Sesame is queen of oil seed crops and widely cultivated in Asia and Africa. The aim of this study was to develop a mini sub core set representing the diverse germplasm of sesame and to assess the genetic diversity, population structure and phylogenetic relationship of the resulted sub core set to be used in whole genome resequencing platform. One hundred twelve accessions out of 277 accessions were selected by the PowerCore program. A total of 155 alleles were captured from the 158 alleles detected in the primary core population, and rare alleles and specific alleles were also maintained in the sub core set accessions representing almost 100% of the primary core population. Among the sub core set accessions, four sub populations were observed with some admixture accessions. Although the genetic diversity of Pop-1 which includes most accessions from Korea is relatively lower than that of other three sub populations, it can maintain maximum number of accessions in the sub core set with the same percentage as in the primary core set probably because of the specific features of these accessions. Based on this framework of genetically defined populations, the effective use and conservation management of Sesamum indicum for crop improvement might be possible.

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.

Rice is the most important staple food crop of almost half of the world`s population. In rice, seed longevity is major factor for production and storage potential of seeds. But it is faced with grain degradation and loss of seed viability. Lipoxygenases(LOX) are a family of enzymes related to the seed longevity. LOX activity in rice grain is present in a bran-milling fraction. It is also observed that rice embryos contains three isozymes activites, Lox1, Lox2 and Lox3. Among those, the Lox3 isozyme is known as the major component in the embryonic tissue. In this study, genetic structure variability of three seed longevity related genes, Lox1, Lox2 and Lox3 were examined by using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels in the exon regions identified through haplotyping analysis would be useful to develop new varieties with improved storage ability of rice in the future molecular breeding.

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.

‘진상’은 공주대학교에서 2013년도에 육성한 고품질 저아밀로스 품종으로 주요특성과 수량성을 요약하면 다음과 같다. 1.‘진상’은 중서부평야 보통기 보비재배에서 출수기가 8월 11일로 ‘추청’보다 약 11일 빠른 중생종으로, 이삭길이는 19 cm로 ‘추청’과 비슷한 수준이었으나, 간장은 75.2 cm로 ‘추청’보다 짧다. 2.‘진상’의 정현비율은 81.2%로 ‘추청’과 비슷한 수준이며 현미길이와 폭이 각각 4.86 mm, 2.91 mm로 ‘추청’에 비해 약간 길고, 넓은 단원형 품종이다. 현미 천립중은 20.91 g 수준이며, 수량성은 457 kg/10a로 ‘추청’과 비슷하였다. 3.‘진상’은 중간찰벼로서 투명도가 중간 정도의 불투명 배유 특성이고, 알칼리 붕괴도는 6.4 정도이며, 아밀로스함량은 11.9%로 대조품종 19.1%보다 낮고, 도요 식미기로 측정한 밥 윤기치는 대조품종인 ‘추청’보다 높게 나타났다.

Amaranths (Amaranthus sp.) are cosmopolitan and include grain, vegetable, ornamental and weed types. Forteen simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 59 accessions of cultivated amaranth from Asian countries. A total of 63 alleles were detected with an average of 4.5 per locus. The averaged values of gene diversity and polymorphism information content (PIC) were 0.35 and 0.33, respectively. Alleles per locus in accessions from South Asia was 4.35, whereas 2.93 and 3.79 alleles per locus were found in Nepal and India, respectively. The mean gene diversity in Central Asia and East Asia was 0.36 and 0.28, respectively, whereas the mean PIC values were 0.27 and 0.22, respectively. The genetic diversity and PIC of the India amaranths were higher than that of other Asian countries. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 56.16% in contrast to 43.84% for the within-population component. The overall FST value was 0.56, reflecting genetic differentiation within Asian amaranths. These findings could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

Vitamin E and phytosterols are both valuable nutrients that act as antioxidants in human bodies. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. In this study, 119 rice accessions of diverse origin were genotyped using 232 SSR markers to identify marker–trait associations with Vitamin E and phytosterols in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.3361. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 81 marker–trait associations were identified using 232 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping. The results from this association mapping study will be the basis for improving rice nutritional quality.