• Title/Summary/Keyword: Genome-wide

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Replication of the Association of the 6q22.31c Locus near GJA1 with Pulse Rate in the Korean Population

  • Kim, Nam-Hee;Kim, Young-Jin;Oh, Ji-Hee;Cho, Yoon-Shin
    • Genomics & Informatics
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    • v.10 no.2
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    • pp.106-109
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    • 2012

  • Pulse rate is known to be related to diverse phenotypes, such as cardiovascular diseases, lifespan, arrhythmia, hypertension, lipids, diabetes, and menopause. We have reported two genomewide significant genetic loci responsible for the variation in pulse rate as a part of the Korea Association Resource (KARE) project, the genomewide association study (GWAS) that was conducted with 352,228 single nucleoride polymorphisms typed in 8,842 subjects in the Korean population. GJA1 was implied as a functionally causal gene for pulse rate from the KARE study, but lacked evidence of replication. To re-evaluate the association of a locus near GJA1 with pulse rate, we looked up this signal in another GWAS conducted in a Health Examinee-shared cohort of 3,703 samples. Not only we were able to confirm two pulse rate loci (1q32.2a near CD46 and 6q22.13c near LOCL644502) identified in the KARE GWAS, we also replicated a locus (6q22.31c) near GJA1 by the lookup in the Health Examinee GWAS. Considering that the GJA1-encoded protein is a major component of cardiac gap junctions, a functional study might be necessary to validate its genuine molecular biological role in the synchronized contraction of the heart.

  • https://doi.org/10.5808/GI.2012.10.2.106 인용 PDF KSCI

Current status and prospects to identify mutations responsible for mutant phenotypes by using NGS technology (NGS 기술 활용 돌연변이체 해석 및 연구현황)

  • Jung, Yu Jin;Ryu, Ho Jin;Cho, Yong-Gu;Kang, Kwon Kyoo
    • Journal of Plant Biotechnology
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    • v.43 no.4
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    • pp.411-416
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    • 2016

  • Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions absent in the reference cannot be identified by simple alignment. In this review, we report the current status and prospects in identification of genes in mutant phenotypes, by using the methods MutMap, MutMap-Gap, and MutMap+. These methods delineate a candidate region harboring a mutation of interest, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. These methods are likely to prove useful for cloning genes that exhibit significant structural variations, such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

  • https://doi.org/10.5010/JPB.2016.43.4.411 인용 PDF KSCI

Cytological Analyses of Iris ruthenica K. Gawl. (Iridaceae), an Endangered Species in Korea

  • Choi, Bokyung;Temsch, Eva M.;Weiss-Schneeweiss, Hanna;So, Soonku;Myeong, Hyeon-Ho;Jang, Tae-Soo
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2019.10a
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    • pp.24-24
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    • 2019

  • Iris L. is a perennial genus comprising approximately 300 species worldwide, with the greatest number of endemic species occurring in Asia. Iris is one of the largest genera in the family Iridaceae and includes ca. 15 species native to Korea. Although chromosome number change, karyotype restructuring, and genome size variation play an important role in plant genome diversification, understanding the karyotype variation in Korean Iris species has been hampered by the wide range of base chromosome number (x = 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22) reported to date. This study documents the chromosome numbers, karyotype structure and genome size variation in Iris ruthenica K. Gawl., an endangered species in Korea obtained using classic Feulgen staining and flow cytometry. The chromosome number of all investigated plants from the nine populations was 2n = 42. All individuals studied possessed metacentric and submetacentric chromosomes. The genome size of the I. ruthenica in eight wild populations ranged from 2.39 pg/1C to 2.45 pg/1C ($2.42{\pm}0.02pg/1C$: $mean{\pm}SD$). This study provides the first report of genome size variation in Iris ruthenica in Korea. This study lays foundation for cytogenetic further analyses employing by fluorescence in situ hybridization (FISH) to better understand the chromosomal evolution in this species and in the whole genus.

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