• 한국육종학회지
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• 제42권2호
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• pp.151-156
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• 2010

The mutants of sugary-2 (su-2), floury (flo), shrunken-1 (shr-1), and dull-1 (du-1) were crossed to waxy (wx) to produce $F_2$ seeds. Chi-square analysis on the segregating ratio of the $F_2$ seeds revealed that flo, su-2, and shr-1 were independently transmitted with wx, while wx was epistatic over du-1. The floury and sugary-2 were crossed to Hwasunchalbyeo, a waxy variety, and then the $F_4$ of floury-waxy and sugary-2-waxy seeds were developed, respectively. As the parents phenotypes of sugary-2 and floury, the grains of these two lines showed lower hardness and grain weight than normal grain of Hwacheongbyeo. For alkali digestive value (AVD), the sugary-2-waxy showed lower ADV than Hwacheongbyeo. For the gel consistency of grain flours, the floury was medium like Hwacheongbyeo, while those of the sugary-2, floury-waxy, and sugary-2-waxy were soft like Hwasunchalbyeo. The amylose contents in the grains of the sugary-2 and floury were decreased to ~15% whereas that of Hwacheongbyeo was 19.1%. All the lines showing waxy endosperm (Hwasunchalbyeo, floury-waxy, and sugary-2-waxy) showed less than 4% amylose contents. Interestingly, the free sugar content in the brown rice was increased to 9.27% in the sugary-2-waxy, showing transgressive segregation phenomenon where the free sugar contents in its parents, sugary-2 and Hwasunchalbyeo, were 5.98% and 3.98% respectively. Also, the floury-waxy showed transgressive segregation phenomenon, containing 6.15% of free sugar content in the grains.

• Animal Bioscience
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• 제35권9호
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• pp.1289-1302
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• 2022

The next generation sequencing has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the male-specific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in Bos taurus, 5 and 7 in Bubalus bubalis, 5 and 24 in Ovis aries, 5 and 19 in Capra hircus, 10 and 16 in Sus scrofa, 46 and 18 in Equus caballus. While in Vicugna pacos only 10 loci are reported in the PAR region. The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.

• Animal Bioscience
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• 제37권4호
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• pp.622-630
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• 2024

Objective: Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). Methods: Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. Results: The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. Conclusion: This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

• Asian-Australasian Journal of Animal Sciences
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• 제25권2호
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• pp.183-188
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• 2012

To investigate the influence of the prolactin receptor 3 (PRLR3) gene and the retinol-binding protein 4 (RBP4) gene on the production traits of swine, genotyping was performed on 156 and 141 Berkshire pigs, respectively, that were carefully selected for economic traits. The frequencies of allele A in the PRLR3 locus and allele B in the RBP4 locus were 0.50 and 0.42, respectively. Neither locus was in the Hardy-Weinberg equilibrium. After a genotype was assigned to the individuals whose parents had the homozygous genotype, a statistical analysis was conducted for 291 pigs. The animals with the PRLR3 and RBP4 genotypes included 182 and 227 head, respectively. Even though the genotypic effects of PRLR3 (p<0.05) and RBP4 (p<0.01) had a significant influence on the pigs' back fat thickness, the interaction of both genes was not highly significant in terms of the back fat thickness (p = 0.1235). While the estimated epistasis effects of aaBB and aaBb decreased the back fat thickness and reduced the growth rate, the effects of AAbb and aabb increased the growth rate. Despite the insignificant difference in the PRLR genotypes in terms of the days to 90 kg and the average daily gain, the back fat thickness showed a significant difference (p<0.05), and the additive effect of allele A and the dominant effect of the hetero-genotype were -0.377 and 1.206 mm, respectively. The RBP4 genotypes had a very significant effect (p<0.01) on the back fat thickness, the days to 90 kg, and the average daily gain. The additive effects of allele B of the RBP4 locus on the back fat thickness, the days to 90 kg, and the average daily gain were 0.70 mm, -1.3 days and 6.2 g, respectively. Moreover, the dominant effects of the heterozygote for those traits were 0.63 mm, 9.9 days and -45.0 g, respectively. Allele A of the PRLR3 locus favorably influenced the back fat thickness, the days to 90 kg of the body weight, and the average daily gain and its dominant effect unfavorably influenced those traits. Allele B of RBP4 showed an incremental growth rate and back fat thickness, which could lower the lean meat percentage in the carcass. The RBP4 hetero-genotype negatively affected the pork production. These results strongly imply that the selection of allele A of PRLR3 and allele B of RBP4 would produce highly productive pigs in the Berkshire breed. Careful selection of allele B of RBP4 is required because of the increase in the back fat thickness.

• Molecules and Cells
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• 제24권1호
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• pp.16-26
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• 2007

Wild progenitor species provide potential gene sources for complex traits such as yield and multiple resistances to biotic and abiotic stresses, and thus are expected to contribute to sustainable food supplies. An introgression line 'IR71033-121-15' was derived from a wild species Oryza minuta (2n = 48, BBCC, Acc No. 101141) at IRRI. Introgression analysis using 530 SSR and STS markers revealed that at least 14 chromosomal segments distributed over 12 chromosomes had been introgressed from O. minuta. An $F_{2:3}$ population from the cross between IR71033 and Junambyeo (a Korean japonica cultivar) consisting of 146 lines was used for quantitative trait loci (QTL) analysis of 16 agronomic traits. A total of 36 single-locus QTLs (S-QTLs) and 45 digenic epistasis (E-QTLs) were identified. In spite of it's inferiority of O. minuta for most of the traits studied, its alleles contributed positively to 57% of the QTLs. The other QTLs originated from either parent, IR71033 or Junambyeo. QTLs for phenotypically correlated traits were mostly detected on introgressed segments. Fourteen QTLs corresponded to QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Twenty-two QTLs controlling yield and its components had not been detected in previous QTL studies. Of these, thirteen consisted of potentially novel alleles from O. minuta. QTLs from O. minuta introgression could be new sources of natural variation for the genetic improvement of rice.

• Molecules and Cells
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• 제24권1호
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• pp.83-94
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• 2007

During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with $F_2$ and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

• Current Research on Agriculture and Life Sciences
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• 제4권
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• pp.12-17
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• 1986

고추 육종(育種)의 기초자료(基礎資料)를 얻고자 $342{\times}$김장고추, 馬山${\times}$Hungarian wax 그리고 마산(馬山)${\times}$제주(濟州) 등(等) 3조합(組合)의 친(親), $F_1$, $F_2$ 그리고 $BCF_1$ 세대(世代)에 대(對)해 적숙(赤熟)된 과실(果實)을 수집(收穫)하여 1생(生) 건과중(乾果重)을 구성(構成)하는 형질(形質)들의 잡종강세(雜種强勢), 유전성분(遺傳成分) 및 상관관계(相關關係)를 조사(調査)한 결과(結果)를 요약(要約)하면 다음과 같다. 평균(平均) Heterosis는 거의 모든 형질(形質)에서 정(正)의 값을 나타내었고 평균(平均) Heterobeltiosis는 $342{\times}$김장고추조합(組合)을 제외(除外)하고는 거의 부(負)의 값을 나타내었다. 또한 근교약세(近交弱勢)도 정(正)의 값을 보여 $F_2$에서의 무게감소가 있는 것으로 나타났다. 형질발현(形質發現)에는 각(各) 조합(組合)의 형질(形質)에 따라 중복적(重複的) 혹(或)은 보족적(補足的)으로 상위성(上位性)이 작용(作用)하였으며 $F_2$에서 과중(果重)과 과육중(果肉重)은 광의(廣義) 및 협의(狹義)의 유전력(遺傳力)이 높았으며 기타형질(其他形質)은 전반적(全般的)으로 낮았다. 각(各) 과중구성요소간(果重構成要素間)의 형질상관(形質相關)은 생(生) 건과중(乾果重)에서 모두 정(正)의 유의(有意)한 상관(相關)을 보였다.

• 식물병연구
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• 제18권4호
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• pp.317-323
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• 2012

본 연구는 국내 고추 주산지의 P. capsici의 균주에 대한 병원성과 균주별 역병 저항성 유전 양식을 구명하고자 수행하였다. 이병성 재료 '#308'과 역병 저항성 재료 'CM334' 및 이들의 $F_1$, $F_2$ 그리고 'Kataguma'(Sakata Korea) 고추 총 5종의 공시 재료에 이천, 음성, 부안, 임실, 영양 지역에서 수집한 P. capsici 각각의 균주와 국립농업유전자원센터에서 분양받은 PA-159(KACC No. 40482)를 포함하여 총 6종의 고추 P. capsici 균주를 사용하여 접종하였다. 접종 농도는 $1{\times}10^5spores/ml$로 관주 접종하였고 이들의 기내 특성, 이병률, $F_2$ 후대 집단의 역병저항성 분리 기대비를 분석하였다. 이병성 재료 '#308'과 저항성 'CM334', $F_1$의 비분리세대는 균주별 군내 비교에서는 각각 고추 역병의 발병도는 4.94-5.00, 1.00-1.07, 1.01-1.08을 보여 P. capsici 균주별 군내 비교에서 공시재료간 역병 저항성 차이는 명확히 구분할 수 있다. 또한 $F_2$ 분리세대의 역병 발병도의 경향은 1.79-2.31을 보여 P. capsici 군내 비교의 차이가 없고 저항성과 이병성 재료간에 유의한 차이를 보여 본 연구에서 사용된 6종의 P. capsici 균주 모두 역병 저항성 검정을 위한 균주로 활용 가능한 것으로 나타났다. 하지만 $F_2$ 분리세대의 균주별 군간 비교에서 PA-159 균주를 중심으로 이천 균주, 부안 균주, 임실 균주가 포함된 집단과 이보다 높은 병원성을 지닌 영양 균주와 음성 균주로 구분되었다. 각 균주별 $F_2$ 세대의 역병 저항성에 대한 분리 기대비를 분석하였는데, PA-159 균주는 3:1 또는 9:3:3:1의 분리비를 보여 1-2개의 유전자가 관여하는 것으로 나타났다. 반면 음성 균주와 영양 균주는 11:5, 이천 균주는 12:3:1의 분리비를 보여 유전자간 상호작용이 있는 것으로 나타났다.