• Title/Summary/Keyword: Quantitative Genetics

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What Holds the Future of Quantitative Genetics? - A Review

  • Lee, Chaeyoung
    • Asian-Australasian Journal of Animal Sciences
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    • v.15 no.2
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    • pp.303-308
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    • 2002
  • Genetic markers engendered by genome projects drew enormous interest in quantitative genetics, but knowledge on genetic architecture of complex traits is limited. Complexities in genetics will not allow us to easily clarify relationship between genotypes and phenotypes for quantitative traits. Quantitative genetics guides an important way in facing such challenges. It is our exciting task to find genes that affect complex traits. In this paper, landmark research and future prospects are discussed on genetic parameter estimation and quantitative trait locus (QTL) mapping as major subjects of interest.

BcSNPdb: Bovine Coding Region Single Nucleotide Polymorphisms Located Proximal to Quantitative Trait Loci

  • Moon, Sun-Jin;Shin, Hyoung-Doo;Cheong, Hyun-Sub;Cho, Hye-Young;NamGoong, Sohg;Kim, Eun-Mi;Han, Chang-Su;Sung, Sam-Sun;Kim, Hee-Bal
    • BMB Reports
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    • v.40 no.1
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    • pp.95-99
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    • 2007
  • Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

Mapping Quantitative Trait Loci for Meat Quality on Pig Chromosome 3, 4 and 7

  • Zuo, Bo;Xiong, YuanZhu;Su, YuHong;Deng, ChangYan;Zheng, Rong;Jiang, Siwen
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.3
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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.

Identification of novel susceptibility genes associated with bone density and osteoporosis in Korean women

  • Bo-Young Kim;Do-Wan Kim;Eunkuk Park;Jeonghyun Kim;Chang-Gun Lee;Hyun-Seok Jin;Seon-Yong Jeong
    • Journal of Genetic Medicine
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    • v.19 no.2
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    • pp.63-75
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    • 2022
  • Purpose: Osteoporosis is a common calcium and metabolic skeletal disease which is characterized by decreased bone mass, microarchitectural deterioration of bone tissue and impaired bone strength, thereby leading to enhanced risk of bone fragility. In this study, we aimed to identify novel genes for susceptibility to osteoporosis and/or bone density. Materials and Methods: To identify differentially expressed genes (DEGs) between control and osteoporosis-induced cells, annealing control primer-based differential display reverse-transcription polymerase chain reaction (RT-PCR) was carried out in pre-osteoblast MC3T3-E1 cells. Expression levels of the identified DEGs were evaluated by quantitative RT-PCR. Association studies for the quantitative bone density analysis and osteoporosis case-control analysis of single nucleotide polymorphism (SNPs) were performed in Korean women (3,570 subjects) from the Korean Association REsource (KARE) study cohort. Results: Comparison analysis of expression levels of the identified DEGs by quantitative RT-PCR found seven genes, Anxa6, Col5a1, Col6a2, Eno1, Myof, Nfib, and Scara5, that showed significantly different expression between the dexamethason-treated and untreated MC3T3-E1 cells and between the ovariectomized osteoporosis-induced mice and sham mice. Association studies revealed that there was a significant association between the SNPs in the five genes, ANXA6, COL5A1, ENO1, MYOF, and SCARA5, and bone density and/or osteoporosis. Conclusion: Using a whole-genome comparative expression analysis, gene expression evaluation analysis, and association analysis, we found five genes that were significantly associated with bone density and/or osteoporosis. Notably, the association P-values of the SNPs in the ANXA6 and COL5A1 genes were below the Bonferroni-corrected significance level.

Prenatal diagnosis of an unbalanced translocation between chromosome Y and chromosome 15 in a female fetus

  • Lee, Dongsook;Park, Heeju;Kwak, Sanha;Lee, Soomin;Go, Sanghee;Park, Sohyun;Jo, Sukyung;Kim, Kichul;Lee, Seunggwan;Hwang, Doyeong
    • Journal of Genetic Medicine
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    • v.13 no.2
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    • pp.95-98
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    • 2016
  • We report the prenatal diagnosis of an unbalanced translocation between chromosome Y and chromosome 15 in a female fetus. Cytogenetic analysis of parental chromosomes revealed that the mother had a normal 46,XX karyotype, whereas the father exhibited a 46,XY,der(15)t(Y;15) karyotype. We performed cytogenetic analysis of the father's family as a result of the father and confirmed the same karyotype in his mother and brother. Fluorescence in situ hybridization and quantitative fluorescent-polymerase chain reaction analysis identified the breakpoint and demonstrated the absence of the SRY gene in female members. Thus, the proband inherited this translocation from the father and grandmother. This makes the prediction of the fetal phenotype possible through assessing the grandmother. Therefore, we suggest that conventional cytogenetic and molecular cytogenetic methods, in combination with family history, provide informative results for prenatal diagnosis and prenatal genetic counseling.

Mapping of Quantitative Trait Loci on Porcine Chromosome 7 Using Combined Data Analysis

  • Zuo, B.;Xiong, Y.Z.;Su, Y.H.;Deng, C.Y.;Lei, M.G.;Zheng, R.;Jiang, S.W.;Li, F.E.
    • Asian-Australasian Journal of Animal Sciences
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    • v.17 no.10
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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.

Biochemical Performance and Quantitative Assessment of F1 Hybrid of Two Ecoraces of Tropical Tasar Silkworm Antheraea Mylitta Drury (Lepidoptera: Saturniidae)

  • Lokesh, Gangadharaiah;Tirkey, Sushma Rani;Srivastava, Ashok Kumar;Kar, Prasant Kumar;Sinha, Manoj Kumar
    • International Journal of Industrial Entomology
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    • v.26 no.2
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    • pp.67-73
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    • 2013
  • Antheraea mylitta Drury is basically a crossbreeding species, as such it seems to be potentially a good material for the exploitation of heterosis. In the present study F1 hybrid of wild ecorace Laria (L) and semi-domestic Daba (D) was raised and evaluated for various quantitative traits and biochemical parameters during larval stage. Improved fecundity ($+18{\pm}1.8%$ and higher egg hatching rate ($+10.96{\pm}1.3%$) was recorded in the F1hybrid ($L{\times}D$). Biochemical parameters studied in the hemolymph, midgut and fatbody of the larva showed significantly higher (P<0.05) total proteins and carbohydrate concentration besides digestive enzyme activity. Correspondingly SDS-PAGE revealed more number of protein bands in the hemolymph sample of F1s, ranging between 29 kDa to 66 kDa compared to parental lines. The present study demonstrates the positive heterosis effect in the F1 hybrid of Laria ${\times}$ Daba. Biochemical analysis indicates that, there is possibilities of exploitation of hybrids with specific parents targeted for desirable commercial traits (silk yield and fecundity). Moreover, most of these biochemical parameters can be used as markers to analyze the genetic improvement in the tasar silkworms.

Plasma Post-operative miR-21 Expression in the Prognosis of Gastric Cancers

  • Ma, Guo-Jian;Gu, Rong-Min;Zhu, Ming;Wen, Xu;Li, Jin-Tian;Zhang, Yuan-Ying;Zhang, Xiao-Mei;Chen, Sen-Qing
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.12
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    • pp.7551-7554
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    • 2013
  • Tumor-associated microRNAs have been detected in serum or plasma, but whether plasma microRNA-21 (miR-21) could be a potential circulating biomarker for gastric cancer (GC) prognosis in Chinese is still uncertain. Real-time quantitative reverse transcription PCR (qRT-PCR) was employed in this study to compare the relative expression of miR-21 between pre-operative and post-operative paired plasmas from 42 patients with primary GCs. The results showed that the expression levels of miR-21 in the post-operative plasmas were significantly reduced by an average of 18.2 times in all patients when compared to the pre-operative plasmas, and by 22.1 times in the subgroup of patients without family history, while only 1.76 times in the subgroup of patients with a family history. With respect of clinicopathological characteristics, the plasma miR-21 expression was highly associated with differentiation degree and lymph node metastasis rate. The results suggested plasma miR-21 could be a novel potential biomarker for GC prognosis and evaluation of surgery outcomes, especially in patients without a family history.

Relationship between Differential Expression of Estrogen Receptor and Follicle Stimulating Hormone Receptor Genes in Ovary and Heterosis of Egg Number Traits in Chickens

  • Wang, Hui;Sun, Dongxiao;Yu, Ying;Wang, Dong;Zhang, Yi;Zhang, Yuan
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.3
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    • pp.325-330
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    • 2008
  • In order to understand the molecular mechanism of heterosis of reproduction traits in chickens, we used the quantitative real-time reverse transcriptional polymerase chain reaction (Quantitative real-time RT-PCR) technique to investigate the differential expression of estrogen receptor (ESR) and follicle stimulating hormone receptor (FSHR) genes in 32-week-old ovaries of inbred chickens and their hybrid offspring in $4{\times}4$ diallel crosses, which involved White Plymouth Rock (E), CAU Brown (D), Silkies (C) and White Leghorn (A). We found that there were significant differences in mRNA expression of ESR and FSHR genes not only between hybrids and their parental lines (p<0.01), but also among different crosses (p<0.01). Furthermore, positive correlations between differential expression of both ESR and FHSR in hybrids and heterosis percentages of 32-week-old and 42-week-old egg number traits were significant at p<0.05. Our results suggested that differential expression of ESR and FSHR genes in the ovaries of inbred chickens and their hybrids could play roles in the formation of heterosis of egg number traits to some extent.

Techniques for Evaluation of LAMP Amplicons and their Applications in Molecular Biology

  • Esmatabadi, Mohammad javad Dehghan;Bozorgmehr, Ali;zadeh, Hesam Motaleb;Bodaghabadi, Narges;Farhangi, Baharak;Babashah, Sadegh;Sadeghizadeh, Majid
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.17
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    • pp.7409-7414
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    • 2015
  • Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.