These experiments were to investigate the variations of rye on forage quality, productivity and β-carotene concentration affected by maturity in Pyeongchang region. Limited information are available about how forage quality and β-carotene content are affected by various factors. Samples were collected from rye harvested every 5 days, from April 25 to May 31 (April 25, April 30, May 4, May 9, May 15, May 21, May 25 and May 31). Dry matter (DM) content, plant height, DM yield and total digestible nutrient (TDN) yield increased continuously with the progressed maturity. However, crude protein (CP) content, in vitro dry matter digestibility (IVDMD) and relative feed value (RFV) decreased markedly with the delay of harvesting, while TDN content decreased from April 25 till May 15, then followed by a stable fluctuation. Conversely, acid detergent fiber (ADF) and neutral detergent fiber (NDF) value increased and then fluctuated slightly after blooming stage. For quality of plant parts, stem contained the lowest CP content and RFV value, and the highest ADF and NDF contents compared with other parts, while the grain showed the higher CP, IVDMD, RFV and lower fiber contents than others. With the plant matured, leaf proportion decreased while stem and grain proportion increased, and feed value of all the three parts decreased till blooming stage and followed by a stable phase. β-carotene concentration showed its highest on jointing stage, and then fell down sharply on the sequential stages. In conclusion, harvest around May 15 (blooming) is proper for forage rye if directly consumed by livestock as green chop in Pyeongchang under the consideration of both nutritive yield and forage quality.

Hay-making is one of the most common way for forage preservation in livestock industry. The quality and production of hay could be affected by various factors. This experiment was conducted to investigate the effect of tedding time and frequency on drying rate and feed value of forage rye (Secale cereale L.) hay. Rye was harvested on heading stage using mower conditioner. Hay was tedded at each set hour(09:00, 13:00 and 17:00) and sampled at each set hour to determine dry matter (DM) content. After two months’ preservation, CP (crude protein), ADF (acid detergent fiber), NDF (neutral detergent fiber), IVDMD (in vitro dry matter digestibility), TDN (total digestible nutrient), RFV (relative feed value), DM loss, visual scores and total fungi count were determined for estimation of hay quality. Tedding was necessary for both speeding up drying rate and improving forage quality. Tedding at 17:00 showed lower NDF content (p<0.05), and also higher RFV value was found compared with tedding at 9:00 and 13:00 (p<0.05). On the other hand, it was observed that more DM losses would be found when tedding later (p<0.05). Tedding in 1~3 times per day were lower in ADF and NDF content (p<0.05), increased CP, TDN and RFV (p<0.05), got less DM loss (p<0.05), and contained less fungi during conservation compared with no tedding (p<0.05). On the other hand, tedding too frequent caused more DM loss (p<0.05). In conclusion, for shorter drying process and higher quality of forage rye hay, tedding at 13:00∼17:00 for 1∼2 times per day was recommended in this study.

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.

Aroma in rice (Oryza sativa L.) results from the loss of function of the betaine aldehyde dehydrogenase (Badh2) gene on chromosome 8. An 8-bp deletion in exon 7 of Badh2 was reported to be the main allele functionally associated with fragrance. The discovery of new functional alleles will provide additional genetic resources to improve fragrant rice. In this study, we sequenced the Badh2 gene in 30 rice accessions and filtered the Badh2 polymorphisms from whole genome re-sequence data of 295 rice accessions. Seven alleles were detected from the sequence data. Six of the seven were known alleles and one was a novel allele (badh2-E12). The novel allele was a 3-bp deletion in exon 12. Five functional markers, targeting six of the seven alleles, were identified. Fourteen accessions were selected to test the utility of these markers. The five molecular markers reliably distinguishing this fragrant rice from other fragrant or non-fragrant rice accessions. Analysis of two F2 rice population validated the genetic markers FME12-3 and FME14I as functional markers. These two markers co-segregated with the fragrance phenotype. These markers will be used in a Badh2 diversity study and to breed improved fragrant rice accessions via marker-assisted selection.

BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcription region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP P11483(T/A)ishighlycorrelatedwithsalttoleranceindex(STI)(P<10-4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (P23036, P25390) explain 97% of aroma variation in our germplasm. It indicated that there are no overlapping functions between the two homology genes. In addition, a large LD block was detected in BADH2 region, however, no large LD blocks in a 4-Mb region of BADH1. Only BADH2 region shown significant bias Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (P23036) of BADH2, while both of the BADH1 alleles (SNP P11483(T/A)) did not show large extended LDblock. All these results suggested that BADH2 was identified as a domesticated gene during rice evolution, while BADH1 was not selected by human beings.

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remain as a great challenge, it is important to establish piratical ways to manage them. A core collection, by definition, refers to a subset of entire population but preserves most of the possible genetic diversity, enhancing the efficiency for germplasm utilizations. Here we reports the whole genome resequencing of the 137 Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in Korean genebank of Rural Development Administration (RDA). We implemented the Illumna HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8x depth using Nipponbare as a reference. Comparisons of the sequences with the reference genome yield more than 15 million(M) single nucleotide polymorphisms (SNPs) and 1.3M insertion/deletion (INDELs). Phylogenetic and population analyses using 2,046,529 high quality SNPs successfully assigned each rice accessions to the relevant subgroups, suggesting those SNPs comprehensively capture evolutionary signatures accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for 4 exemplary agronomic traits from the KRIC_CORE manifest the utility of KRICE_CORE, identifying previously defined gene or novel genetic polymorphisms that potentially regulate the important phenotypes. This study provides strong evidences that the size of KRICE_CORE is small but contains such a high genetic and functional diversity across the genome. Thus those resequencing results will be useful for future breeding, functional and evolutionary studies in the post-genomic era.

Rice is the staple food for more than half the world’s population. It is known that Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. Here, we performed Genome-Wide Association Study(GWAS) with high-resolution density SNPs and InDels to identify natural allelic variation in zinc increase from Heuristic or core rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of zinc in 137 core accessions of brown rice grain were wide, from 7.86ppm to 31.76ppm, with mean 18.97ppm. In particular, GWAS result show that the high peak found in Chromosomes (1, 4, 6, 8). The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

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

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.

2-acetyl-1-pyrroline (2AP) was widely known as the principal aroma compound, it development in rice has been reported due to the loss of function of betaine aldehyde dehydrogenase gene (badh2) on chromosome 8. In previous study, a lot of haplotypes have been found of this gene, while only limited haplotypes have been proved as functional mutations. A total of 137 core set accessions, and additional 45 germplasms have been employed in this study. Finally, two new mutations have been found (3bp deletion in exon12 and C/A SNP in exon 10), and 23 haplotypes have been detected, most of them had strong relations with aroma formation. According to the sequence results, five functional markers have been developed, the markers showed a highly efficient in discriminating the special aromatic rice varieties, and displayed perfect co-segregation with the trait of fragrance in F2 population. Those new markers developed in the present study would be useful in molecular breeding of fragrant rice varieties. Based on the haplotypes, the further research is in progress.

AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.

Aroma development in rice has been reported due to the lack of function of betaine aldehyde dehydrogenase gene (badh2) on rice chromosome 8. A lot of functional markers have been designed based on the InDels, such as 7bp deletion in exon 2, 803bp deletion in exon 4 and 5, 8bp deletion in exon 7, and 3bp insertion in exon 13. Although there were a lot of functional SNPs, other InDels have not been detected by a PCR-based marker. Here we developed a simple, co-dominant, functional cleaved amplified polymorphic sequence (CAPS) marker for fragrance trait based on 1bp insertion in exon 14. The developed marker showed a high efficiency in discriminating that special aromatic rice variety, and displayed perfect co-segregation with the trait of fragrance in the F2 population. This new marker developed in the present study would be useful in molecular breeding of fragrant rice varieties.