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.

In Africa, rice is the fastest demanding staple food with a high growth rate of consumption at 4.5% per annum. Currently Africa occupies 32% of world rice imports, and pressure on rice is expected to rise in the near future. Faced with this deficit, Korea has launched the rice breeding project through Korea-Africa Food & Agriculture Cooperation Initiative (KAFACI) of which goal is to increase rice productivity through accelerated development of improved germplasm and varieties in Africa. As of 2013, the ten African member countries joined the rice breeding projects of KAFACI program; they are Cameroon, DR Congo, Ghana, Kenya, Malawi, Mali, Nigeria, Sudan, Tanzania, and Uganda. We adopted the breeding strategy of intervarietal cross and anther culture to speed up high-yielding secondary populations using the Korean and African germplasm. Korean germplasm is composed of 1) temperate japonicas adaptable to tropical conditions of short-day length and high temperature 2) wide-cross derivatives from African wild species, O.glaberrima and O,longistaminata, and 3) tongil-type varieties. These germplasm is evaluated for adaptability in Africa and African partners make crosses with local germplasm with the best selections. Korea produce double-haploid populations from these crosses for another cycle of selection for high-yielding lines in Africa. Inter-varietal crosses and double-haploid technology could accelerate the development of high-yielding germplasm and new rice varieties in Africa within short project period.

Genetic resources play a great role in crop breeding because of containing a broad array of useful genes. Currently, the harder are rice breeders trying to develop new rice cultivars with the improved traits, they are more often handicapped by the limited availability of germplasm resources. Thus, a desirable core or heuristic (HS) set of germplasm with maximum genetic diversity can be usefully exploited to breakthrough the present and future challenges of the rice breeding. As such we previously developed the rice HS sets of 166 diverse accessions out of a total 24,368 rice germplasms. Here, we report a large-scale analysis of the patterns of genome-wide genetic variations accumulated in the HS as well as Korean rice over the time. We characterized a total of about 11.8 millions of single nucleotide polymorphisms (SNPs) across the rice genome from resequencing a total of 295 rice genomes including 137 HS and 158 KB rice sets, with an average of approximately 10x depth and > 90% coverage. Using about 460,000 high-quality SNPs (HQSNPs), we specified the population structure, confirming our HS set covers all the rice sub-populations. We further traced the relative nucleotide variabilities of HQSNPs and found the level of the diversity was dynamically changing across the KB genome, which reveals the selection history of KB lines in the past and present. In addition, the results of our genome wide association study (GWAS) suggests that our HS can be also a good reservoir of valuable alleles, pinpointing those alleles underlying the important rice agronomical traits. Overall, the resequencing of our HS set re-illuminates the past, present of the germplasm utilization, which will support the Korean rice breeding in the future.

We are currently developing a high-throughput single nucleotide polymorphism (SNP) genotyping service at IRRI to accelerate progress in rice breeding by providing rapid and cost-effective marker services. SNP marker development and validation is being performed based on cloned genes and QTLs, GWAS hits, and whole genome sequence data to identify predictive SNP markers at important genes for key traits for the breeding programs. Trait-based and targeted SNPs are being deployed in sets of 24 and 96 SNPs on a Fluidigm EP1 system. At the same time, 384 SNP sets and a 6K SNP chip developed by Susan McCouch at Cornell University are being used for higher density genome scans on an Illumina system. Genotyping by sequencing (GBS) approaches with 96 and 384 barcoded samples per sequence lane are also being evaluated in comparison to SNP array technology based on the number of loci, call rates, turnaround times, and cost per sample. An efficient sample processing workflow with an integrated LIMS is also being optimized to enable high throughput genotyping with sample tracking to minimize errors. Moreover, web-based SNP data analysis tools have been deployed through the IRRI Galaxy workbench to speed up SNP data analysis. Future efforts will focus on large-scale deployment of GBS across breeding materials to enable QC genotyping, tracking of donor introgressions, and integration of genome-wide prediction into the variety development pipelines. The large-scale application of high-density markers will help transform IRRI’s rice breeding programs and increase the rate of genetic gain towards developing high-yielding, stress-tolerant varieties for target environments and market segments

‘안미’는 농촌진흥청 국립식량과학원과 국제미작연구소 간의 협력으로 분자육종법을 이용하여 2010년에 육성한 중만생 고품질 복합내병충성 품종이다. 지역적응시험을 3개년(2008~2010)간 수행한 결과, ‘안미’는 중부평야지에서 보통기 보비재배 시 출수기는 8월 15일로 ‘화성’보다 5일 늦은 중만생종으로 쌀수량은 보통기 표준재배에서 5.76 MT/ha로 ‘화성’보다 11% 증수되었다. ‘안미’는 ‘화성’에 비해 간장(77 cm)은 작고 수당립수는 많으나 등숙비율은 다소 낮았다. ‘안미’는 현미 장폭비가 1.84인 단원형이며 백미는 심복백 발현이 거의 없어 맑고 투명하다. ‘안미’의 알카리 붕괴도와 단백질 함량은 ‘화성’과 비슷하고 아밀로스 함량은 조금 낮았반면, 식미평가에서 밥맛은 매우 양호하였다. ‘안미’의 재배시험 과정 중 위조현상은 관찰되지 않았으며 성숙기 하위엽 노화는 늦은 편이었다. ‘안미’는 ‘화성’에 비해 수발아에 둔감하였고 내랭성 평가 중 적고는 나타나지 않았으나 임실율은 다소 낮았다. ‘안미’는 도열병, 벼흰잎마름병(K₁, K₂, K₃), 줄무늬잎마름병 및 벼멸구에 강한 저항성을 발현하였다.

NGS costs are decreasing rapidly, and beneficial application of the technology to plant genomics seems inevitable. Trying to interpret the agriculturally important traits like yield is actively in progress all across the globe. However, the current stage of bio-informatic technology as applied to the interpretation of agricultural trait appears not yet at a level of maturity to justify widespread plant genome sequencing for user-friendly molecular breeding. It is necessary to construct dense mutation block (DMB) based molecular breeding system for selecting plants with optimal agricultural performance; as well as for identifying useful quantitative trait loci (QTLs). Firstly, we screened and selected DMBs-specific INDEL markers obtained from SNV density profiles using 42 genome sequences of Korean cultivar and public sequences of 24 japonica rice cultivars. Secondly, we analyzed the genetic similarity between 288 Korean cultivars using 113 DMB-specific INDEL markers, which could differentiate on agarose gel by PCR. And we are going to integrate 360 INDEL markers up to 30 per each chromosome. Finally, we selected 40 founder lines considering the importance of the breeding, the purpose of use, and plant ecotype. To construct rice nested association mapping population we crossed each founder lines with the pollen of Hwayoungbyeo which was most commonly used in korean rice breeding program. F2 seed multiplication and generation iteration are ongoing.

The transfer of a biotic resistance gene from indica rice cultivars into japonica cultivars by conventional breeding methods often difficult due to high sterility of the progenies, poor plant type, and linkage drag. Molecular markers provide opportunities to map resistance genes and accelerate the application of marker-assisted backcross(MAB) breeding through the precise transfer of target genomic regions into the recurrent parent. The basis of MAB breeding is to transfer a specific gene/allele of the donor parent into the recurrent parent genome while selecting against donor introgressions across the rest of the genome. The effectiveness of MAB breeding depends on the availability of closely linked DNA markers for the target locus, the size of the population, the number of backcrosses and the position and number of markers for background selection. We have successfully developed Bph18 version of the commercially cultivated japonica elite cultivar by using MAB and incorporating the resistance gene Bph18 that conferred enhanced resistance to BPH. MAB breeding provides a new opportunity for the selective transfer of biotic resistance genes into elite indica rice cultivars devoid of linkage drag. In additon, molecular markers precisely estimate the introgression of chromosome segments from donor parents and can speed up the recipient genome recovery via background selection.

A set of nine Korean rice germplasm (KRG) along with the six indica lines were screened under irrigated non-stress and drought stress situations at IRRI in dry season (DS) 2011. The experiment received mild to moderate drought stress. Under irrigated situation, among all lines, IRRI119 yielded highest followed by PSBRc80 and PSBRc14. Among nine KRG, Hanareumbyeo yielded highest followed by Gayabyeo. Yield of Hanareumbyeo was similar to high yielding indica lines. Under drought, PSBRc14 provided the highest yield among indica lines and Hanarembyeo provided highest yield among nine KRG. Among nine KRG, Hanarembyeo provided the highest yield both under irrigated non-stress and drought stress situation. Parental polymorphism was performed with 125 SSR markers taking six KRG and three drought tolerant donors and polymorphic markers and japonica lines background specific markers were identified. The polymorphic markers in the region of three QTLs (DTY1.1, DTY2.2, DTY3.1) will be used for foreground genotyping for QTL introgression and background specific markers will be used for background genotyping. Sixteen rice germplasm could be separated into two main groups, japonica and indica groups by cluster analysis. The japonica and indica groups also classified as two subgroups, respectively. Based on results of screening of japonica lines under irrigated non-stress and drought stress situations, two KRG- Hanarembyeo and Jinmibyeo were selected for introgression of three QTLs (DTY1.1, DTY2.2 and DTY3.1) associated with grain yield under drought stress.

The Brown planthopper (BPH) is one of the most serious pests of rice affecting rice yield and quality throughout the country. AA genome wild rice, O.rufipogon is a useful source of insect resistance to BPH. To broaden the BPH resistance in the existing quality japonica cultivars, crossess were made between a highly susceptible quality rice cultivar, Ilpumbyeo, and five accessions (acc.106109, 106286, 106424,105908,80671) of O.rufipogon. Among 126 F8 RIL lines evaluated for Bph resistance at NICS, the highly resistant 22 introgression lines were identified and Ilpumbyeo*2/O.rufipogon (acc.105908) showed different genotype at the marker loci of Bph1, Bph18 and the resistance reaction to BPH in the BC1F2 population fitted to 3:1 segregation mode, indicating the possible new dominant resistance gene might be involved. Polymorphism between Ilpumbyeo and resistant line was low with 36 (27%) SSR markers among 130 markers detected. Currently mapping population of BC2F2 is established and SSR marker analysis will be carried out to find out the resistance loci.

중모1001'은 중북부중간지 및 중산간지 고품질 벼를 육성할 목적으로 1994년 하계에 초형이 좋은 SR14694-57-4-2-1-3-2-2 계통을 부본으로 하고 단간이며 쌀알이 깨끗한 철원52호를 모본으로 인공교배하여 2007년 육성된 조생 내도복 고품질 중간모본으로 주요 특성과 수량성을 요약하면 다음과 같다. 1. 보통기 보비재배에서 출수기는 평균 8월 5일로 '오대벼' 보다 4일 늦은 조생종이다. 2. 간장은 73 cm이며, 주당수수는 13개, 수

Bacterial blight(BB) caused by Xanthomonas oryzae pv. oryzae(Xoo) is one of the most economically destructive bacterial diseases of rice in worldwide. Utilization of resistant cultivars carrying resistant gene(s) is relatively an effect method to control this disease. About 34 resistant genes for BB resistance have been identified in many countries. Among them, Xa1 and Xa3 genes against bacterial blight have been incorporated into improved korean japonica rice varieties. Now, Ilmi carrying Xa1 gene and severial cultivars carrying Xa3 gene are widely grown in our country. In recent year, xa5, Xa21 and Xa23 genes are using in rice breeding programs for japonica resistant cultivars to bacterial blight. Resistant cultivars incorporated with a diverse single gene and two, three, or the more major gene necessite in the future.

야생벼은 재배벼의 친환경적성을 강화시킬 수 있는 병해충 저항성 및 불량환경에 견딜 수 있는 유용한 유전자들의 보고로 알려져 왔다. 국내에서 육성된 벼 품종인 '화성'(AA게놈)와 야생벼인 Oryza. minuta(BBCC 게놈; Acc.=101141)간의 교잡을 통하여 종간잡종 후대들이 육성되었다. 불화합성과 초기분리세대의 극심한 불임을 극복하기 위해 배주배양으로 F1 개체를 확보하였으며, '화성'으로의 여교잡을 수 차례 실시하였다. 확립된 계통들에 대

Arabidopsis thaliana Ca2+/H+ 수송체 유전자인 CAX 1(cation exchanger 1)이 도입된 벼 형질전환체에 대한 연구결과를 요약하면 다음과 같다. Agrobacterium 이용 형질전환 CAX 1 벼 T5 세대를 대상으로 CAX 1밴드가 도입되었음을 확인하였다. 농업적인 특징인 수장, 수수 및 간장은 모품종(일품)과 유사하였으며, 종자의 칼슘 함량도 높았다. 미립의 크기와 천립중은 모품종보다 약간 크나 거의 일치하고, 저온저항성과 도열병에 대한 내병성이 나타났다. T5 세대에서 형질이 안정적으로 발현되면서 모품종과 유사하고 농업적 형질이 우수한 3 계통을 선발하였다. 앞으로 T6 세대에 대한 특성조사를 거쳐 Ca2+ 함량이 안정적으로 높게 유지되는 계통을 선발하여 세대육성하면 칼슘과 관련된 유전자의 내재해성 작물의 기초자료 이용되어 질 수 있을 것으로 사료된다.