• Communications for Statistical Applications and Methods
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• v.16 no.4
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• pp.713-722
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• 2009

The estimation of odds ratio and corresponding confidence intervals for case-control data have been done by traditional generalized linear models which assumed that the logarithm of odds ratio is linearly related to risk factors. We adapt a lower-dimensional approximation of Gu and Kim (2002) to provide a faster computation in nonparametric method for the estimation of odds ratio by allowing flexibility of the estimating function and its Bayesian confidence interval under the Bayes model for the lower-dimensional approximations. Simulation studies showed that taking larger samples with the lower-dimensional approximations help to improve the smoothing spline estimates of odds ratio in this settings. The proposed method can be used to analyze case-control data in medical studies.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.591-599
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• 2020

Phytophthora root and stem rot reduce soybean yields worldwide. The use of R-gene type resistance is currently crucial for protecting soybean production. The present study aimed to identify the genomic location of a gene conferring resistance to Phytophthora sojae isolate 2457 in the recombinant inbred line population developed by a cross of Daepung × Daewon. Singlemarker analysis identified 20 single nucleotide polymorphisms associated with resistance to the P. sojae isolate 2457, which explained ~67% of phenotypic variance. Daewon contributed a resistance allele for the locus. This region is a well-known location for Rps1 and Rps7. The present study is the first, however, to identify an Rps gene locus from a major soybean variety cultivated in South Korea. Linkage analysis also identified a 573 kb region on chromosome 3 with high significance (logarithm of odds = 13.7). This genomic region was not further narrowed down due to lack of recombinants within the interval. Based on the latest soybean genome, ten leucine-rich repeat coding genes and four serine/ threonine protein kinase-coding genes are annotated in this region, which all are well-known types of genes for conferring disease resistance in crops. These genes would be candidates for molecular characterization of the resistance in further studies. The identified R-gene locus would be useful in developing P. sojae resistant varieties in the future. The results of the present study provide foundational knowledge for researchers who are interested in soybean-P. sojae interaction.

• Genes and Genomics
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• v.40 no.12
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• pp.1351-1361
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• 2018

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 $F_{12}$ recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.55 no.5
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• pp.557-566
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• 2022

The Japanese eel Anguilla japonica is a highly valued research object that is important for aquaculture in Asia, including the Republic of Korea. However, few studies have been conducted analyzing parentage using microsatellite markers derived from the Japanese eel. We acquired Japanese eel genome data using next generation sequencing technology, and constructed a draft genome comprising 1,087 Mbp. Using the Simple Sequence Repeat Identification Tool program, 444,724 microsatellites were identified. Of these, 1,842 microsatellites located in the 3' untranslated region, which are stably inherited, were finally selected. Ninety-six primers were selected to validate polymorphism at these microsatellites, and 9 primers were finally identified for multiplex analysis. Using multiplex polymerase chain reaction with three different fluorescence chemistries, we performed parentage analysis of an artificial Japanese eel population. CERVUS software was used to calculate the logarithm of the odds (LOD) scores and the confidence of the parentage assignments. The results presented here show that 83 out of 85 paternity cases were assigned at 95% confidence to a candidate father and mother with LOD scores ranging from 4.79 to 28.2. This study provided a microsatellite marker-based assay for parentage analysis of Japanese eels, which will be useful for selective breeding and genetic diversity studies.

• Asian Journal of Turfgrass Science
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• v.22 no.1
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• pp.85-100
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• 2008

Gray leaf spot (GLS) is a serious fungal disease caused by Pyricularia oryzae Cavara, recently reported on the important turf and forage species, perennial ryegrass (Lolium perenneL.). This fungus also causes rice blast, which is usually controlled by host resistance, but durability of resistance is a problem. Few instances of GLS resistance have been reported in perennial ryegrass. However, two major QTL for GLS resistance have been detected on linkage groups 3 and 6 in an Italian x perennial ryegrass mapping population. To confirm that those QTL are still detectable in the next generation and can function in a different genetic background, a resistant segregant from this population has been crossed with an unrelated susceptible perennial clone, to form a new mapping population segregating for GLS resistance. QTL analysis has been performed in the new population, using two different ryegrass field isolates and RAPD, RFLP, and SSR marker-based linkage maps for each parent. Results indicate the previously identified QTL on linkage group 3 is still significant in the new population, with LOD and percent of phenotypic variance explained ranging from 2.0 to 3.5 and 5% to 10%, respectively. Also two QTL were detected in the susceptible parent, with similar LOD and phenotypic variance explained. Although the linkage group 6 QTL was not detected, the major QTL on linkage group 3 appears to beconfirmed. These results will add to our understanding of the genetic architecture of GLS resistance in ryegrass, which will facilitate its use in perennial ryegrass breeding programs.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.1
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• pp.43-50
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• 2016

Quantitative trait locus (QTL) is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC). F1 samples (n = 595) were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM) of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3) for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001) and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003). Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007) and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027) were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1649-1659
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• 2012

Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1555-1561
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• 2016

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [$L^*$], redness [$a^*$], and yellowness [$b^*$]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects $b^*$ value (logarithm of odds [LOD] = 47.5, $p=1.60{\times}10^{-49}$) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences $a^*$ value (LOD = 14.2, $p=6.14{\times}10^{-16}$). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and $a^*$ ($P_{MGA}=1.69{\times}10^{-28}$; $P_{QTDT}=2.40{\times}10^{-25}$). The strongest associations were between BCDO2 g.9367 A>C and $b^*$ ($P_{MGA}=3.56{\times}10^{-66}$; $P_{QTDT}=1.68{\times}10^{-65}$). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.