast Asia. In our study, SSR markers helped improve our understanding of the genetic diversity, genetic relationships, and population structure of the two cultivated types of P. frutescens and their weedy types in East and Southeast Asia.
Sa, Kyu Jin,Ko, Woo Ri,Kim, O. Gyeom,Ma, Shi Jun,Choi, Hong-Jib,Lee, Ju Kyong 한국유전학회 2016 Genes & Genomics Vol.38 No.9
<P>This study assessed the genetic and phenotypic variation of 90 super sweet corn inbred lines and performed association analyses of six agronomical traits using 100 simple sequence repeats (SSR), ultimately detecting 590 alleles, with an average of 5.90 alleles per locus. The average genetic diversity and Polymorphism information content values were 0.54 and 0.50, respectively. Using population structure analysis, inbred lines were divided into three major groups and one admixed group. Association analysis was performed with a general linear model using a Q-matrix (Q GLM) and a mixed linear model using Q and K-matrices (Q + K MLM). Q GLM found 33 marker-trait associations involving 20 SSR markers that were associated with six agronomic traits. Q + K MLM identified four marker-trait associations involving three markers that were associated with traits of days of tasseling (DT) and days of silking (DS). Q GLM and Q + K MLM detected four significant marker-trait associations (SMTAs), with a level of significance of P < 0.01. In overlapping SMTAs, phi051 was associated with DT, umc1708 was associated with DS, and umc2341 was associated with two traits: DT and DS. The detection of loci associated with traits in this study may provide greater opportunities to improve quality by marker-assisted selection (MAS). Finally, these results will be helpful for breeders in choosing parental lines for crossing combinations as well as markers for using MAS in super sweet corn breeding programs in Korea.</P>
( Kyu Jin Sa ),( Tak Ki Hong ),( Ju Kyong Lee ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.2
We evaluated genetic diversity and population structure in 32 Canadian maize inbred lines and performed association analysis for five agronomical traits and 50 simple sequence repeat (SSR) markers. Genetic diversity analysis revealed a total of 381 alleles at the 50 SSR loci. The average number of alleles per locus was 7.6. The average genetic diversity and polymorphic information content values were 0.709 and 0.676, respectively. The average major allele frequency was 0.414. Population structure analysis indicated that these maize inbred lines were comprised of four major groups and one admixed group based on a membership probability threshold of 0.80. A general linear model showed 20 marker-trait associations involving 12 SSR markers associated with the four agronomic traits except for leaf length. For these marker-trait associations, phi056, mmc0022, bnlg1621, bnlg1695, phi116, and bnlg1028 were associated with only one trait. The other nc005, bnlg1012, phi065, and umc1982 were associated with two traits. Two SSR markers, mmc0111 and umc1038, were associated with three traits. These results will help in optimizing the choice of parents for crossing combinations, as well as in selecting markers for marker-assisted selection for maize improvement.
Kyu Jin Sa,Byong Wan Kim,Seung Hun Choi,Jong Yeol Park,Ki Jin Park,Ju Kyong Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Our study is performed to confirm the level of genetic diversity and population structure with 80 maize inbred lines (40 waxy inbred lines and 40 flint inbred lines) and to explain the genetic basis of agronomic traits using an association mapping. The 200 SSR loci are confirmed a total of 1,610 alleles in total 80 maize inbred lines. The average number of alleles per locus was 8.05. The average GD was 0.72. The average PIC value was 0.68. The average MAF was 0.40. Population structure was revealed for K=2. Total 80 maize inbred lines were divided by groups I, II and admixed group. The 14 waxy inbred lines were assigned to group I. The 45 inbred lines include 5 waxy inbred lines and 40 flint inbred lines were contained to group II. The 21 waxy inbred lines were contained in the admixed group with lower than membership threshold 0.8. Association mapping between 200 SSR markers and 10 phenotypic traits of waxy/flint maize inbred lines were performed by Q GLM and Q+K MLM. In significant level at 0.01, 72 SSR markers were associated with 10 phenotypic traits using Q GLM. The 4 marker-trait association were detected in Q+K MLM. The results derived from this study will be used for designing efficient new maize breeding programs.