Resequencing 295 accessions of heuristic and Korean breeding rice deciphers the milestones for breeding and domestication history of Korean rice

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

A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies

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.

Development of new markers to genotype the functional insertion of badh2, a gene responsible for fragrance in aromatic rice

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.

Effects of concentrated rigid inclusions defects on the in-plane impact behavior of hexagonal honeycombs

Qiang He,Wenxian Tang,Jian Zhang,Xiaorong Wang 대한기계학회 2017 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.31 No.10

Hexagonal honeycombs have exhibited significant advantages in energy absorption and they are increasingly used as absorbers under crush conditions. The in-plane crushing process of imperfect hexagonal honeycombs with concentrated rigid inclusions defects is simulated using finite element simulations. In each case, a constant velocity is applied to an impact plate which then crushed the honeycomb. Simulation results indicate that the defect location has a great influence on the deformation modes, especially at low and moderate velocity. After analyzing the apparent reflection about dynamic response at the impact end, the respective influences of local fraction of inclusions and foil thickness (relative density) on the crushing plateau stress on account of the crushing velocity are further discussed. Furthermore, the energy absorption capacity under constant velocity loading is studied. Due to the distribution of the concentrated rigid inclusions defects, the energy absorption can be controlled effectively.

Numerical study on the dynamic behavior of circular honeycomb structure with concentrated filling inclusions defects

Qiang He,Jun Feng,Honggen Zhou,Guizhong Tian 대한기계학회 2018 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.32 No.8

Circular honeycombs are extensively used to absorb impact energy considering its good energy absorption properties. Rather than focusing on the existing perfect honeycomb, effects of concentrated filling inclusions on the in-plane dynamic behavior of circular honeycomb structure are studied in detail by using finite element simulations. The crushing model of honeycomb under in-plane impact is established which then is used to investigate the influences of packing ratio, defect distribution area and impact velocity on the deformation mode and the plateau stress. Investigation results show that the deformation model of imperfect honeycomb can still be classified into three types: Quasi-static mode, transition mode and dynamic mode; However, the value of packing ratio and defect location may seriously influence localized deformed band of transition mode; The plateau stress of the honeycomb relies on the defect location except for the packing ratio; The filling inclusions defect concentrated in sub-region 2 is more beneficial to improve the energy-absorption capacity; Especially under middle or low impact velocities, it displays higher sensitivity; The crushing plateau stress of honeycomb with a = 0.36 and defect concentrated in sub-region 2 is even improved about 56.9 % under impact velocity 100 m/s. These results can provide valuable suggestions in the study and design of other honeycomb structures.

Genome‑wide association study of vitamin E using genotyping by sequencing in sesame (Sesamum indicum)

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.

Impact of WS2 Nanoparticles on Nitrile Butadiene Rubber Properties

Qiang He,Guangfei Wang,Bo Zheng,Wei Zhou,Yanbin Zhang 한국섬유공학회 2020 Fibers and polymers Vol.21 No.5

WS2/nitrile butadiene rubber (NBR) nanocomposite was prepared by mechanical blending. The vulcanization andmechanical behavior, contact angle with water, friction and wear properties, as well as thermal stability were measured toinvestigate the influence of nano WS2 content on the NBR. Moreover, scanning electron microscopic (SEM) and elementdispersive spectrum analysis (EDS) were used to analyze the tensile failure mechanism of the WS2/NBR nanocomposite. Results showed that the tensile strength, elongation at break and contact angle with water of the vulcanized rubber reachedtheir maxima when the content of nano WS2 was 10 parts. Furthermore, fast vulcanization rate and the minimum friction andwear properties were also observed. The tear strength, rebound resilience and electrical resistivity decreased with theincrement of WS2 content, while the hardness and thermal stability increased. Investigation on tensile fracture showed thatcrack growth was mainly caused by stress concentration.

Discovery of a novel fragrant allele and development of functional markers for fragrance in rice

Qiang He,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Aroma in rice (Oryza sativa L.) results from the loss of function of the betaine aldehyde dehydrogenase (Badh2) gene on chromosome 8. An 8-bp deletion in exon 7 of Badh2 was reported to be the main allele functionally associated with fragrance. The discovery of new functional alleles will provide additional genetic resources to improve fragrant rice. In this study, we sequenced the Badh2 gene in 30 rice accessions and filtered the Badh2 polymorphisms from whole genome re-sequence data of 295 rice accessions. Seven alleles were detected from the sequence data. Six of the seven were known alleles and one was a novel allele (badh2-E12). The novel allele was a 3-bp deletion in exon 12. Five functional markers, targeting six of the seven alleles, were identified. Fourteen accessions were selected to test the utility of these markers. The five molecular markers reliably distinguishing this fragrant rice from other fragrant or non-fragrant rice accessions. Analysis of two F2 rice population validated the genetic markers FME12-3 and FME14I as functional markers. These two markers co-segregated with the fragrance phenotype. These markers will be used in a Badh2 diversity study and to breed improved fragrant rice accessions via marker-assisted selection.

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.