• Mycobiology
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• v.49 no.6
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• pp.589-598
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• 2021

White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18 × KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value ≤ .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value ≤ .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.33-33
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• 2022

Rice (Oryza sativa L.) is a widely studied domesticated model plant. Seed awning is an unfavorable trait during rice harvesting and processing. Hence, awn was one of the target characters selected during domestication. However, the genetic mechanisms underlying awn development in rice are not well understood. In this study, we analyzed the genes for awn development using a mapping population derived from a cross between the Korean indica cultivar 'Milyang23' and NIL4/9 (derived from a cross between 'Hwaseong' and O. minuta). Two quantitative trait loci (QTLs), qAwn4 and qAwn9 were mapped on chromosome 4 and 9, respectively, increased awn length in an additive manner. Through comparative sequencing analyses parental lines, LABA1 was determined as the causal gene underlying qAwn4. qAwn9 was mapped to a 199-kb physical region between markers RM24663 and RM24679. Within this interval, 27 annotated genes were identified, and five genes, including a basic leucine zipper transcription factor 76 (OsbZIP76), were considered candidate genes for qAwn9 based on their functional annotations and sequence variations. Haplotype analysis using the candidate genes revealed tropical japonica specific sequence variants in the qAwn9 region, which partly explains the non-detection of qAwn9 in previous studies that used progenies from interspecific crosses. This provides further evidence that OsbZIP76 is possibly a causal gene for qAwn9. The O. minuta qAwn9 allele was identified as a major QTL associated with awn development in rice, providing an important molecular target for basic genetic research and domestication studies. Our results lay the foundation for further cloning of the awn gene underlying qAwn9.

• Animal Bioscience
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• v.37 no.4
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• pp.576-590
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• 2024

Objective: The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. Methods: A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-year-season, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. Results: A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. Conclusion: Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

• Journal of Animal Science and Technology
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• v.54 no.5
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• pp.323-329
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• 2012

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sires using bovine 10K mapping chip in Hanwoo (Korean cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cut-off p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, a single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The number of significant SNP at a threshold of P<0.001 was 3, 5, 5 and 4 loci for live weight at 6, 12, 18 and 24 months, respectively. For live weight at different ages, significant SNP were spread out across chromosome but some of significant SNP (rs29012453 and rs29012456 on BTA24) had shown highly significant effects. As for the distribution of size of SNP effects, few loci for live weight at different age had moderate effects (6~11%) but most of significant loci had small effects (2 to 5% of additive genetic variance) against total additive genetic variance. In conclusion, live weight at different age might be affected by few loci with moderate effect and many loci with small effects across genome in Hanwoo.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.21-21
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• 2017

Severe lodging has recurrently occurred at strong typhoon's hitting in recent climate change. The identification of quantitative trait loci (QTLs) and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To identify QTLs for lodging resistance, the tropical japonica line, Chugoku 117 and the improved indica variety, Habataki were selected as the donor parent, as these had thick and strong culms compared with the temperate japonica varieties in Japan such as Koshihikari. By using chromosome segment substitution lines (CSSLs) in which chromosome segments from the japonica variety were replaced to them from Habataki, we identified the QTLs for strong culm on chrs. 1 and 6, which were designated as STRONG CULM1 (SCM1) and STRONG CULM2 (SCM2), respectively. By using recombinant inbred lines (BILs) derived from a cross between Chugoku 117 and Koshihikari and introgression lines, we also identified the other QTLs for strong culm on chrs. 3 and 2, which were designated as STRONG CULM3 (SCM3) and STRONG CULM4 (SCM4), respectively. Candidate region of SCM1 includes Gn1 related to grain number. SCM2 was identical to APO1, a gene related to the control of panicle branch number, and SCM3 was identical to FC1, a strigolactone signaling associated gene, by performing fine mapping and positional cloning of these genes. To evaluate the effects of SCM1~SCM4 on lodging resistance, the Koshihiakri near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of Habataki (NIL-SCM1, NIL-SCM2) and the another Koshihikari NIL with the introgeressed SCM3 or SCM4 locus of Chugoku 117 (NIL-SCM3, NIL-SCM4) were developed. Then, we developed the pyramiding lines with double or triple combinations derived from step-by-step crosses among NIL-SCM1 NIL-SCM4. Triple pyramiding lines (NIL-SCM1+2+3, ~ NIL-SCM1+3+4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.

• Korean Journal of Agricultural Science
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• v.40 no.2
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• pp.155-162
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• 2013

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sire using bovine 10K mapping chip in Hanwoo (Korean Cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cutoff p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, GWAS for five genetic mode (additive, dominant, overdominant, recessive and codominant) was implemented in this study. Three SNPs (rs29018694, ss46526851 and rs29018222) at a threshold p< $1.11{\times}10^{-5}$ were detected on BTA12 and BTA21 for dressing percentages in codominant and recessive genetic mode. The G allele for rs29018694 has 4.9% higher dressing percentage than A allele, while the T allele for ss46526851 has 2.57 % higher dressing percentage than C allele. Therefore, rs29018694 SNP showed a bigger effect than the other two SNPs (ss46526851 and rs29018222) in this study. In conclusion, this study identifies three loci with moderate effects and many loci with infinitesimally small effect across genome in Hanwoo.