• Asian-Australasian Journal of Animal Sciences
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• 제19권8호
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• pp.1085-1089
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• 2006

The objectives of this study were to confirm a location of the calpastatin (CAST) gene in chromosome 2 and to detect associations of genetic variations with economic traits in the porcine CAST gene as a candidate gene for growth and meat quality traits in pigs. Calpastatin is a specific endogenous inhibitor of calpains. The calpain protease system is ubiquitous, and is involved in numerous growth and metabolic processes. Three single nucleotide variations were identified within a 1.6 kb fragment of the porcine CAST gene and these polymorphisms were used for genetic linkage mapping. Linkage and QTL mapping were performed with the National Livestock Research Institute (NLRI) reference families using eight microsatellites and SNP makers in the CAST gene. The porcine CAST gene was mapped adjacent to the markers, SW395 and SW1695 on SSC2 with LOD scores of 15.32 and 8.50, respectively. According to the QTL mapping, a significant association was detected at 82 cM between SW395 and CAST-Hinf I for weight at the age of 30 weeks. In addition, an association study was performed with the $F_2$ animals of NLRI reference families for Hinf I, Msp I and Rsa I polymorphisms in the CAST gene. Two polymorphisms, CAST-Rsa I and CAST-Hinf I, showed significant correlation for growth traits at p<0.01 and p<0.05, respectively.

• Asian-Australasian Journal of Animal Sciences
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• 제16권3호
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• pp.320-324
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• 2003

The objective of this study was to localize QTL affecting meat quality in a pig family of three generations. All animals were genotyped for twenty-four microsatellites on SSC3 (Sus scrofa chromosome 3), SSC4 and SSC7. One hundred and forty $F_2$ offsprings were scored for eleven meat quality traits. Least square regression interval mapping revealed quantitative trait loci (QTL) effect for meat pH (m. Semipinalis Capitis, SC) on SSC4 and SSC7; for moisture (m. Longissimus Dorsi, LD) on SSC3. Furthermore, there was suggestive evidence for a QTL on SSC4 affecting intramuscular fat (IMF) content that nearly approached the chromosomewise (p=0.05) significance threshold.

• Asian-Australasian Journal of Animal Sciences
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• 제20권12호
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• pp.1805-1811
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• 2007

A simulation study was conducted to evaluate the effect of reciprocal cross on the detection and characterization of parent-of-origin (POE) QTL in $F_2$ QTL populations. Data were simulated under two different mating designs. In the one-way cross design, six $F_0$ grand sires of one breed and 30 $F_0$ grand dams of another breed generated 10 $F_1$ offspring per dam. Sixteen $F_1$ sires and 64 $F_1$ dams were randomly chosen to produce a total of 640 $F_2$ offspring. In the reciprocal design, three $F_0$ grand sires of A breed and 15 $F_0$ grand dams of B breed were mated to generate 10 $F_1$ offspring per dam. Eight $F_1$ sires and 32 $F_1$ dams were randomly chosen to produce 10 $F_2$ offspring per $F_1$ dam, totaling 320 $F_2$ offspring. Another mating set comprised three $F_0$ grand sires of B breed and 15 $F_0$ grand dams of A breed to produce the same number of $F_1$ and $F_2$ offspring. A chromosome of 100 cM was simulated with large, medium or small QTL with fixed or different allele frequencies in parental breeds. A series of tests between Mendelian and POE models were applied to characterize QTL as Mendelian, paternal, maternal or partial expression QTL. The overall detection powers were similar between the two mating designs. However, the proportions of paternally expressed QTL that were declared as paternal QTL type were greater in the reciprocal cross design than in the one-way cross, and vice versa for Mendelian QTL. When QTL alleles were segregating in parental breeds, a significant proportion of Mendelian QTL were spuriously declared POE QTL, suggesting that care must be taken to characterize imprinting QTL in a QTL mapping population with a small number of $F_1$ parents.

• 한국가금학회:학술대회논문집
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• 한국가금학회 2003년도 제20차 정기총회 및 학술발표회
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• pp.135-137
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• 2003

본 연구는 한국 재래닭에 대한 유전적 특성에 근거한 표지유전자 및 재래닭 특이유전자와 경제형질간의 연관성을 분석하고자 실시하였다. 연구의 수행을 위해 DNA 초위성체에 의한 경제형질 연관 QTL 지도를 작성하는 것을 목표로 하며, 실험재료로서는 현재 국내의 재래닭을 계통화하여 개량하고 있는 집단으로부터 QTL mapping을 위한 기준집단을 조성하여 이들로부터 경제형질을 조사하고 특정 경제형질 연관 QTL을 탐색하기 위한 연구 설계 및 기준집단을 조성하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1350-1353
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• 2004

To further investigate the regions on porcine chromosome 7 that are responsible for economically important traits, phenotypic data from a total of 287 F2 individuals were collected and analyzed from 1998 to 2000. All animals were genotyped for eight microsatellite loci spanning the length of chromosome 7. QTL analysis was performed using interval mapping under the line-cross model. A permutation test was used to establish significance levels associated with QTL effects. Observed QTL effects were (chromosomewide significance, position of maximum significance in centimorgans): Birth weight (<0.01, 3); Carcass length (<0.05, 80); Longissimus muscle area (<0.01, 69); Skin percentage (<0.01, 69); Bone percentage (<0.01, 74); Fat depths at shoulder (<0.05, 54);Mean fat depth (<0.05, 81); Moisture in m. Longissimus Dorsi (<0.05, 88). Additional evidence was also found which suggested QTL for dressing percentage and fat depths at buttock. This study offers confirmation of several QTL affecting growth and carcass traits on SSC7 and provides an important step in the search for the actual major genes involved in the traits of economic interest.

• Asian-Australasian Journal of Animal Sciences
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• 제25권5호
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• pp.613-620
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• 2012

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

• Plant Resources
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• 제3권3호
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• pp.184-193
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• 2000

Soybean [Glycine max (L.) Merr.] seed weight is a important trait in cultivar development. Objective of this study was to identify and confirm quantitative trait loci (QTLs) for seed weight variation in the F2 and F2:3 generations. QTLs for seed weight were identified in F2 and F2:3 generations using interval mapping (MapMaker/QTL) and single-factor analysis of variance (ANOVA). In the F2 plant generation (i.e., F3 seed), three markers, OPL9a, OPM7a, and OPAC12 were significantly (P<0.01) associated with seed weight QTLs. In the F2:3 plant row generation (i.e., F4 seed), five markers, OPA9a, OPG19, OPL9b, OPP11, and Sat_085 were significantly (P<0.01) associated with seed weight QTLs. Two markers, OPL9a and OPL9b were significantly (P<0.05) associated with seed weight QTLs in both generations. Two QTLs on USDA soybean linkage group C1 and R were identified in both F2 and F2:3 generations using interval mapping. The linkage group C1 QTL explained 16% of the variation in seed weight in both generations, and the linkage group R QTL explained 39% and 41% of the variation for F2 and F2:3 generation, respectively. The linkage group C2 QTL identified in F2:3 generation explained 14.9% of variation. Linkage groups C1, C2 and R had previously been identified as harbouring seed size QTLs. The consistency of QTLs across generations and populations indicates that marker-assisted selection is possible in a soybean breeding program.

• Plant Breeding and Biotechnology
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• 제1권1호
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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.

• Asian-Australasian Journal of Animal Sciences
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• 제21권5호
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• pp.617-623
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• 2008

A fine-mapping method exploiting linkage disequilibrium was used to detect quantitative trait loci (QTL) on the X chromosome affecting milk production, body conformation and productivity traits. The pedigree comprised 22 paternal half-sib families of Black-and-White Holstein bulls in the Netherlands in a grand-daughter design for a total of 955 sons. Twenty-five microsatellite markers were genotyped to construct a linkage map on the chromosome X spanning 170 Haldane cM with an average inter-marker distance of 7.1 cM. A covariance matrix including elements about identical-by-descent probabilities between haplotypes regarding QTL allele effects was incorporated into the animal model, and a restricted maximum-likelihood method was applied for the presence of QTL using the LDVCM program. Significance thresholds were obtained by permuting haplotypes to phenotypes and by using a false discovery rate procedure. Seven QTL responsible for conformation types (teat length, rump width, rear leg set, angularity and fore udder attachment), behavior (temperament) and a mixture of production and health (durable prestation) were detected at the suggestive level. Some QTL affecting teat length, rump width, durable prestation and rear leg set had small numbers of haplotype clusters, which may indicate good classification of alleles for causal genes or markers that are tightly associated with the causal mutation. However, higher maker density is required to better refine the QTL position and to better characterize functionally distinct haplotypes which will provide information to find causal genes for the traits.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.286-286
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• 2022

The properties of starch play an important role in determining the palatability of rice. In addition, the gelatinization temperature (GT) of rice starch is an important factor in determining the quality of rice because it is related to the cooking time and texture of rice. For the development of high-quality rice, it is important to understand the genetic basis of palatability-related traits, and QTL analysis is an effective method to explain the genetic basis of variation in complex traits. QTL mapping related to alkali digestion value (ADV) of brown and milled rice was performed using the 120 Cheongcheong/Nagdong double haploid (CNDH) line. As a result, 12 QTLs related to ADV were detected, and 20 candidate genes were selected from the RM588-RM1163 region of chromosome 6 through screening by gene function analysis. The comparison of the relative expression level of candidate genes showed that OsSS1q6 is highly expressed in CNDH lines with high ADV in both brown rice and milled rice. In addition, OsSS1q6 has high homology with starch synthase 1 protein, and interact with various starch biosynthesis-related proteins, such as GBSSII, SBE, and APL. Therefore, we suggest that OsSS1q6 identified through QTL mapping could be one of the various genes involved in the GT of rice by regulating starch biosynthesis. This study can be used as basic data for breeding high-quality rice and provides a new genetic resource that can increase the palatability of rice.