• Asian-Australasian Journal of Animal Sciences
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• v.19 no.12
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• pp.1691-1695
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• 2006

The identification method that inflects real time ultrasound (RUT) and the potential application of marker assisted selection (MAS) for improvement of a cow population of Hanwoo (Korean Native cattle) was studied. The averages of RUT longissimus muscle area, RUT fat thickness, and RUT marbling score scanned at the 13th rib were 55.78 $cm^2$, 3.70 mm and 3.83 scores, respectively. We investigated the effects of the two SNPs (Kpn2 I and Msp I) in the leptin gene on carcass traits for Hanwoo cows by using ultrasound measurements. Genotype CC of the Kpn2 I had a significantly higher effect on back fat thickness (4.23 mm) and longissimus muscle area (57.57 $cm^2$) than genotype TT (3.14 mm, 53.93 $cm^2$, respectively, p<0.05). Genotype AA of the Msp I had a significantly higher effect only on marbling score (5.37) than genotype AB (3.57, p<0.05) and BB (3.37, p<0.05). Significant effects of SNPs in the leptin gene were found for the ultrasound measures of body composition in live cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.4
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• pp.458-462
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• 2005

The study was aimed at detecting polymorphism of the fifth intron in lipoprotein lipase (LPL) gene and analyzing association between the polymorphism and productive traits. A pair of primers was designed for amplifying the fifth intron. Sequence analysis indicated that a G1171C substitution existed in Large White breed. The mutation was detected by PCR-AfaI-RFLP. Polymorphism analysis in a pig resource family showed that there existed significant effects on carcass and meat quality traits. Thoraxwaist fat thickness of BB genotype was significantly higher (14.2%, p<0.05) than that of AA on carcass traits, while BB genotype was significantly lower (3.6% p<0.01, 4.1% p<0.01; 2.3% p<0.01, 1.9% p<0.01; 1.8% p<0.01, 1.4% p<0.05) than AA and AB genotype in pH of m. Longissimus Dorsi (LD), m. Biceps Femoris (BF), m. Semipinali Capitis (SC). The allelic frequencies were also significantly different between indigenous Chinese breeds and exotic breeds. Data analyzed revealed that the mutation locus affected production traits mostly by additive effects. Based on these results, it is necessary to do more studies on LPL gene before making the LPL locus into the application of marker-assisted selection (MAS) programs.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.566-574
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• 2015

Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.474-481
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• 2009

The purpose of this study was to identify the quantitative trait loci (QTL) associated with gel consistency (GC), and to evaluate the relationships between GC and physico-chemical properties related to eating quality in rice. A total of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong' and 26 varieties were used for this study. The 120 DH lines were divided into four groups, soft (61~100 mm), medium (41~60 mm), hard (26~40 mm) and whole population, according to the gel length. A negative correlation between GC and amylose content was observed only in the soft group. The GC negatively correlated with lipid content in the medium, and the whole population, but positively correlated with lipid content in the soft group. The positive correlation between GC and protein content was observed in the soft group, while negative correlations were observed in the medium group and the whole population. Two significant QTLs regarding GC were detected on chromosomes 4 and 11. They collectively explained 23% of phenotypic variation with LOD score of 3.1 and 2.9, respectively. The DNA markers of S4026 and RM287 were tightly linked to GC in the DH population and 26 varieties, respectively.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.267-267
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• 2022

Glutinous rice is a key grain quality trait occupying an important part during rice processing in most rice growing areas. Amylose content (AC) of rice determine eating quality which is one of the major traits in rice breeding program. In this study, a gene pyramiding approach was used to introduce two dull genes, responsible for low amylose contents, for glutinous rice breeding using marker assisted selection (MAS). Two dull genes were located on chromosome 6 (wx-mq, AC: 12.7 %) and chromosome 10 (du1, AC: 10.3%), respectively. To test whether these two dull genes have an epistatic interaction, we developed an F₂ population by crossing two nearly isogenic lines(NILs) harboring wx-mq and du1. Gene based marker and KASP marker were used to select NILs(NIL-nor, NIL-wxmq, NIL-du1, and NIL-wxmq/du1) from the F2 population. A two-way ANOVA revealed an epistatic interaction between the two genes in the F2 population. The mean of Amylose contents for NIL-nor, NIL-wxwq, NIL-(du1, and NIL-wxmq/du1 were 17.3%, 12.5%, 9.7%, and 7.2%, respectively. This interaction was confirmed by an analysis of NILs indicating that both genes are involved in the same genetic mechanism controlling amylose contents. This result will be useful for rice breeding related to amylose content.

• Journal of Animal Science and Technology
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• v.54 no.1
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• pp.1-8
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• 2012

This study aimed to investigate the single nucleotide polymorphisms (SNPs) of the porcine MC4R gene and validate the effect of the MC4R genotype for marker assisted selection (MAS). Six amplicons were produced to analyze the entire base sequences of the porcine MC4R gene and six SNPs were detected (c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, c.892A>G-Asp298Asn, and c.*430A>T). Linkage disequilibrium (LD) of the six SNPs was analyzed by performing haploid analysis. There was a perfect linkage disequilibrium in c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, and c.*430A>T. Only the c.892A>G (Asp298Asn) SNP showed a very low LD with an $r^2$ value of 0.028 and the D' value of 0.348. As a result, the two SNPs-c.707A>G (Arg236His) and c.892A>G (Asp298Asn)-were selected to extract the genotype frequencies from the 5 pig breeds by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotype analysis method. The SNP frequency of c.707A>G (Arg236His) indicated the presence of the A (His) allele only in Yorkshire, while the G allele was fixed in the KNP, Landrace, Berkshire, and Duroc. Association analysis was carried out in 484 pigs with the c.707A>G (Arg236His) SNP and the meat quality traits of four different pig cross populations: a significant association was noted in crude fat, sirloin moisture, meat color, and the degree of red and yellow coloration. The frequency of the c.892A>G(Asp298Asn) SNP genotype varied among the breeds; while Duroc showed the highest frequency of the A (Asn) allele, KNP showed the highest frequency of the G (Asp) allele. Association analysis was carried out in 1126 pigs with the c.892A>G (Asp298Asn) SNP and the meat quality traits of four pig populations: a highly significant linkage was noted in the back-fat thickness (P<0.002). It was found that the back-fat thickness was higher in individuals with the AA genotype than in those with the AG or GG genotype. Thus, in this study, we verified that the c.892A>G (Asp298Asn) SNP in the pig MC4R gene has a sufficient effect as a gene marker for MAS in Korean pork industry.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.577-584
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• 2007

Adipocyte-specific secretory factor(ADSF)/resistin, an hormone, is a small cysteine-rich protein secreted from adipose tissue and ADSF/resistin has been implicated in modulating adipogenesis in human and rodents. Although the exact role of ADSF/resistin in bovine has not been identified, it may have directly or indirectly involved in adipocyte differentiation. The objective of this study was to investigate its DNA polymorphism associated with carcass traits in Korean Native Cattle(Hanwoo). To investigate DNA polymorphism in Hanwoo ADSF/resistin gene, blood samples were taken from 295 Hanwoo steers belonging to progeny testing at Hanwoo Improvement Center in Korea. Seven single nucleotide polymorphisms(SNPs) were found in intron regions but not in any other regions including promoter (1.7kb) and 4 exons. The highest frequency among SNPs was C186A(0.16/0.84) following G964A (0.156/0.884). The significant correlation(P<0.05) between the SNPs and economic traits was found on 764Ains associated with marbling but not from any other SNPs determined.  A computer simulation was also conducted to assess the efficiency of marker assisted selection(MAS) versus the conventional breeding scheme.  Results revealed that MAS was more efficient as a breeding tool compared to the conventional. In conclusion, ADSF/Resistin gene is one of candidate genes to evaluate the quality, especially marbling score, in Hanwoo.

• Korean Journal of Breeding Science
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• v.51 no.3
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• pp.190-200
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• 2019

It is reported that the absence of lipoxygenase-3 (LOX-3) may contribute to a reduction in stale flavor after the storage of rice. To improve the quality of stored rice of the Korean japonica rice cultivar, we conducted a breeding program to develop near-isogenic rice without LOX-3 in the genetic background of Saenuri, a mega variety of Korea. In the first step of the breeding program, we used a donor parent of LOX-3 null, Daw Dam, and a recurrent japonica parent, Sindongjin, to develop HR27873-AC12 by backcross (BC₁), color test for introgression of lox-3, and anther culture for rapid fixation. In the second step, we used the donor parent, HR27873-AC12, and the recurrent parent, Saenuri, to develop HR28896-31-3-1-1 by backcross (BC₁), marker-assisted selection (MAS) for lox-3, and phenotypic selection (PS) for agronomic traits. Finally, in the third step, we developed HR30960-186-2-1-2-1 (Jeonju624), derived from a cross between Saenuri and HR28896-31-3-1-1, by MAS for lox-3 and PS with high selection pressure for agronomic characteristics. Jeonju624 was confirmed with the introgression of lox-3 by molecular marker. Jeonju624 was a mid-late maturing rice with similar agronomic characteristics to Saenuri, lodging tolerance with short culm, erect plant architecture, and resistance to bacterial blight and rice stripe virus. The yield components of Jeonju624 were mostly similar to Saenuri, except for the 1,000-grain weight of brown rice. The appearance of the grain of Jeonju624 was better than that of Saenuri, and the characteristics of cooked rice were similar to those of Saenuri. In the genetic background analysis using 406 KASP (Kompetitive Allele-Specific PCR) markers, Jeonju624 was confirmed to be the near-isogenic line (NIL) of Saenuri with a 95.8% recovery rate. Jeonju624 is the NIL of Saenuri without LOX-3, and overcomes the linkage drag of Daw Dam with similar agronomic characteristics and genetic background to Saenuri. Jeonju624 can be utilized as a practical cultivar to improve the quality of stored rice, breeding material for the introgression of lox-3, and genetic material to elucidate the effect of introgressed genes.

• Korean Journal of Breeding Science
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• v.51 no.4
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• pp.448-453
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• 2019

'Haedamssal' is an early maturing and rice stripe virus disease-resistant cultivar adaptable for early-transplanting cultivation that was developed by the rice breeding team of the Department of Southern Crop, NICS, RDA, in 2014. This cultivar was derived from the cross YR25869 (YR21247-B-B-B-49-1/Sasanishiki BL4//Koshihikari) and YR25868 (Unkwang//YR21247-B-B-B-49-1/Sasanishiki BL4) made in the 2005/2006 winter season and was advanced to the F₅ generation by a bulk breeding method using rapid generation advance. To incorporate rice stripe virus resistance, marker-assisted selection on the RSV gene was conducted in 3-way and 6-way cross F₁ generation using the tightly linked marker RM6897. From testing in the replicated yield trial in 2011, a promising line YR26258-B-B-B-33-3 was selected and it was designated as 'Milyang276'. A local adaptability test of 'Milyang276' was performed at three locations from 2012 to 2014 and it was named as 'Haedamssal', which was a good eating quality variety. The culm length was 67 cm in yield trials, which was 4 cm shorter than 'Jopyeong'. The number of spikelets per panicle was lower than 'Jopyeong', whereas the number of tillers per hill was higher. This variety was resistant to RSV disease, bacterial blight, and leaf blast disease. The milled rice yield of 'Haedamssal' was 5.48 MT per ha at the early transplanting in the local adaptability test. 'Haedamssal' is well adapted to early transplanting cultivation in the southern plain area (Registration No. 6811).

• Journal of Animal Science and Technology
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• v.52 no.1
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• pp.9-16
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• 2010

A previous study has shown that the g.17924G>A polymorphism of fatty acid synthase (FASN) is associated with unsaturated fatty acid composition in the Hanwoo beef, hence this study was conducted to evaluate the effect of single nucleotide polymorphisms (SNPs) within FASN gene on the selection phenotypes of Hanwoo breeding stock. A total of 925 progeny test steers were used to genotype g.11280G>A, g.13125T>C, and g.17924G>A polymorphisms and significant associations were found among g.11280G>A, g.17924G>A, and carcass traits, such as carcass weight, backfat thickness, and beef quantity index. No significant association was found between g.13125T>C and carcass traits. Although the degree of linkage disequilibrium (LD) was not strong among g.11280G>A, g.13125T>C, and g.17924G>A in the LD analysis, four major haplotype classes were formed with the genotypic information within the FASN gene; the frequencies of the halpotypeswere -GCG-[0.378], -ATG-[0.301], -GTA-[0.191], and -ACG-[0.063], respectively. Phenotypic association was performed among these haploptypes, and the haplotype 2 (-ATG-)was significantly associated with higher carcass weight when compared to the other haplotypes, i.e. haplotype 1 (-GCG-) and haplotype 3 (-GTA-). A copy number of the FASN haplotype 3 (-GTA-) had also a significant association with carcass weight of subjects. In conclusion, it was observed that two polymorphisms (g.11280G>A and g.17924G>A) and their haplotypes within the FASN gene are consistently associated with carcass traits. Therefore, it is desirable to use the FASN polymorphisms for pre-selection program as genetic marker with improved carcass yield and beef quality of the Hanwoo sire at the Hanwoo Improvement Center as well as for commercial Hanwoo producers, the FASN genotypic information can be used for a part of selecting Hanwoo dam for superior calf production.