• Journal of The Korean Society of Grassland and Forage Science
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• v.43 no.3
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• pp.168-176
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• 2023

Silicon (Si) has the potential to improve plant growth and stress tolerance. The study aimed to explore Si-involving plant responses and molecular characterization of different Si-responsive genes in alfalfa. In this study, the exogenous supplementation of Si enhanced plant growth, and biomass yield. Si-acquisition in alfalfa root and shoot was higher in Si-supplemented compared to silicon deficient (-Si) plants, implying Si-acquisition has beneficial on alfalfa plants. As a consequence, the quantum efficiency of photosystem II (Fv/Fm) was significantly increased in silicon-sufficient (+Si) plants. The quantitative gene expression analysis exhibited a significant upregulation of the Lsi1, Lsi2, Lsi3, NIP5;1, and NIP6;1 genes in alfalfa roots, while BOR1, BOR4, NIP2, and NIP3 showed no significant variation in their expression. The MEME results further noticed the association of four motifs related to the major intrinsic protein (MIP). The interaction analysis revealed that NIP5;1 and Lsi1 showed a shared gene network with NIP2, BOR1, and BOR4, and Lsi2, Lsi3 and NIP3-1, respectively. These results suggest that members of the major intrinsic proteins (MIPs) family especially Lsi1, Lsi2, Lsi3, NIP5;1, and NIP6;1 genes helped to pass water and other neutral solutes through the cell membrane and those played significant roles in Si uptake and transport in plants. Together, these insights might be useful for alfalfa breeding and genome editing approaches for alfalfa improvement.

• Journal of Animal Science and Technology
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• v.57 no.8
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• pp.28.1-28.7
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• 2015

Background: The physiologic characteristics of the cashmere trait and many of the differentially expressed genes relevant to hair cycling have been extensively studied, whereas genes involved in the prenatal development of hair follicles have been poorly investigated in cashmere goats. The aim of this study, therefore, was to quantify the time-course changes in the expressions of $TR{\alpha}$ and CRABPII genes in the fetal skin of Chinese cashmere goats at the multiple embryonic days (E70, E75, E80, E90, E100, E120 and E130) using real-time quantitative PCR (RT-qPCR). Results: RT-qPCR showed that $TR{\alpha}$ was expressed at E70 with relatively high level and then slightly decreased (E75, E80, and E90). The highest expression of $TR{\alpha}$ mRNA was revealed at E130 (P > 0.05). The expression pattern of CRABPII mRNA showed an 'up-down-up' trend, which revealed a significantly highest expression at E75 (P < 0.05) and was down-regulated during E80 to E120 (P < 0.05) and mildly increased at E130, subsequently. Conclusion: This study demonstrated that $TR{\alpha}$ and CRABPII genes expressed in different levels during prenatal development of cashmere. The present study will be helpful to provide the comprehensive understanding of $TR{\alpha}$ and CRABPII genes expressions during cashmere formation and lay the ground for further studies on their roles in regulation of cashmere growth in goats.

• Horticultural Science & Technology
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• v.35 no.3
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• pp.333-343
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• 2017

Bloomless cucumber fruits are commercially produced by grafting onto the pumpkin stocks (Cucurbita moschata) to restricted silicon ($SiO_2$) absorption. Inhibition of silicon absorption in bloomless stocks is conferred by a mutant allele of the CmLsi1 homologous to Lsi1 in rice. In this study, we characterized the Lsi1 homologs in pumpkin (C. moschata) and its cold-tolerant wild relative C. ficifolia ('Heukjong') in order to develop a DNA marker for selecting a bloomless trait and to establish the molecular basis for breeding bloomless stock cultivars of C. ficifolia. A Cleaved amplified polymorphic sequence (CAPS) marker (CM1-CAPS) was designed based on a non-sysnonymous single nucleotide polymorphism (SNP, C>T) of the CmLsi1 mutant-type allele, and its applicability for Marker-assisted selection (MAS) was confirmed by evaluating three bloom and five bloomless pumpkin stock cultivars. Quantitative RT-PCR of the CmLsi1 for these stock cultivers implied that expression level of the CmLsi1 gene does not appear to be associated with the bloom/bloomless trait and may differ depending on plant species and tissues. A full length cDNA of the Lsi1 homolog [named CfLsi1($B^+$)] of 'Heukjong' (C. ficifolia), was cloned and sequence comparison between CmLsi1($B^+$) and CfLsi1($B^+$) revealed that there exists total 24 SNPs, of which three were non-synonymous. Phylogenetic analysis of CfLsi1($B^+$) and Lsi1 homologs further revealed that CfLsi1($B^+$) is closesly related to Nodulin 26-like intrinsic proteins (NIPs) and most similar to CpNIP1 of C. pepo than C. moschata.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.8-19
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• 2017

Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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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.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1353-1362
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• 2016

Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.5
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• pp.638-642
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• 2017

Objective: This study aimed to validate the statistical evidence from the genome-wide association study (GWAS) as true-positive and to better understand the effects of the glycophorin C (GYPC) gene on serum hemoglobin traits. Methods: Our initial GWAS revealed the presence of two single nucleotide polymorphisms (SNPs) (ASGA0069038 and ALGA0084612) for the hemoglobin concentration trait (HGB) in the 2.48 Mb region of SSC15. From this target region, GYPC was selected as a promising gene that associated with serum HGB traits in pigs. SNPs within the GYPC gene were detected by sequencing. Thereafter, we performed association analysis of the variant with the serum hemoglobin level in three pig populations. Results: We identified one SNP (g.29625094 T>C) in exon 3 of the GYPC gene. Statistical analysis showed a significant association of the SNP with the serum hemoglobin level on day 20 (p<0.05). By quantitative real-time polymerase chain reaction, the GYPC gene was expressed in eight different tissues. Conclusion: These results might improve our understanding of GYPC function and provide evidence for its association with serum hemoglobin traits in the pig. These results also indicate that the GYPC gene might serve as a useful marker in pig breeding programs.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.4
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• pp.432-440
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• 2019

Global climate change exerts adverse effects on maize production. Among abiotic stresses, drought stress during the tasseling stage (VT) can increase anthesis-silking intervals (ASI) and decrease yield. We performed an evaluation of ASI and yield using a drought-sensitive line (Ki3) and a drought-tolerant line (Ki11) to analyze the correlation with ASI and yield. Moreover, the de novo data of Ki11 were analyzed to find putative novel transcripts related todrought stress in tropical maize. A total of 182 transcripts, with a log2 ratio >1.5, were found by comparing drought conditions to a control. The top 40 transcripts of high expression levels in the de novo analysis were selected and analyzed with PCR. Of the 40 transcripts, six novel transcripts were detected by quantitative real-time PCR (qRT-PCR) using seedling and VT stage samples. Five transcripts (transcripts_1, 12, 34, 35, and 40) were up-regulated in the Ki11 shoot at seedling stage, and transcripts_1, 12, and 40 were up-regulated at the re-watering stage after 12 h of drought stress. The transcripts_32 and 34 were up-regulated at the VT stage. Hence, transcript_34 possibly plays a significant role in drought tolerance during the seedling and VT stages. The transcript_32 was identified as chloramphenicol acetyltransferase (CAT) by Pfam domain analysis. The function of the other transcripts remained unknown. Further characterization of these novel transcripts in genetic regulation will be of great value for the improvement of maize production.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.274-283
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• 2020

Seed dormancy is an adaptive trait in which seeds do not germinate under unfavorable environmental conditions. Low dormancy seeds are easily germinated under optimal environmental conditions, and these characteristics greatly reduce the yield and quality of crops. In the present study, we compared the pre-harvest sprouting (PHS) rate of two cultivars, Joun and Jopyeong, using the Winkler scale after heading day and temperature of the test. The PHS rate increased as the Winkler scale after heading day increased from 700℃ to 1100℃ and the temperature of the test increased. In all conditions, the PHS rate of Jopyeong was higher than that of Joun. RNA-sequencing was used to analyze the cause of the high PHS rate. We analyzed the biological metabolic processes related to the abscisic acid (ABA) metabolite pathway using the KEGG mapper with selected differentially expressed genes in PHS seeds. We found that the expression of ABA biosynthesis genes (OsNCEDs) was down-regulated and that ABA catabolic genes (OsCYP707As) was up-regulated in PHS seeds. However, the quantitative real-time PCR results showed that Joun had a higher expression of OsNCEDs than that of Jopyeong, but OsCYP707As did not yield a significant result. Joun displayed higher ABA content than that of Jopyeong not only during ripeness time but also during PHS treatment. Taken together, we provided evidence that the ABA content remaining in the seed is important to the PHS rate, which is determined by the expression level of the ABA biosynthesis gene OsNCEDs.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.10
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• pp.1471-1477
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• 2017

Objective: Since athletic performance is a most importance trait in horses, most research focused on physiological and physical studies of horse athletic abilities. In contrast, the molecular analysis as well as the regulatory pathway studies remain insufficient for evaluation and prediction of horse athletic abilities. In our previous study, we identified AXL receptor tyrosine kinase (AXL) gene which was expressed as alternative spliced isoforms in skeletal muscle during exercise. In the present study, we validated two AXL alternative splicing transcripts (named as AXLa for long form and AXLb for short form) in equine skeletal muscle to gain insight(s) into the role of each alternative transcript during exercise. Methods: We validated two isoforms of AXL transcripts in horse tissues by reverse transcriptase polymerase chain reaction (RT-PCR), and then cloned the transcripts to confirm the alternative locus and its sequences. Additionally, we examined the expression patterns of AXLa and AXLb transcripts in horse tissues by quantitative RT-PCR (qRT-PCR). Results: Both of AXLa and AXLb transcripts were expressed in horse skeletal muscle and the expression levels were significantly increased after exercise. The sequencing analysis showed that there was an alternative splicing event at exon 11 between AXLa and AXLb transcripts. 3-dimentional (3D) prediction of the alternative protein structures revealed that the structural distance of the connective region between fibronectin type 3 (FN3) and immunoglobin (Ig) domain was different between two alternative isoforms. Conclusion: It is assumed that the expression patterns of AXLa and AXLb transcripts would be involved in regulation of exercise-induced stress in horse muscle possibly through an $NF-{\kappa}B$ signaling pathway. Further study is necessary to uncover biological function(s) and significance of the alternative splicing isoforms in race horse skeletal muscle.