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Phenotypic characterization and genetic mapping of an open-hull sterile mutant in rice.
Gileung Lee,Yoye Yu,Rihua Piao,Aeri Han,Sunghan Kim,Hee-Jong Koh 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Rice hulls remain closed throughout the ripening period to maintain internal humidity of the grains. An Open-hull sterile mutant was induced by N-methyl-N-nitrosourea(MNU) treatment on Sinsunchalbyeo rice, a japonica type. This mutant showed open hulls even in the ripening stages and fully mature grains. In addition, several altered characteristics were observed, including of narrowed palea, decreased grain size, partial pollen sterility and erect panicle. Microscopic analysis showed that the palea was positioned slightly inside the lemma, and the size of palea decreased in the mutant. Genetic analysis of F2 and F3 segregation populations derived from the cross between the Open-hull sterile mutant (Oryza sativa ssp. japonica) and Milyang23 (O. sativa ssp. indica) indicated that the Open-hull trait was controlled by a single recessive allele. The fine-mapping with STS (sequence tagged site) markers revealed that the mutant gene was located on the short arm of chromosome 3. We were able to narrow it down until 30.6Kb where three candidate genes were found.
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Fine mapping of gem controlling the enlarged embryo character in rice (Oryza sativa L.)
Gileung Lee,Mi-Ok Woo,Yoye Yu,Hee-Jong Koh 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Rice embryo contains valuable materials which are related to human health and industrial material, thus controlling embryo size is more and more important in the field of rice breeding. Especially, main health-aid components such as γ -aminobutyric acid (GABA), tocopherol and vitamins showed positive-correlation with embryo size. We obtained three enlarged embryo character mutants derived from Hwacheongbyeo (Korean japonica cultivar) by treatment of chemical mutagen, N-methyl-N-nitrosourea(MNU). These three mutants were named according to their embryo size as ge-m, ge, ge-s. The result of allelism test between Hwacheongbyeo, ge-m, ge and ge-s represented that the embryo size of ge and ge-s was controlled by the same gene(Giant embryo, GE). Through GE locus sequencing of three mutants, we found that each of ge and ge-s mutant has a point mutation, causing non synonymous amino acid substitution. On the other hand, ge-m mutant, the embryo of which featured intermediate size in between those of Hwacheongbyeo and ge, turned out to be non-allelic to the GE locus, suggesting it is likely a novel gene, which influences rice embryo development through a different mechanism than GE gene. Fine mapping of ge-m is currently in progress. 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.
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Lee, Gileung,Piao, Rihua,Lee, Yunjoo,Kim, Backki,Seo, Jeonghwan,Lee, Dongryung,Jang, Su,Jin, Zhuo,Lee, Choonseok,Chin, Joong Hyoun,Koh, Hee-Jong Springer US 2019 Rice Vol.12 No.1
<P><B>Background</B></P><P>Although embryo accounts for only 2–3% of the total weight of a rice grain, it is a good source of various nutrients for human health. Because enlarged embryo size causes increase of the amount of nutrients and bioactive compounds stored within rice grain, giant embryo mutants of rice (<I>Oryza sativa</I> L.) are excellent genetic resources for improving the nutritional value of rice grains.</P><P><B>Results</B></P><P>Three giant embryo mutants, including <I>large embryo</I> (<I>le</I>), <I>giant embryo</I> (<I>ge</I>) and <I>super</I>-<I>giant embryo</I> (<I>ge</I><SUP><I>s</I></SUP>), with variable embryo size were used in this study. We investigated whether genes controlling embryo size in these mutants (<I>le</I>, <I>ge</I> and <I>ge</I><SUP><I>s</I></SUP>) were allelic to each other. Although <I>ge</I> and <I>ge</I><SUP><I>s</I></SUP> was allelic to <I>GIANT EMBRY</I> (<I>GE</I>), <I>le</I> was not allelic to <I>ge</I> and <I>ge</I><SUP><I>s</I></SUP> in allelism test. The <I>GE</I> gene carried a unique nucleotide substitution in each of the two mutants (<I>ge</I> and <I>ge</I><SUP><I>s</I></SUP>), resulting in non-synonymous mutations in exon 2 of <I>GE</I> in both mutants. However, the <I>GE</I> gene of the <I>le</I> mutant did not carry any mutation, suggesting that the enlarged embryo phenotype of <I>le</I> was governed by another gene. Using map-based cloning, we mapped the <I>LE</I> gene to the short arm of chromosome 3. The <I>le</I> mutant showed mild enlargement in embryo size, which resulted from an increase in the size of scutellar parenchyma cells. The <I>LE</I> encodes a C3HC4-type RING finger protein and was expressed to relatively high levels in seeds at a late developmental stage. Knockdown of <I>LE</I> expression using RNA interference increased the embryo size of rice grains, confirming the role of <I>LE</I> in determining the embryo size.</P><P><B>Conclusion</B></P><P>Overall, we identified a new gene controlling embryo size in rice. Phenotypic and molecular characterization results suggest that the <I>le</I> mutant will serve as a valuable resource for developing new rice cultivars with large embryos and nutrient-dense grains.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12284-019-0277-y) contains supplementary material, which is available to authorized users.</P>
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Su Jang,Gileung Lee,Chang Soo Yoo,Hee-Jong Koh 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
The number of spikelets per panicle in rice is determined by characters of the panicle such as the number of primary branches (PB) and secondary branches (SB) and panicle length (PL). It is a quantitative traits controlled by several genes. In this study, the nucleotide polymorphism and haplotype diversity of coding region of genes related to number of spikelets per panicle (SPP), including APO1, APO2, FON1, DEP1, GN1a, GHD8, HD1, and SP1, were analyzed using 45 varieties which showed significant phenotypic variations for PL, PB, SB and SPP. Significant correlations were observed among all the panicle traits. A total of 151 polymorphisms, including 114 SNPs and 26 indels were detected in coding region of 8 genes which constructed 52 haplotypes. Neutrality tests revealed that population subdivision event or balancing selection occurred in locus of APO2, FON1, and HD1 whereas no significant deviation from neutrality was detected in the other genes, suggesting a neutral evolution. Based on the results of GLM association analysis, 34 polymorphic sites in 6 genes were significantly related with the 4 panicle related-traits.
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Genotypic variation of embryo dent of rice grains
Yunjoo Lee,Gileung Lee,Rihua Piao,Sunmi Jang,Hee-Jong Koh 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
As the market demand on functionality rice has been increasing, embryo rice in which embryo residue remains even after milling has come to comsumers’ attention because rice embryo contains several functionality components. Consequently, development of rice varieties for higher rate of embryo adhesion to grains after milling has become one of the breeding objectives for quality improvement. In this study, we observed embryo dent of 49 commercial varieties and analyzed the relationship between embryo dent and grain size and shape. Embryo dent of rice grains varied 0.27 (Keunnun)~0.59 (Daerip 1) mm. Varieties Jinbu, Jinbo, Heugseol, Obong, Unkwang, and Cheongnam showed relatively deeper embryo dent, suggesting that they will be applicable in breeding for embryo rice. Embryo dent was correlated positively with grain width (r=0.53**) and grain size(r=0.34*), and negatively with grain width/length ratio (r= -0.38**). Strategies for breeding embryo rice were discussed in relation to embryo dent, grain size and shape.
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QTL analysis for eight agronomic characters in two rice (Oryza sativa) populations
Jeonghwan Seo,Sunghan Kim,Gileung Lee,Sheryl Sierra,Hee-Jong Koh 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
The HWC-line of rice showed wide compatibility with both indica and japonica cultivars, tall culm length, long and slender grain shape. For QTL analysis, two F2 populations were derived from the crosses between the HWC-line and each of two Korean variety, Dasanbyeo (Korean Tongil-type cultivar) and Hwacheongbyeo (temperate japonica cultivar), respectively. A total of 190 F2 plants were evaluated in each of two F2 populations. Eight agronomic characters were measured for QTL analysis in F2 populations and parents. Two molecular linkage maps were constructed. In the F2 population from cross between HWC-line / Dasanbyeo (HD) cross, 93 STS markers and 13 SSR markers were mapped on 12 chromosomes, covering a total length of 1942.6 cM, with an average distance of 18.33cM between adjacent markers. In the F2 population from HWC-line / Hwacheongbyeo (HH) cross, 28 STS markers, 29 SSR markers and 1 FNP marker were mapped on 11 chromosomes, spanning a total length of 925.53cM, with an average distance of 15.96cM between adjacent markers. In the F2 population from HD cross, 16 M-QTLs and 1 E-QTL were detected for culm length, spikelets per panicle, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 7 QTLs of spikelet fertility, grain length, grain width and grain shape were newly identified in this study. In the F2 population from HH cross, 15 M-QTLs were detected for culm length, panicle length, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 6 QTLs of culm length, grain length, grain width and grain shape were newly identified in this study. The QTLs identified in this study would provide basic information on putative functional genes related agronomic characters and facilitate breed new rice cultivar.
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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.
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