• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.10-10
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• 2017

Rice consumption has been continuously decreasing as the eating habits of Koreans have become westernized and diversified. The per capita annual rice consumption in Korea has dropped sharply from 136.4 kg in 1970 to 61.9 kg in 2016. The Korean government, therefore, has been trying to promote rice consumption by invigorating the processed food industry using rice flour. To facilitate the market for processed rice foods, it is essential to develop proper milling technology in terms of flour particle size and damaged starch content to produce high quality rice flour at competitive cost. Dry milling and wet milling are the two major processes used to produce rice flour. Although the dry milling process is relatively simple with a lower production cost, damaged starch content increases because of the high grain hardness of rice. In wet milling, the quality of rice flour is improved by reducing flour particle size as well as damaged starch content through soaking procedures. However, the production costs are high because of the additional expenses associated with the disposal of waste water, sterilization and drying of the wet flour. Recently developed technologies such as jet milling and cryogenic milling also require expensive investment and production. Therefore, developing new rice cultivars with dry milling adaptability as well as good processing properties is an important goal of rice breeding in Korea. 'Suweon 542' is a floury endosperm mutant line derived from sodium azide treatment on a high-yield, early maturing, and non-glutinous japonica rice cultivar, 'Namil'. Compared with the wild type, after dry milling process, the grain hardness of 'Suweon 542' was significantly lower because of its round and loosely packed starch granules. Also, the flour of 'Suweon 542' had significantly smaller particles and less damaged starch than 'Namil' and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Recently, through collaborations with nine universities and food companies, a total of 21 kinds of processed prototypes, using the dry milling flour of 'Suweon 542', were evaluated. In the production of major rice processing products, there was no significant quality difference between the flours prepared by wet milling and dry milling. Although the amount of water added to the dough was slightly increased, it was confirmed that the recipe applying the wet flour could be used without significant change. To efficiently transfer the floury endosperm characteristics of 'Suweon 542' to other commercial rice cultivars, it is essential to develop DNA marker tightly linked to the target gene. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from 'Suweon 542'/'Milyang 23' showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of 'Suweon 542' was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population. Through further physical mapping, a co-segregate and co-dominant DNA marker with the locus, flo7(t) was successfully developed, by which, thereby, breeding efficiency of rice cultivars having proper dry milling adaptability with high yield potential or useful functional materials would be improved. 'Suweon 542' maintained the early maturity of the wild type, Namil, which can be used in rice-wheat double cropping systems in Korea not only for improved arable land but also for sharing flour production facilities. In addition to the high susceptibility against major rice diseases, nevertheless, another possible drawback of 'Suweon 542' is the high rate of viviparous under prolonged rainfall during the harvesting season. To overcome susceptibility and vivipary of 'Suweon 542', the progeny lines, derived from the crosses 'Suweon 542' and 'Jopyeong', an early maturing rice cultivar with multiple resistance against rice blast, bacterial blight, and rice strip virus, and 'Heugjinju', a anthocyanin pigment containing black rice cultivar, were intensively evaluated. As the outputs, three dry milling suitable rice elite lines, 'Jeonju614', 'Jeonju615', and 'Jeonju616' were developed.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.4
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• pp.448-457
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• 2015

Developing rice lines with various amylose contents is necessary to diverse usages of rice in terms of raw materials for processed food production, and thereby to promote rice consumption in Korea. A rice mutant line, 'Namil(SA)-dull1' was established through sodium azide mutagenesis on 'Namil', a non-glutinous Korean Japonica rice cultivar. Namil(SA)-dull1' had dull endosperm characteristics and the evaluated amylose content was 12.2%. A total of 94 F2 progenies from a cross between 'Namil(SA)-dull1' and 'Milyang23', a non-glutinous Tongil-type rice cultivar, was used for genetic studies on the endosperm amylose content. Association analyses, between marker genotypes of 53 SSR anchor markers and evaluated amylose contents of each 94 F2:3 seeds, initially localized rice chromosome 6 as the harboring place for the modified allele(s) directing low amylose content of 'Namil(SA)-dull1'. By increasing SSR marker density on the putative chromosomal region followed by association analyses, the target region was narrowed down 0.94 Mbp segment, expanding from 28.95 Mbp to 29.89 Mbp, on rice chromosome 6 pseudomolecule. Among the SSR loci, RM7555 explained 84.2% of total variation of amylose contents in the $F_2$ population. Further physical mapping on the target region directing low amylose content of 'Namil(SA)-dull1' would increase the breeding efficiency in developing promising rice cultivars with various endosperm characteristics.

• Korean Journal of Breeding Science
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• v.50 no.4
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• pp.387-395
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• 2018

This study was conducted to identify DNA markers related to resistance to herbicide containing mesotrione in Tongil type rice. Two Tongil type elite lines; Milyang154 and Suweon382, showed resistance to mesotrione, whereas the others were susceptible at 20 days after mesotrione application, and severe growth inhibition was observed in the remaining 13 lines. As a result of analysis of mesotrione resistance using 190 $F_2$ populations derived from a cross of Hanareum2 (susceptible) and Milyang154 (resistant), the mesotrione resistance locus was shown to be a single dominant gene with a 3:1 segregation ratio ($X^2=1.19$, P=0.31). To identify a DNA marker closely linked to the mesotrione resistance gene, bulked segregant analysis (BSA) was adopted. The DNA marker RM3501 was identified on chromosome 2 with a recombinant value of 0.53 to the mesotrione resistance gene. Mst1(t) was located between SSR (simple sequence repeat) markers RM3501 and RM324 with a physical map distance of 10.2 Mb-11.4 Mb on chromosome 2. The band pattern of agarose gel electrophoresis of the SSR marker RM3501 showed the same segregation pattern with respect to mesotrione treatment in 20 Tongil type varieties and a $BC_2F_2$ segregation population derived from a cross between Unkwang (resistant) and Hanareum2 (susceptible). Thus, the RM3501 DNA marker could be used in breeding programs for Marker Assisted Selection in mesotrione resistant rice breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.704-711
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• 2020

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc×Erhualian F₂ population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study. Methods: A whole-genome sequences association study was performed in the F₂ population. Genotyping was performed for 1,020 individuals (19 F₀, 68 F₁, and 933 F₂). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits. Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified. Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Molecules and Cells
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• v.24 no.1
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• pp.83-94
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• 2007

During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with $F_2$ and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.6
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• pp.772-779
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• 2013

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size ($N_e$) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of $r^2$ were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and $N_e$ was 73 at five generations ago.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6397-6403
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• 2014

Background: Aberrant promoter hypermethylation has been recognized in human breast carcinogenesis as a frequent molecular alteration associated with the loss of expression of a number of key regulatory genes and may serve as a biomarker. The E-cadherin gene (CDH1), mapping at chromosome 16q22, is an intercellular adhesion molecule in epithelial cells, which plays an important role in establishing and maintaining intercellular connections. The aim of our study was to assess the methylation pattern of CDH1 and to correlate it with the expression of E-cadherin, clinicopathological parameters and hormone receptor status in breast cancer patients of Kashmir. Materials and Methods: Methylation specific PCR (MSP) was used to determine the methylation status of CDH1 in 128 invasive ductal carcinomas (IDCs) paired with the corresponding normal tissue samples. Immunohistochemistry was used to study the expression of E-cadherin, ER and PR. Results: CDH1 hypermethylation was detected in 57.8% of cases and 14.8% of normal adjacent controls. Reduced levels of E-cadherin protein were observed in 71.9% of our samples. Loss of E-cadherin expression was significantly associated with the CDH1 promoter region methylation (p<0.05, OR=3.48, CI: 1.55-7.79). Hypermethylation of CDH1 was significantly associated with age at diagnosis (p=0.030), tumor size (p=0.008), tumor grade (p=0.024) and rate of node positivity or metastasis (p=0.043). Conclusions: Our preliminary findings suggest that abnormal CDH1 methylation occurs in high frequencies in infiltrating breast cancers associated with a decrease in E-cadherin expression. We found significant differences in tumor-related CDH1 gene methylation patterns relevant to tumor grade, tumor size, nodal involvement and age at diagnosis of breast tumors, which could be extended in future to provide diagnostic and prognostic information.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1565-1574
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• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.6
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• pp.453-456
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• 2005

This study was carried out to select DNA markers closely linked to brown planthopper (BPH) resistance gene originated from a rice cultivar 'Cheongcheong­byeo'. For the mapping of resistant gene to BPH, a doubled-haploid (DH) population was developed by anther culture of $F_1$ plants from a cross 'Cheongcheong­byeo/Nagdongbyeo'. In BPH bioassay and marker screen­ing for the DH population, the segregation of resistant and susceptible plants to BPH fitted to a 1:1 ratio. A total of 310 RAPDs of 520 markers showed polymorphism in parental survey using 'Cheongcheongbyeo' and 'Nag­dongbyeo'. In the analysis of relationship between BPH resistance and marker pattern for 40 DH lines, the OPE16 produced a specific dominant fragment, 700 bp, which was closely linked with BPH resistance gene of 'Cheong­cheongbyeo'. Based on the linkage analysis using 7 markers, BPH resistance of 'Cheongcheongbyeo' was mapped on chromosome 12, which was closely linked with $OPE16_{700}$ at a distance of 4.6 cM.