• Title/Summary/Keyword: Gene-set analysis

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First Report of Tomato Spotted Wilt Virus in Oxypetalum coeruleum in Korea (옥시페탈룸에서 발생한 토마토반점위조바이러스 국내 첫 보고)

  • Eseul, Baek;Peter, Palukaitis;Ju-Yeon, Yoon
    • Research in Plant Disease
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    • v.28 no.4
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    • pp.231-236
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    • 2022
  • Oxypetalum coeruleum, commonly known as Tweedia, is a perennial herbaceous plant of the Apocynaceae family native to southern Brazil and Uruguay. Tweedia plants are grown as one of the most popular ornamental flowers for floral arrangement in Korea. In May 2021, several tweedia plants in a single greenhouse in Gimje, Jeollabuk-do were found to show virus-like symptoms including necrotic rings, vein-clearing, chlorotic mottle, and mosaic on the leaves, and necrosis on the stems. Here, we have identified tomato spotted wilt virus (TSWV) in symptomatic tweedia leaves by applying high-throughput RNA sequencing. In the result, a single infection by TSWV was verified without mixed infections of different virus species. To confirm the presence of TSWV, a reverse transcription polymerase chain reaction was performed with a specific primer set to the N gene of TSWV. The complete genomic sequence of L, M, and S segments of TSWV 'Oxy' isolate were determined and deposited in GenBank under accession numbers LC671525, LC671638, and LC671639, respectively. In the phylogenetic tree analysis by maximum likelihood method, 'Oxy' isolate showed a high relationship with TSWV 'Gumi' isolate from Gerbera jamesonii in Gyeongsangbuk-do, Korea; for all three RNA segments. To our knowledge, this is the first report of TSWV infection of O. coeruleum in Korea.

Pupal Drone Extracts for Anti-wrinkle and Skin-lightening Materials (수벌번데기 추출물의 주름개선 및 미백효과 구명)

  • Kim, Jung-Eun;Kim, Do-Ik;Koo, Hui-Yeon;Kim, Hyeon-Jin;Kim, Seong-Yeon;Lee, Yoo-Beom;Moon, Jae-Hak;Choi, Yong-Soo
    • Journal of Life Science
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    • v.30 no.5
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    • pp.428-433
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    • 2020
  • In this study, we created pupal stage extracts of Apis mellifera L. drones for use in cosmetic materials. The effect of the drone pupae extract (DPE) on HDF cells was assessed for analysis of anti-wrinkle activity by collagen or collagenase gene expression, and the skin-lightening effect was studied by in vitro tyrosinase inhibition and B16F10 melanoma assay; the two cells were found to be non-cellular when the concentration of DPE was 100 ㎍/ml. Albutin concentration (positive control) in the whitening test was set at a capacity of 100 ug/ml and m-melanocyte stimulating hormone (α-MSH). A melanin-producing induction material was set at a concentration of 100 nM, and the expression of collagen type I and MMP1 collagenase was measured using HDF cells. MMP1 expression was seen to reduce in a concentration-dependent manner in treatment with DPE. Inhibiting melanin generation with B16F12 cells indicated a tendency to decrease in the DPE treatment group. Both L-Tyrosine and L-DOPA as DPE were used in an in vitro tyrosinase induction test to demonstrate the effects of tyrosinase suppression on concentrations. The higher the concentration of DPE, the greater the wrinkle reduction and whitening effect. In conclusion, it was found that DPE is an effective smoothing and whitening material by increasing collagen generation and inhibiting collagenase expression and reducing melanin production.

Verification of ET and AI Derived Offspring Using on the Genetic Polymorphisms of Microsatellite and Coat Color Related Genes in Jeju Black Cattle (제주흑우 집단에서 모색 관련 유전자와 microsatellite marker의 다형현상을 이용한 수정란이식 및 인공수정 유래 후대우 검증)

  • Han, Sang-Hyun;Ko, Jin-Cheul;Kim, Young-Hoon;Kim, Nam-Young;Kim, Jae-Hwan;Ko, Moon-Suck;Jeong, Ha-Yeon;Cho, In-Cheol;Yang, Young-Hoon;Lee, Sung-Soo
    • Journal of Life Science
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    • v.20 no.3
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    • pp.381-387
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    • 2010
  • To find offspring of Jeju Black cattle (JBC) produced by embryo transfer (ET) and artificial insemination (AI), a molecular genetic study was carried out in candidate cattle populations collected from cattle farms in Jeju Island, Korea. The genetic marker set was composed of 11 ISAG microsatellite (MS) markers, 11 SAES MS markers selected by our preliminary analysis for population diversity of JBC and two major coat color related genes: MC1R and ASIP. The results showed a combined non-exclusion probability for first parent (NE-P1) that was higher than that recommended by ISAG (above 0.9995), and a combined non-exclusion probability for sib identity of $5.3{\times}10^{-10}$. Parentage analysis showed that the cases identified the candidate's father only (77.0%), mother only (54.0%), and both parents (40.5%) in the candidate offspring population. The ET and AI calves were identified as 14.7% in the in vitro fertilized eggs provided and 32.4% in total population, respectively. However, the result from ISAG marker analysis showed 3 identical allele-combinations in 7 calves, and that from ISAG/SAES MS marker combination also showed 1 identical allele-combination in 2 calves. Data from MS and coat-color gene analyses provided information for complete identification of all animals tested. Because the present JBC population was mostly bred using small nuclear founders through bioengineering techniques such as AI and ET, the genetic diversity levels obtained from MS analysis in the JBC population were relatively lower than those of other cattle populations, including Hanwoo. The results suggested that the more efficient marker combinations, including coat color related genotypes, should be studied and used for constructing a system for identification and molecular breeding of JBC as well.

Assessment Selective Breeding Effect of Israeli carp (Cyprinus carpio) from Korea (국내 이스라엘 잉어의 선발육종효과 평가)

  • Kim, Jung Eun;Hwang, Ju-ae;Kim, Hyeong Su;Im, Jae Hyun;Lee, Jeong-Ho
    • Korean Journal of Ichthyology
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    • v.32 no.4
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    • pp.210-221
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    • 2020
  • Since the introduction of Israeli carp into Korea for farming in 1973, there are no breeding studies on developing Korea Israeli carp (domestic) so far. This study performed gene-based cross-breeding studies to restore genetic diversity of lowered Israeli carp through continuous inbreeding, and for rapid growth and better scales. This study produced four cross-breeding groups (F1) using Koean Israeli carp and Chinese Songpu mirror carp for the improvement of growth and scale of Israeli carp in Korea. And mating scheme for breeding groups was set in consideration of the morphological analysis and genetic distance of broodstock. In addition, this study used microsatellite markers and genotype data to analyze genetic diversity and parentage analysis. As a result, the average NA and HE values of Korean select broodstock are 8.3 and 0.743, and F1 is 13.0 and 0.764. This study shows that the genetic diversity of F1 has been recovered over Korean Israeli carp through breeding between Korean Israeli carp and Chinese Songpu mirror carp. Common Israeli carp in Korea reached 1.7 kg in 17 months, and improved Israeli carp reached to 2.2 kg. The KC (Korea×China, KC) group was 2.52 and broodstock group was 3.15. F1 showed lower scale score (0.63) than broodstock. The improved carp (F1; CK, KC) had 20% better scales than the parent group (F0), which improved 27% in weight and 25% in scales compared to common Israeli carp. The Israeli carp developed by the genetics-based breeding grew quicker and had improved genetic diversity and fewer scales, which will be of great value for Korean Israeli aquaculture industry due to good marketability.

Developmental Genetic Analysis of Avian Primordial Germ Cells and the Application to Poultry Biotechnology

  • Kagami, H.
    • Korean Journal of Poultry Science
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    • v.28 no.2
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    • pp.135-142
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    • 2001
  • A novel sterategy has been established to determine the origin of the Primordial Germ Cells (PGCs) in avian embryos directly and the developmental fate of the PGCs for the application to Poultry biotechnology. Cells were removed from 1) the centre of area pellucida, 2) the outer of area pellucida and 3) the area opaca of the stage X blastoderm (Eyal-Giladi & Kochav, 1976). When the cells were removed from the centre of area pellucida, the mean number of circulating PGCs in blood was significantly decreased in the embryo at stage 15 (Hamburger & Hamilton, 1951) as compared to intact embryos. When the cells were replenished with donor cells, no reduction in the PGCs number was observed. The removal of cells at the outer of area pellucida or at the area opaca had no effect on the number of PGCs. In case, another set of the manipulated embryos were cultured ex vivo to the hatching and reared to the sexual maturity, the absence of germ cells and degeneration of seminiferous tubules was observed in resulting chickens derived from the blastoderm in which the cells were removed from the centre of the area pellucida. It was concluded that the avian Primordial Germ cells are originated at the center of area pellucida. Developmental ability of the cells to differentiate into somatic cells and germ cells in chimeras were analyzed. Somatic chimerism was detected as black feather attributed from donor cells. Molecular identification by use of female - specific DNA was performed. It was confirmed that the donor cells could be differentiated into chimeric body and erythrocytes. Donor cells retained the ability to differentiate into germline in chimeric gonads. More than 70% of the generated chimeras transmitted donor derived gametes to their offspring indicating that the cells at the center of area pellucida had the high ability to differentiate into germ cells. A molecular technique to identify germline chimerism has been developed by use of gene scan analysis. Strain specific DNA fragments were amplified by the method. It would be greatly contributed for the detection of germline chimerism. Mixed- sex chimeras which contained both male and female cells were produced to investigate the developmental fate of male and female cells in ovary and testes. The sex combinations of donor and recipient of the resulting chimeras were following 4 pairs; (1) chimeras (ZZ/ZZ) produced by a male donor (ZZ) and a male recipient (ZZ), (2) chimeras (ZW/ZW) produced by a female donor (ZW) and a female recipient (ZW), (3) chimeras (ZZ/ZW) Produce by a male donor (ZZ) and a female recipient (ZW), (4) chimeras (ZW/ZZ) produced by a female donor (ZW) and a male recipient (ZZ). It was found that genetically male avian germ cells could differentiate into functional ova and that genetically female germ cells can differentiate into functional spermatozoa in the gonad of the mixed- sex chimeras. An ability for introduction of exogenous DNA into the PGCs from stage X blastoderms were analyzed. Two reporter genes, SV-$\beta$gal and RSV-GFP, were introduced into the PGCs. Expression of bacterial/gal was improved by complexing DNA with liposome detectedcc in 75% of embryos at 3 days embryos. At the embryos incubated for 1 day, expression of the GFP was observed all the embryos. At day 3 of incubation, GFP was detected in about 70% of the manipulated embryos. In case of GFP, expression of the transgene was detected in 30 %e of the manipulated embryos. These results suggested that the cells is one of the most promising vectors for transgenesis. The established strategy should be very powerfull for application to poultry biotechnology.

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Analysis of Genetic Diversity and Population Structure for Core Set of Waxy and Normal Maize Inbred Lines using SSR Markers (SSR 분자마커를 이용한 찰옥수수 및 종실용 옥수수 자식계통들의 핵심집단에 대한 유전적 다양성 및 집단구조 분석)

  • Sa, Kyu Jin;Kim, Jin-Ah;Park, Ki Jin;Park, Jong Yeol;Goh, Byeong Dae;Lee, Ju Kyong
    • Korean Journal of Breeding Science
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    • v.43 no.5
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    • pp.430-441
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    • 2011
  • Maize is divided into two types based on the starch composition of the endosperm in the seed, normal maize(or non-waxy maize) and waxy maize. In this study, genetic diversity and population structure were investigated among 80 waxy maize and normal inbred lines(40 waxy maize inbred lines and 40 normal maize inbred lines) using 50 SSR markers. A total of 242 alleles were identified at all the loci with an average of 4.84 and a range between 2 and 9 alleles per locus. The gene diversity values varied from 0.420 to 0.854 with an average of 0.654. The PIC values varied from 0.332 to 0.838 with an average of 0.602. To evaluate the population structure, STRUCTURE 2.2 program was employed to confirm genetic structure. The 80 waxy and normal maize inbred lines were separated with based on the membership probability threshold 0.8, and divided into groups I, II and admixed group. The 13 waxy maize inbred lines were assigned to group I. The 45 maize inbred lines including 7 waxy maize inbred lines and 38 normal maize inbred lines were assigned to group II. The 22 maize inbred lines with 20 waxy maize inbred lines and 2 normal maize inbred lines were contained in the admixed group. The cluster tree generated using the described SSR markers recognized three major groups at 31.7% genetic similarity. Group I included 40 waxy maize inbred lines and 11 normal maize inbred lines, and Group II included 27 normal maize inbred lines. Group III consist of only 2 normal maize inbred lines. The present study has demonstrated the utility of SSR analysis for the study of genetic diversity and the population structure among waxy and normal maize inbred lines. The information obtained from the present studies would be very useful for designing efficient maize breeding programs in Maize Experiment Station, Kangwon Agricultural Research and Extension Services.

Identification of a Locus Associated with Resistance to Phytophthora sojae in the Soybean Elite Line 'CheonAl' (콩 우수 계통 '천알'에서 발견한 역병 저항성 유전자좌)

  • Hee Jin You;Eun Ji Kang;In Jeong Kang;Ji-Min Kim;Sung-Taeg Kang;Sungwoo Lee
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.68 no.3
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    • pp.134-146
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    • 2023
  • Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ2 = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

Studies on Genetic Analysis by the Diallel Crosses in $F_2$ Generation of Cowpea(Vigna sinensis savi.) (동부 Diallel Cross$ F_2$세대의 유전분석에 관한 연구)

  • Kim, J.H.;Ko, M.S.;Chang, K.Y.
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.28 no.2
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    • pp.216-226
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    • 1983
  • Genetic studies on the $F_2$ generation of a set of half diallel crosses involving six cowpea varieties were conducted. by the randomized block design with three replications to determine combining ability, gene action and the relationships between parents and their $F_2$ hybrids. The 12 agronomic characters namely, days to flowering, days from flowering to maturity, days to maturity, diameter of stem, length of internode, number of branches per plant, length of pod, number of pods per plant, number of grains per pod, number of grains per plant, 100 grain weight and grain weight per plot were observed, and the $F_2$ generation of this diallel set of crosses was analysed for each character according to the method by Jinks and Hayman. The results obtained are summarized as follows: 1. Vr-Wr graphical analyses; The following seven characters, days to flowering, number of branches per plant, length of pod, number of pods per plant, number of grains per plant, 100 grain weight and grain weight per plot appeared to be partially dominant, and over dominance was found for days from flowering to maturity, days to maturity, length of internode and number of grains per pod. But diameter of stem indicated partial dominance near complete dominance. 2. Estimates of genetic variance components; In the degree of dominance,. eight characters, that is, days to flowering, days from flowering to maturity, days to maturity, length of internode, number of pods per plant, number of grains per pod, number of grains per plant and grain weight per plot were expressed larger than 1. And the characters, days from flowering to maturity, number of branches per plant and number of grains per plant as the degree of mean dominance ($H_1$/D) were found to be negative value over other characters. On the other hand, apprent asymmetry of dominance-recessive allele ($H_2$ /$4H_1$) produced comparatively estimates with lower value on days from flowering to maturity, length of internode, number of branches per plant and number of grains per pod. 3. Analyses of combining ability; Mean square value of GCA(general combining ability) appeared to be more important than those of SCA (specific combining ability) for most characters, and among them, grain weight per plot showed the highest mean square value in GCA and SCA. 4. Effect of combining ability; Variety 178 was expressed as the highest GCA effects in five characters (days to flowering days to maturity, number of pods per plant, number of grains per plant and grain weight per plot). SCA effects were differed from parents, characters and crosses, but crosses between TVu 1857 $\times$ TVu 2885 and TVu 2702 $\times$ J78 were shown to be highly with SCA effects on yield.

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A Study of the Factors Influencing Behavioral Intention for Organic Food: Using the Theory of Planned Behavior (유기농식품에 대한 소비자의 구매의도 영향요인 분석 계획적 행동이론을 중심으로)

  • Choi, Hwa-Sun;Lee, Kwang-Keun
    • Journal of Distribution Science
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    • v.10 no.2
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    • pp.53-62
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    • 2012
  • Well-being is a reflection of current sociocultural trends that focus on the quality of life based on economic growth. Furthermore, organic food is believed to help people maintain good health and therefore leads to increased consumption of organic foods. Therefore, consumer interest in organic food is increasing, causing its market to grow, and this trend will be maintained in the future. The abuse of agricultural pesticides, gene manipulation, and bovine spongiform encephalopathy has caused consumers to worry about food safety. The well-being trend has also contributed to consumers' growing interest inorganic food and organic agricultural products. A consumer's choice offood is a complex processes affected by various factors. In particular, organic food is considered an individualistic merit good, considering the consumers' preferences related to certification policies. Therefore, various factors such as personal characteristics and sense of value could affect consumers' decisions. This research focused on an analysis of the factors influencing consumers' purchasing intention for organic food on the basis of an increase in organic food consumption. The research method was based on the theory of planned behavior (TPB). Factors such as consumer characteristics regarding food consumption, purchasing frequency, and other factors affecting purchasing intention were presented. The hypothesis was set using advanced research and stated that it is easier to forecast purchasing intentions by combining the theory of planned behavior and personal characteristics of consumer. The results show that two dimensions, attitude and perceived behavioral control, have statistically significant influence on the purchasing intention. It can be said that a positive attitude toward organic foods in particular increases the possibility of purchasing intention. In addition, consumers who consume more organic food products are more likely to have positive attitudes, and, in the past, purchasing frequency has positively influenced purchasing intention of organic foods. Consumers' negative feelings about the non-purchase of organic foods also showed a negative influence on purchasing intentions. In other words, even though consumers feel uncomfortable when not consuming organic food products, they do not try to purchase such products because of this feeling of discomfort. Furthermore, the subjective norm and the behavioral control of food-related involvement do not have a statistically significant influence on the purchasing intention or attitudes. This research verified the influence of factors related to purchasing intention. This study has several limitations: (1) even though consumers' responses can change based on the type of food, the types of food were not classified in this study; (2) future studies are necessary to analyze the attitudes of consumers on the basis of their purchasing experiences with organic foods.

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Production of Transgenic Pigs with an Introduced Missense Mutation of the Bone Morphogenetic Protein Receptor Type IB Gene Related to Prolificacy

  • Zhao, Xueyan;Yang, Qiang;Zhao, Kewei;Jiang, Chao;Ren, Dongren;Xu, Pan;He, Xiaofang;Liao, Rongrong;Jiang, Kai;Ma, Junwu;Xiao, Shijun;Ren, Jun;Xing, Yuyun
    • Asian-Australasian Journal of Animal Sciences
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    • v.29 no.7
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    • pp.925-937
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    • 2016
  • In the last few decades, transgenic animal technology has witnessed an increasingly wide application in animal breeding. Reproductive traits are economically important to the pig industry. It has been shown that the bone morphogenetic protein receptor type IB (BMPR1B) A746G polymorphism is responsible for the fertility in sheep. However, this causal mutation exits exclusively in sheep and goat. In this study, we attempted to create transgenic pigs by introducing this mutation with the aim to improve reproductive traits in pigs. We successfully constructed a vector containing porcine BMPR1B coding sequence (CDS) with the mutant G allele of A746G mutation. In total, we obtained 24 cloned male piglets using handmade cloning (HMC) technique, and 12 individuals survived till maturation. A set of polymerase chain reactions indicated that 11 of 12 matured boars were transgene-positive individuals, and that the transgenic vector was most likely disrupted during cloning. Of 11 positive pigs, one (No. 11) lost a part of the terminator region but had the intact promoter and the CDS regions. cDNA sequencing showed that the introduced allele (746G) was expressed in multiple tissues of transgene-positive offspring of No.11. Western blot analysis revealed that BMPR1B protein expression in multiple tissues of transgene-positive $F_1$ piglets was 0.5 to 2-fold higher than that in the transgene-negative siblings. The No. 11 boar showed normal litter size performance as normal pigs from the same breed. Transgene-positive $F_1$ boars produced by No. 11 had higher semen volume, sperm concentration and total sperm per ejaculate than the negative siblings, although the differences did not reached statistical significance. Transgene-positive $F_1$ sows had similar litter size performance to the negative siblings, and more data are needed to adequately assess the litter size performance. In conclusion, we obtained 24 cloned transgenic pigs with the modified porcine BMPR1B CDS using HMC. cDNA sequencing and western blot indicated that the exogenous BMPR1B CDS was successfully expressed in host pigs. The transgenic pigs showed normal litter size performance. However, no significant differences in litter size were found between transgene-positive and negative sows. Our study provides new insight into producing cloned transgenic livestock related to reproductive traits.