• Korean Journal of Agricultural Science
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• v.39 no.4
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• pp.477-482
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• 2012

Low-temperature germination is one of the major determinants for stable stand establishment in the rice direct seeding method in temperate regions and at high altitude areas. Quantitative trait loci (QTL) controlling low-temperature germinability in rice were identified using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon and the Korean japonica cultivar, 'Hwaseongbyeo'. The germination rate at $15^{\circ}C$ was measured to represent low-temperature germination and used for QTL analysis. The germination rate at $15^{\circ}C$ for 7 days of Oryza rufipogon and Hwaseongbyeo was 93.3 and 28.7%, respectively, and that of progenies ranged from 0 to 48%. A linkage map was constructed using 135 simple sequence repeat (SSR) markers. Five putative QTLs associated with low-temperature germination were detected on chromosomes 1, 3, 4, 10 and 11. The QTL, qltg10 on chromosome 10 accounted for 19.2% of the total phenotypic variation for low-temperature germinability. Four additional QTL, accounted for 10.4 - 15.1% of the total phenotypic variation. The O. rufipogon alleles in all detected QTLs loci increased the low-temperature germination rate. No QTL associated with low temperature germinability has been detected near the qltg10 QTL in this study suggesting that qltg10 is a new QTL. The locus, qltg10 is of particular interest because of its independence from undesirable height and maturity effects. The DNA markers linked to the QTL for low temperature germinability would be useful in selecting lines with enhanced low temperature germinability in rice breeding program.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.5
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• pp.607-613
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• 2019

Objective: Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods: We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results: A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion: These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.

• 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.

• Plant Breeding and Biotechnology
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• v.1 no.1
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• pp.1-8
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• 2013

Low-temperature stress is an important factor controlling the growth and development of rice (Oryza sativa L.) in temperate region. In this study, a molecular linkage map consisting of 136 SSR markers was employed to identify QTL associated with cold tolerance at the seedling stage. 80 recombinant inbred lines (RILs) from an intersubspecific cross between Milyang23 (O. sativa ssp. Indica) and Hapcheonaengmi3, a japonica weedy rice and the parents were evaluated for leaf discoloration and SAPD value of seedlings. Rice plants were grown for 15 days in the low-temperature condition (13/20℃ day/night) and the control condition (25/20℃ day/night) in the growth chamber. The degree of leaf discoloration showed a highly significant correlation with the SPAD value in the low-temperature plot (r = -0.708, P < 0.0001). A total of four QTLs for SPAD were identified and the phenotypic variance explained by each QTL ranged from 5.4 to 16.0%. Two QTLs detected in the control condition were located on chromosomes 2 and 5, respectively. Two QTL on chromosomes 1 and 4 were detected at the low-temperature condition and Hapcheonaengmi3 alleles increased the SPAD values at these loci. Substitution mapping was conducted to delimit the position of qSPA-4 using introgression lines derived from the same cross. Results indicated that qSPA-4 was located in a 810-Kb region flanked by RM16333 and RM16368. The results indicated that Hapcheonaengmi3 contains QTL alleles that are likely to improve cold tolerance of Indica rice.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.206-206
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• 2022

Sustainable agriculture is a potential strategy to enable agricultural cultivation systems to feed the growing population under climate change. Sustainable agriculture consists of environment-friendly farming methods that allow the production of crops with minimal harm to the ecosystem. Early establishment in rice might be helpful to adopt sustainable agriculture with less inputs, such as water and phosphorus fertilizer. Two QTLs conferring tolerance to abiotic stress and low nutrition condition, DTY4.1 and Pup1, respectively, are effective for good establishment in the early growth stage under low water and phosphorus fertilizer application. We developed 'Sechanmi' and 'MSI 1-DTY' harboring Pup1 and DTY4.1 into MS11, a japonica rice variety adaptable to tropical regions, using Marker-Assisted Backcrossing (MABC). MS 11-PD lines were developed to meet the demand for less water and P fertilizer application throughout the growth stage of rice. In the F5 generation, water-saving or rainfed cultivation was performed in different P (phosphorus) content. Irrigation was applied only when severe drought was observed one month after transplanting. There was no significant difference observed between the parents and MS11-PD lines in low P conditions. However, MS11-PD lines had more tillers in P-supplied conditions compared to that of the parents 40 and 50 days after transplanting. Under the same amount of P, MS11-PD lines might have higher phosphorus uptake capacity than the parents, increasing the number of tillers and showing better early establishment. The better vegetative growth stage is one of the factors that can potentially increase production by way of higher number of panicles. Through this breeding strategy, it is possible to attain sustainable agriculture by applying less P and water to address the need of a growing population.

• 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.

• Korean Journal of Plant Resources
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• v.30 no.2
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• pp.213-218
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• 2017

Rice is the staple food of at least half of the world's population. Due to global warming, the weather is difficult to forecast nowadays. Therefore, it is necessary to breed various breeding to respond to such changes in the environment. This study was conducted to analyze the QTL about plant form, culm length, ear number and ear length by using 120 lines by anther culture, a cross between the Indica variety Cheongcheong and Japonica variety Nagdong. DNA marker was selected on the QTLs gene, and the following results were obtained. CNDH (Cheongcheong Nagdong Doubled Haploid) lines frequency distribution table curves about culm length, ear number and ear length exhibited showed a continuous variation close to a normal distribution. QTL analysis result, on culm length qPlL1-1 and qPlL1-2 were detected on the chromosome 1 and qPlL5 was detected on the chromosome 5. However, on ear length qPL2, qPL3 and qPL10, were detected on the chromosome 2, 3 and 10, while on ear number qPN1-1 and qPN1-2 were detected on the chromosome 1, qPN9 was detected on the chromosome 9. The QTLs related to culm length was found to chromosomes 5 and LOD scores were 3.81. The QTLs related to ear length was found to chromosomes 2 and 3 LOD scores were 7.13 and 3.20. The QTLs related to ear number was found to chromosome 9 and LOD scores were 4.27. Twenty two (22) Japonica cultivars and 12 Indica cultivars were analyzed polymorphisms, using selected 9 markers from the result about plant form analysis. RM5311, RM555 and RM8111 about the culm length, the ear length and number of ear were selected on the standard of Cheongcheong and Nagdong. Each rate of concordances about the culm length, the ear length and number of ear are 44.11%, 41.17% and 44.11%.

• Proceedings of the Korean Society of Crop Science Conference
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• 2000.04a
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• pp.34-35
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• 2000

• International Journal of Industrial Entomology and Biomaterials
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• v.19 no.1
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• pp.143-154
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• 2009

Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

• Proceedings of the Korean Society of Crop Science Conference
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• 2005.10b
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• pp.134-135
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• 2005