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Qiang He,Byung-Kook Yun,Min-Young Yoon,Xiao-Qiang Wang,Feng-Peng Li,Aye-Aye Khaing,Won-Hee Ra,Win Htet Oo,Cheol-Soon Park,Sun-Kyung Min,Wei Tong,Jie Yu,Bu-Woong Choi,Eun-Beom Heo,Khandakar Md.Rayhanul 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.
Association study of vitamin E content in rice using whole genome re-sequencing
Xiao-Qiang Wang,Qiang He,Wei Tong,Byung-Kook Yun,Young-Sang Lee,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Rice is the major food for half of the world population. The nutrition component in rice is critical for improvement of people’s health. Vitamin E serves as important antioxidant by quenching the free radical intermediates and thus protects the cell membrane. Because of the high nutritional value and the benefits of vitamin E in human health, increasing the tocochromanol content of major agricultural crops has long been in the focus of breeding programs and genetic engineering approaches. The key genes involved in tocopherol biosynthesis have been elucidated in Arabidopsis and other model organisms. Quantitative trait locus (QTL) study performed in Arabidopsis suggested that some of these key genes and a few additional loci contribute to natural tocopherol variations. Identifying such genetic variations in rice, enrich our understanding of the genetic mechanisms controlling tocopherol variation, which can be directly applied to rice breeding programs. In this study, we used genome-wide association mapping with high-resolution density SNPs of rice core set to identify natural allelic variations, which contribute to tocopherol increase in rice
Wei Tong,Qiang He,Xiao-Qiang Wang,Min-Young Yoon,Won-Hee Ra,Feng Peng Li,Jie Yu,Win Htet Oo,Sun-Kyung Min,Buung Choi,Eun-Beom Heo,Byoung-Kook Yun,Kyu-Won Kim,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.
Qiang He,Jae-Wan Park,Yoo-Hyun Cho,Soon-Wook Kwon,Young-Sang Lee,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Aroma development in rice has been reported due to the lack of function of betaine aldehyde dehydrogenase gene (badh2) on rice chromosome 8. A lot of functional markers have been designed based on the InDels, such as 7bp deletion in exon 2, 803bp deletion in exon 4 and 5, 8bp deletion in exon 7, and 3bp insertion in exon 13. Although there were a lot of functional SNPs, other InDels have not been detected by a PCR-based marker. Here we developed a simple, co-dominant, functional cleaved amplified polymorphic sequence (CAPS) marker for fragrance trait based on 1bp insertion in exon 14. The developed marker showed a high efficiency in discriminating that special aromatic rice variety, and displayed perfect co-segregation with the trait of fragrance in the F2 population. This new marker developed in the present study would be useful in molecular breeding of fragrant rice varieties.
Resequencing reveals different domestication rate for BADH1 and BADH2 in rice (Oryza sativa)
Qiang He,Jie Yu,Tae-Sung Kim,Yoo-Hyun Cho,Young-Sang Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcription region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP P11483(T/A)ishighlycorrelatedwithsalttoleranceindex(STI)(P<10-4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (P23036, P25390) explain 97% of aroma variation in our germplasm. It indicated that there are no overlapping functions between the two homology genes. In addition, a large LD block was detected in BADH2 region, however, no large LD blocks in a 4-Mb region of BADH1. Only BADH2 region shown significant bias Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (P23036) of BADH2, while both of the BADH1 alleles (SNP P11483(T/A)) did not show large extended LDblock. All these results suggested that BADH2 was identified as a domesticated gene during rice evolution, while BADH1 was not selected by human beings.
The Efficacy Analysis of Endoscopic Third Ventriculostomy in Infantile Hydrocephalus
He, Zhenhua,An, Caixia,Zhang, Xinding,He, Xiaodong,Li, Qiang The Korean Neurosurgical Society 2015 Journal of Korean neurosurgical society Vol.57 No.2
Objective : To investigate the efficacy of endoscopic third ventriculostomy (ETV) for infantile hydrocephalus. Methods : Retrospectively reviewed the 17 infantile hydrocephalus cases who were treated with ETV between July 2009 and June 2013. The study includes 17 patients (4 Han and 13 Hui) between the ages of 51 and 337 days. Five cases with encephalitis history and 2 cases with cerebral hemorrhage, with the remaining 10 cases congenital hydrocephalus. ETVs were performed for all patients with 1 case failing because the severe ventricle inflammatory adhesion, excessive exudation, and vague basilar artery. Results : Among the 16 successful cases 7 cases improved remarkably : heads and ventricles reduced and cerebral cortexes thickening morphologically. The ventricles of the remaining cases were unchanged. Conclusion : The ethnic minority account for the majority of the patients in this study. ETV is effective for infantile obstructive hydrocephalus.
Qiang He,Feifei Xu,민명현,추상호,김규원,박용진 한국유전학회 2019 Genes & Genomics Vol.41 No.9
Background At least eight structurally related forms of vitamin E occur in nature, four tocopherols and four tocotrienols, all of which are potent membrane-soluble antioxidants. In this study, we detected two major isoforms in sesame (Sesamum indicum L.) seed: γ-tocopherol and β-tocotrienol. The objective of this study is to investigate the genetic basis of these vitamin E isoforms. Methods We conducted a genome-wide association study (GWAS) using 5962 genome-wide markers, acquired from 96 core sesame accessions. The GWAS was performed using generalized linear (GLM) and mixed linear (MLM) models. Results LG08_6621957, on chromosome 8, was detected as having a significant association with γ-tocopherol in both models. It explained 20.9% of γ-tocopherol variation in sesame. For β-tocotrienol, no significant loci were detected according to the two models, but one locus, SLG03_13104062, explained 17.8% of the phenotypic variation. Based on structure and phylogenetic studies, the 96 accessions were clearly clustered into two subpopulations. Conclusion This study on sesame demonstrates and provides an evidence that genotyping by sequencing (GBS) based GWAS can be used to identifying important loci for small growing crops. The significant SNPs or genes could be useful for improving the vitamin E content in sesame breeding programs.
Haplotye analysis and functional study of badh2, a gene responsible for fragrance in aromatic rice
Qiang He,Yoo-Hyun Cho,Tae-Sung Kim,Young-Sang Lee,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
2-acetyl-1-pyrroline (2AP) was widely known as the principal aroma compound, it development in rice has been reported due to the loss of function of betaine aldehyde dehydrogenase gene (badh2) on chromosome 8. In previous study, a lot of haplotypes have been found of this gene, while only limited haplotypes have been proved as functional mutations. A total of 137 core set accessions, and additional 45 germplasms have been employed in this study. Finally, two new mutations have been found (3bp deletion in exon12 and C/A SNP in exon 10), and 23 haplotypes have been detected, most of them had strong relations with aroma formation. According to the sequence results, five functional markers have been developed, the markers showed a highly efficient in discriminating the special aromatic rice varieties, and displayed perfect co-segregation with the trait of fragrance in F2 population. Those new markers developed in the present study would be useful in molecular breeding of fragrant rice varieties. Based on the haplotypes, the further research is in progress.
He, Qiang,You, Hong,Li, Xin-Min,Liu, Tian-Hui,Wang, Ping,Wang, Bao-En Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.4
The high mobility group box-1 (HMGB1) protein and NALP3 inflammasome have been identified to play important roles in inflammation and cancer pathogenesis, but the relationships between the two and cancer remain unclear. The current study investigated the relationship between HMGB1 and the NALP3 inflammasome in THP-1 macrophages. HMGB1 was found unable to activate the NALP3 inflammasome and failed to induce the release of the IL-$1{\beta}$ and IL-18 in THP-1 macrophages. HMGB1 was also found significantly enhanced the activity of ATP to induce IL-$1{\beta}$ and IL-18 by the induction of increased expression of pro-IL-$1{\beta}$ and pro-IL-18. This process was dependent on activation of RAGE, MAPK p38 and NF-${\kappa}B$ signaling pathway. These results demonstrate that HMGB1 promotes the synthesis of pro-IL-$1{\beta}$ and pro-IL-18 in THP-1 macrophages by the activation of p38 MAPK and NF-${\kappa}B$ through RAGE. HMGB1 likely plays an important role in the first step of the release of the IL-$1{\beta}$ and IL-18, preparing for other cytokines to induce excessive release of IL-$1{\beta}$ and IL-18 which promote inflammation and cancer progression.