• Journal of agriculture & life science
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• v.50 no.3
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• pp.99-117
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• 2016

Data on primal cuts were collected from 1,829 steers of Hanwoo progeny testing programs, between 2010 and 2015 for the ssGWAS. SNP data were analyzed by using Illumina Bovine 50K Beadchip. The SNP data that matches with phenotype data was 674 animals. As a first step, the genomic estimated breeding value(GEBV) of the loin and rib cuts were estimated, which was used in the estimation of SNP marker effects and their variances related to the traits. Then, the estimated variance explained by each marker was expressed as a proportion to the total genetic variance. Finally, the SNP loci and their significance to any possible QTL were examined. Among the 20 best SNP loci explaining a larger proportion of SNP variance to the total genetic variance for tender loin yield, the region between 12,812,193 ~ 12,922,313bp on BTA 10 harbored a cluster of SNPs that explained about 7.32 to 7.34% of the total genetic variance. For strip loin yield, a peak for higher effects for multiple SNPs was found in BTA24, between 38,158,543 and 38,347,278bp distances, which explained about 8.36 to 8.56% of the observed variance for this trait. For loin yield had relatively smaller effects in terms of the total genetic variance. Therefore, loin yield might be affected by a few loci with moderate effects and many other loci with smaller effects across the genome.

• Journal of Animal Science and Technology
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• v.53 no.2
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• pp.89-97
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• 2011

In this study, the efficiency of microsatellite (MS) markers for pork quality was examined and further, their suitability to domestic pork industry also was verified, by measuring meat quality parameters of Berkshire breeds. A total of 323 pigs of Berkshire breeds were slaughtered and subjected to meat quality evaluation. In addition, the genomic DNAs from blood samples of slaughtered pigs were used for genotyping analysis of 50 MS markers. The results revealed that Berkshire breeds have excellent meat quality, compared with the popular domestic breeds such as Duroc, Yorkshire, and Landrace. Noticeably, the Berkshire breeds exhibited a significant post-mortem pH24hr ($5.88{\pm}0.01$) and fat content ($2.878{\pm}0.06$). Through the linkage analysis between MS markers, 14 MS markers showed significant association with meat quality traits (p<0.05). Maximum significant differences of 0.55 pH24hr value and 2.04% fat content were observed between the highest and lowest allele populations. If these 14 MS markers are applied to the pork quality diagnosis kit, the synergistic effect can be expected in meat quality parameters such as meat color, fat content, pH 24 hr, cooking loss, drip loss and water-holding capacity.

• Korean Journal of Plant Resources
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• v.36 no.4
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• pp.369-380
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• 2023

Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.8-9
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• 2017

Soybean yield has been low and unstable in Japan and other areas in East Asia, despite long history of cultivation. This is contrasting with consistent increase of yield in North and South America. This presentation tries to describe perspective of breaking stagnation of soybean yield in East Asia, considering the factors of the different yields between regions. Large amount of rainfall with occasional dry-spell in the summer is a nature of monsoon climate and as frequently stated excess water is the factor of low and unstable soybean yield. For example, there exists a great deal of field-to-field variation in yield of 'Tanbaguro' soybean, which is reputed for high market value and thus cultivated intensively and this results in low average yield. According to our field survey, a major portion of yield variation occurs in early growth period. Soybean production on drained paddy fields is also vulnerable to drought stress after flowering. An analysis at the above study site demonstrated a substantial field-to-field variation of canopy transpiration activity in the mid-summer, but the variation of pod-set was not as large as that of early growth. As frequently mentioned by the contest winners of good practice farming, avoidance of excess water problem in the early growth period is of greatest importance. A series of technological development took place in Japan in crop management for stable crop establishment and growth, that includes seed-bed preparation with ridge and/or chisel ploughing, adjustment of seed moisture content, seed treatment with mancozeb+metalaxyl and the water table control system, FOEAS. A unique success is seen in the tidal swamp area in South Sumatra with the Saturated Soil Culture (SSC), which is for managing acidity problem of pyrite soils. In 2016, an average yield of $2.4tha^{-1}$ was recorded for a 450 ha area with SSC (Ghulamahdi 2017, personal communication). This is a sort of raised bed culture and thus the moisture condition is kept markedly stable during growth period. For genetic control, too, many attempts are on-going for better emergence and plant growth after emergence under excess water. There seems to exist two aspects of excess water resistance, one related to phytophthora resistance and the other with better growth under excess water. The improvement for the latter is particularly challenging and genomic approach is expected to be effectively utilized. The crop model simulation would estimate/evaluate the impact of environmental and genetic factors. But comprehensive crop models for soybean are mainly for cultivations on upland fields and crop response to excess water is not fully accounted for. A soybean model for production on drained paddy fields under monsoon climate is demanded to coordinate technological development under changing climate. We recently recognized that the yield potential of recent US cultivars is greater than that of Japanese cultivars and this also may be responsible for different yield trends. Cultivar comparisons proved that higher yields are associated with greater biomass production specifically during early seed filling, in which high and well sustained activity of leaf gas exchange is related. In fact, the leaf stomatal conductance is considered to have been improved during last a couple of decades in the USA through selections for high yield in several crop species. It is suspected that priority to product quality of soybean as food crop, especially large seed size in Japan, did not allow efficient improvement of productivity. We also recently found a substantial variation of yielding performance under an environment of Indonesia among divergent cultivars from tropical and temperate regions through in a part biomass productivity. Gas exchange activity again seems to be involved. Unlike in North America where transpiration adjustment is considered necessary to avoid terminal drought, under the monsoon climate with wet summer plants with higher activity of gas exchange than current level might be advantageous. In order to explore higher or better-adjusted canopy function, the methodological development is demanded for canopy-level evaluation of transpiration activity. The stagnation of soybean yield would be broken through controlling variable water environment and breeding efforts to improve the quality-oriented cultivars for stable and high yield.

• Journal of Life Science
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• v.22 no.12
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• pp.1644-1650
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• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.