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Kim, Backki,Kim, Dong-Gwan,Lee, Gileung,Seo, Jeonghwan,Choi, Ik-Young,Choi, Beom-Soon,Yang, Tae-Jin,Kim, Kwang Soo,Lee, Joohyun,Chin, Joong Hyoun,Koh, Hee-Jong Springer New York 2014 Rice Vol.7 No.-
<P><B>Background</B></P><P>Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between <I>indica</I> and <I>japonica</I> varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties.</P><P><B>Results</B></P><P>A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two <I>indica</I> types and one <I>japonica</I> type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the <I>indica</I> parents and 7.9% from the <I>japonica</I> parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition.</P><P><B>Conclusions</B></P><P>Tongil was derived from a three-way cross among two <I>indica</I> and one <I>japonica</I> varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the <I>indica</I> genome with a small proportion of <I>japonica</I> genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the <I>indica</I> genome.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users.</P>
Genetic Diversity of Rice Landraces Collected in Cordillera Region, Philippines
Backki Kim,Sheryl N. Sierra,Hong-Yeol Kim,Hee-Jong Koh 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Banaue Rice Terraces in the Philippines has been a rich source of genetic diversity of untapped rice landraces in the mountainous region of Cordillera. Although some may have been included into modern breeding programs, significant indica-japonica differentiation among landraces cultivated in the region is not well known. Thus, Cordillera landraces differentiation across different altitude gradient (458 m to 1830 m) will provide great opportunities for improvement on rice genetics. We analyzed the genetic variation among 166 accessions collected in 17 towns in 6 provinces across different altitudes using Subspecies Specific Sequence Tagged Site (SS-STS) and Insertion-Deletion (InDel) markers. Subspecies Prototype Index (SPI) degree of each landrace was used to calculate the genomic inclination of each variety towards subspecies. The 50 molecular markers (24 SS-STS and 26 InDel) that assayed variation in 166 accessions revealed 116 alleles. Gene diversity ranged from 0.04 (R3M23) to 0.50 (S04058) with an average of 0.40. Polymorphism information content (PIC) ranged from 0.04 (R3M23) to 0.37 (S12030, S07047, R10M40, S10001, S04058 and S09040B) with an average of 0.31. Using the control varieties to assign groups, the larger group of 114 Cordillera landraces corresponds to 71% japonica type while the smaller group of 42 corresponds to 26% indica and 3% intermediates. A total of 7 (4%) indica and 9 (6%) japonica type accessions were found above 1500 m. Results of this study suggested that majority of japonica type rice landraces were grown in high altitudes of Banaue Rice Terraces and nearby provinces, and interestingly, indica type rice landraces were cultivated in areas at much higher altitudes (>1500 m) than those categorized by the traditional methods.
Backki Kim,Dong-Gwan Kim,Gileung Lee,Jeonghwan Seo,Ik-Young Choi,Beom-Soon Choi,Tae-Jin Yang,Kwang soo Kim,Joohyun Lee,Joong Hyoun Chin,Hee-Jong Koh 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yielding rice variety derived from a three-way cross between indica and japonica. Tongil contributed to staple food self-sufficiency of Korea, an achievement that was termed the ‘Korean Green Revolution’. In this study, we analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated from Tongil rice. Three parental accessions, two indica and one japonica types, of Tongil rice were also sequenced for approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare; the average SNP frequency of Tongil was 5.77 per kb. Genome composition based on the SNP data by comparing with the three parental genome sequences on sliding window of Nipponbare genome sequence revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent, different from the theoretical expectation in a three-way cross, i.e., 75% indica and 25% japonica parental origins on average. Copy number of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, yield-related QTLs or gene locations, and polymorphic transposon insertions were also comparatively analyzed between Tongil and parents using sequence-based tools. The results indicated that each genetic factor was transferred from parents into Tongil in proportion to the whole-genome composition. The Tongil rice is the first successful superior cultivar derived from indica × japonica hybridization in Korea. Defining of genome structure demonstrates that the Tongil genome is composed mostly of the indica genome with a small proportion of japonica genome introgression. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.
Kim, Backki,Woo, Sunmin,Kim, Mi-Jung,Kwon, Soon-Wook,Lee, Joohyun,Sung, Sang Hyun,Koh, Hee-Jong Elsevier 2018 Food chemistry Vol.241 No.-
<P><B>Abstract</B></P> <P>Flavonoids are naturally occurring phenolic compounds with potential health-promoting activities. Although anthocyanins and phenolic acids in coloured rice have been investigated, few studies have focused on flavonoids. Herein, we analysed flavonoids in a yellow grain rice mutant using UHPLC-DAD-ESI-Q-TOF-MS, and identified 19 flavonoids by comparing retention times and accurate mass measurements. Among them, six flavonoids, isoorientin, isoorientin 2″-<I>O</I>-glucoside, vitexin 2″-<I>O</I>-glucoside, isovitexin, isoscoparin 2″-<I>O</I>-glucoside and isoscoparin, were isolated and fully identified from the yellow grain rice mutant, and the levels were significantly higher than wild-type, with isoorientin particularly abundant in mutant embryo. Significant differences in total phenolic compounds and antioxidant activity were observed in mutant rice by DPPH, FRAP and TEAC assays. The results suggest that the representative six flavonoids may play an important role in colouration and antioxidant activity of embryo and endosperm tissue. The findings provide insight into flavonoid biosynthesis and the possibility of improving functionality in rice.</P> <P><B>Highlights</B></P> <P> <UL> <LI> High level of flavonoids containing rice mutant is reported for the first time. </LI> <LI> 19 flavonoids were identified or tentatively identified in a yellow grain mutant by UHPLC-DAD-ESI-Q-TOF-MS. </LI> <LI> Isoorientin was particularly abundant in embryo tissue. </LI> <LI> Yellow grain mutant showed the high phenolic content and antioxidant activity. </LI> </UL> </P>
QTLs for hybrid fertility and their association with female and male sterility in rice
Reflinur,Backki Kim,Joong Hyoun Chin,Sun Mi Jang,Babul MD Akter,Joohyun Lee,Hee-Jong Koh 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Hybrid sterility is one of the major barrier to the application of wide crosses in plant breeding and is commonly encountered in crosses between indica and japonica rice varieties. Ten mapping populations comprised of two reciprocal F2 and eight BC1F1 populations generated from the cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were used to identify QTLs and to interpret the gametophytic factors involved in hybrid fertility or sterility between two subspecies. Frame maps were constructed using a total of 107 and 144 STS markers covering 12 rice chromosomes in two reciprocal F2 and eight BC1F1 populations, respectively. A total of 15 main-effect QTLs and 17 significant digenic- epistatic interactions controlling spikelet fertility (SF) were resolved in the the entire genome map of F2 BC1F1 populations . Among detected QTLs responsible for hybrid ferility, four QTLs, qSF5.1 and and qS F5.2 on chromosome 5, qSF6.2 on chromosome 6, and qSF12.2 on chromosome 12 were identified as major QTLs since they were located at corresponding position in at least three mapping populations. Loci qSF5.1, qSF6.1 and qSF6.2 were responsible for both female and male sterility, whereas qSF3.1, qSF7 and qSF 12.2 affected the spikelet fertility only through embryosac factors, and qSF9.1 did through pollen factors. Five new QTLs identified in this study will be helpful for understanding the hybrid sterility and for breeding programs via inter-subspecific hybridization.