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.

It is well known that Dharial (Bangladesh origin and weedy rice line) has longer seed longevity than indica and japonica rice varieties. To study the genetic basis of seed longevity of Dharial, we developed 240 BC3F7 backcross recombinant inbred lines derived from the crosses between Dharial (a donor parent) and two korea rice accessions (recurrent parents) including Ilmi and Gopum, respectively. Among these lines, we selected two introgression lines with longer seed longevity and named them Ilmi-NIL and Gopum-NIL. Also, we developed an EMS-induced mutant line from Dharial which has shortened seed longevity, and named it Dharial-EMS. We performed re-sequencing of four rice accessions that are Dharial, Dharial-EMS, Ilmi-NIL, and Gopum-NIL. A total of 706×106 raw reads were generated which provided sequence data over 46x rice genome coverage per each accession. We did genome-wide variation analysis comparing produced re-sequencing data and the re-sequencing data of Ilmi from NABIC database with the Nipponbare reference sequence. By graphical analysis of SNP distribution in rice genome of the five accessions, we could select candidate chromosomal segments introgressed from Dharial in Ilmi-NIL and Gopum-NIL. The introgressed chromosomal segments were in seven regions in Ilmi-NIL and eight regions in Gopum-NIL, and four common introgressed regions between Ilmi-NIL and Gopum-NIL were identified. 2,758 SNPs between Dharial and Dharial-EMS were found in the introgressed regions. Also, we detected 450 genes including at least one SNP among these SNPs. This result will facilitate identification of genes and development of molecular markers for improvement of seed longevity.

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

Chloroplast (cp) DNA sequence data are a versatile tool for plant identification, barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized to infer evolutionary relationship of plant species. Although the overall structure of the chloroplast genome is generally well conserved, a number of mutations have been observed. Thus, documentation of chloroplast sequence variation has also been an valuable asset in plant population and evolutionary studies for over two decades. Recently, advance in chloroplast genome assembly from whole genome NGS data has become available. In the present study, chloroplast variations among 295 diverse origin accessions were detected based on Oryza rufipogon, which thought to be the progenitor of cultivated rice.. Variation calling was carried out using the whole genome re-sequencing data of those accessions along with the five rice reference cp genomes. Phylogenetic and evolution analysis of the six references and 295 accessions were performed using the whole reference genome sequence and the variation data, respectively. Also, nucleotide polymorphisms of 295 rice accessions were validated by using previously characterized 50 ecotypes. Differential SNP frequency across the rice cp genome suggests a regional dependent preferential high variation occurrence during the evolution of chloroplast

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.

고추 탄저병은 국내에서 아주 피해가 심한 병 중의 하나로 본 연구팀은 십수 년 동안 탄저병 저항성에 대해 유전분석을 수행하는 동시에 저항성 품종 육성에 노력을 기울여 왔다. 이전에 사용하였던 탄저병 저항성 소재는 Capsicum baccatum 종의 PBC81 accession이었는데, 이와 가장 교잡화합성이 높았던 C. annuum 종의 SP21 계통을 모친으로 사용하여 종간 교잡을 수행하였고, 이에 대한 BC1F1과 BC1F2 분리집단에서 QTL mapping을 수행하여 두 가지의 탄저병(Colletotrichum acutatum과 C. capsici)에 대한 각각의 저항성 주동 QTL을 탐색함과 동시에 연관된 분자표지를 개발하였다. 본 연구에서는 탄저병 저항성 소재로 PBC81이 아닌 PI594137과 AR을 사용하여 NGS re-sequencing을 수행한 후 대량의 SNP를 탐색하고자 하였다. PI594137은 C. baccatum 종에 속하며, PBC81보다 좀 더 broad spectrum resistance를 보인다. AR은 AVRDC에서 분양 받은 재료인데, C. chinense Jacq. PBC932의 열성 저항성을 C. annuum에 도입한 계통이다. 탄저병 저항성 QTL mapping은 Golden aji(C. baccatum, 탄저병 이병성)와 PI594137의 F2 분리집단과 SP211(C. annuum, 탄저병 이병성)과 AR의 F2 분리집단에서 수행할 계획이어서 각각의 양친 사이(Golden aji vs. PI594137과 SP211 vs. AR)에서 SNP를 탐색하였다. NGS re-sequencing을 통해 읽혀진 염기서열 총 길이는 PI594137이 40.5Gbp, Golden aji가 12.1Gbp, AR이 12.8Gbp, SP211이 11.5Gbp였다. 이 염기서열을 사용하여 생물정보학적 분석((주)씨더스에 의뢰)을 수행하였는데, PI594137과 Golden aji 사이에서 333,816개, AR과 SP211 사이에서 1,218,595개의 SNP를 최종적으로 탐색할 수 있었다. 탐색된 SNP는 탄저병 저항성 QTL mapping 분석에 유용하게 사용될 수 있을 것이다.