• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.280-280
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• 2022

Tiller angle, defined as the angle between the main stem and its side tillers, is one of the main target traits selected inbreeding to achieve the ideal plant type and increase rice yield. Therefore, the discovery and identification of tiller angle-related genes can provide architecture and yield. In the present work, using QTL analysis hence a total of 8 quantitative trait loci (QTLs) were detected based on the phenotype data of tiller angle and tiller crown width in two years. Among them, four QTLs (qTA9, qCW9, qTA9-1, qCW9-1) were overlapped at marker interval RM6235-RM24288 on chromosome 9 with a large effect value regarded as stable major QTL. Twenty tiller angle-related genes were selected from the target region and the relative gene expression levels were checked in five compact type lines, five spreading type lines, and their parental lines. Finally, OsSA URq9 which belongs auxin-responsive SMALL AUXIN UP RNA (SAUR) protein family was selected as a target gene. Overall, this work will help broaden our understanding of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.

• Journal of Life Science
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• v.30 no.10
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• pp.844-850
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• 2020

Disaster-related extreme weather is rapidly increasing due to climate change. In Korea, typhoons accompanied by rainfall usually approach in August and September, causing great damage. The purpose of this study is to find a gene that regulates the heading date of rice in order to avoid loss of harvest from climate change and typhoons. Cheongcheong/Nagdong doubled haploid (CNDH) was used as the plant material to investigate the location of heading-related genes using QTL and sequence analysis by cloning the gene. In the distribution chart, the heading dates, culm lengths, panicle lengths, numbers of panicles, and 1,000-grain weights all have normal distributions. QTL analysis found 13 contigs on chromosome 8. One QTL, named qHd8, was detected on chromosome 8. The range at qHd8 was approximately 7.7 cM, with RM72 and RM404 markers near the peak. There were 13 contigs and 1 ORF. Protein sequence analysis showed that rice was similar to Os08g0341700, AtSFH13, and AtSFH7 proteins. Os08g0341700, which is involved in signal transduction, is similar to phosphatidylinositol transfer-like protein II, and complete information is not available, but it is believed to play a role in the phosphatidylinositol-specific signaling pathway related to Sec14P.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.1
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• pp.1-17
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• 2019

A quantitative trait loci (QTL) analysis of traits related to heading and yield was performed develop rice cultivars that are both early maturing and panicle weight type varieties. Our analysis included 120 strains of the Cheongcheong Nagdong doubled haploid (CNDH) variety. An observational growth experiment was conducted to identify genetic agronomic traits of CNDH. Heading date, ten plant weight, moisture, thousand grain weight, and yield had a normal distribution based on the frequency distribution table of the observational growth data. The QTL analysis found one heading-related and nine yield-related QTLs. The LOD of 2.85 was the largest in QTLs for heading date (QHD), 5.39 in QTLs for ten plant weight (QTPW), 3.92 in QTLs for moisture (QM), 4.80 in QTLs for thousand grain weight (QTGW), and 3.7 in QTLs for yield (QY). Genomic analysis detected 58 candidate genes on chromosome 2, 3, 7, 8, and 10. Among those, we found Rcd1 protein and OsERF3 gene in QM, MtN3 and zinc finger protein genes in QTGW, and OsNAC3 protein gene in QY. If further analysis reveals the presence of genes related to water content, thousand grain weight or yield in the CNDH stains, we can develop a selection of varieties that will be capable of coping with climate change and will contribute to global food problems.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.9
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• pp.1184-1191
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• 2011

We attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the $F_2$ offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model. Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n = 16) and YS (n = 8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic information contents (PIC) values of >0.300 in the $F_2$ groups (n = 252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level. The QTL for crude protein were detected on SSC2, SSC3, SSC6, SSC9 and SSC12; for intramuscular fat and marbling on SSC2, SSC8, SSC12, SSC14 and SSC18; meat color measurements on SSC1, SSC3, SSC4, SSC5, SSC6, SSC10, SSC11, SSC12, SSC16 and SSC18; water content related measurements in pork were detected on SSC4, SSC6, SSC7, SSC10, SSC12 and SSC14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC6, SSC12, SSC13 and SSC16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC12. Our results demonstrated that a QTL linkage map of the $F_2$ design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.

• Journal of Embryo Transfer
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• v.31 no.4
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• pp.313-318
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• 2016

The aim of this study was to identify quantitative trait loci (QTLs) influencing teat number traits in an $F_2$ intercross between Landrace and Korean native pigs (KNP). Three teat number traits (left;right;and total) were measured in 1105 $F_2$ progeny. All experimental animals were genotyped with 173 informative microsatellite markers located throughout the pig genome. We detect that seven chromosomes harbored QTLs for teat number traits: genome regions on SSC1;3;7;8;10;11;and 13. Six of fourteen identified QTL reached genome-wide significance. In SSC7;we identified a major QTL affecting total teat number that accounted for 5.6 % of the phenotypic variance;which was the highest test statistic (F-ratio = 61.1 under the additive model;nominal $P=1.3{\times}10^{-14}$) observed in this study. In this region;QTL for left and right teat number were also detected with genome-wide significance. With exception of the QTL in SSC10;the allele from KNP in all 6 identified QTLs was associated with decreased phenotypic values. In conclusion;our study identified both previously reported and novel QTL affecting teat number traits. These results can play an important role in determining the genetic structure underlying the variation of teat number in pigs.

• Plant Resources
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• v.3 no.3
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• pp.184-193
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• 2000

Soybean [Glycine max (L.) Merr.] seed weight is a important trait in cultivar development. Objective of this study was to identify and confirm quantitative trait loci (QTLs) for seed weight variation in the F2 and F2:3 generations. QTLs for seed weight were identified in F2 and F2:3 generations using interval mapping (MapMaker/QTL) and single-factor analysis of variance (ANOVA). In the F2 plant generation (i.e., F3 seed), three markers, OPL9a, OPM7a, and OPAC12 were significantly (P<0.01) associated with seed weight QTLs. In the F2:3 plant row generation (i.e., F4 seed), five markers, OPA9a, OPG19, OPL9b, OPP11, and Sat_085 were significantly (P<0.01) associated with seed weight QTLs. Two markers, OPL9a and OPL9b were significantly (P<0.05) associated with seed weight QTLs in both generations. Two QTLs on USDA soybean linkage group C1 and R were identified in both F2 and F2:3 generations using interval mapping. The linkage group C1 QTL explained 16% of the variation in seed weight in both generations, and the linkage group R QTL explained 39% and 41% of the variation for F2 and F2:3 generation, respectively. The linkage group C2 QTL identified in F2:3 generation explained 14.9% of variation. Linkage groups C1, C2 and R had previously been identified as harbouring seed size QTLs. The consistency of QTLs across generations and populations indicates that marker-assisted selection is possible in a soybean breeding program.

• Journal of Korean Society of Forest Science
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• v.95 no.4
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• pp.483-494
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• 2006

We conducted QTL mapping for 6-year growths of open-pollinated half-sib progenies from a selected clone 7-1037 in Pinus taeda. With an AFLP marker analysis on haploid DNA samples from the megagametophytes of the open-pollinated seeds, we constructed 20 framework maps spanning a total of 1,869 cM in total length and 18.5 cM in an average interval length between markers. Composite interval mapping reveals that one QTL explains 5.9% of the total phenotypic variation of height, and three QTLs account for 3.9~5.6% of the variation of diameter at breast height (DBH). There are no correlations between the QTLs. The genetic effects of the QTLs are 39.6 cm in height and 7.20~9.41 mm in DBH, respectively, The average effects of gene substitution of the markers closely linked with the QTLs are 44.3 cm in height and 8.38~11.81 m in DBH. Under an assumption that the within-family heritability for the growth traits of loblolly pine is less than 0.2, the QTLs account for 26.8% of the additive genetic variance of the progenies. In terms of relative selection efficiency, the individual selection based on QTL markers could be 5 times as high as phenotypic selection. The results in this study indicate that the QTL mapping method with open-pollinated half-sib family could be more practical and applicable to the conventional seed orchard-based selection work than other mapping methods with a single full-sib family, in particular from the viewpoint that it can provide crucial information for within-family individual selection such as breeding value.

• Communications for Statistical Applications and Methods
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• v.13 no.3
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• pp.525-535
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• 2006

We describe tests for detecting and locating quantitative traits loci (QTL) for traits in Hanwoo. Lod scores and a permutation test have been described. From results of a permutation test to detect QTL, we select major DNA markers of ILSTS098 microsatellite locus in Hanwoo chromosome 2 for further analysis. K-means clustering analysis applied to four traits and eight DNA markers in ILSTS098 resulted in three cluster groups. We conclude that the major DNA markers of BMS1167 microsatellite locus in Hanwoo chromosome 2 are markers 105bp, 113bp and 115bp. Finally, bootstrap testing method has been adapted to calculate confidence intervals and for finding major DNA Markers.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.148-148
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• 2017

Soybean is an important economical resource of protein and oil for human and animals. The genetic basis of seed protein and oil content has been separately characterized in soybean. However, the genetic relationship between seed protein and oil content remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation and linkage mapping to dissect the relationship between seed protein and oil content. A $F_{10:11}$ RIL population containing 222 lines, derived from the cross between two Korean soybean cultivars Seadanbaek as female and Neulchan as male parent, were used in this experiment. Soybean seed analyzed were harvested in three different experimental environments. A genetic linkage map was constructed with 180K SoyaSNP Chip and QTLs of both traits were analyzed using the software QTL IciMapping. QTL analyses for seed protein and oil content were conducted by composite interval mapping across a genome wide genetic map. This study detected four major QTL for oil content located in chromosome 10, 13, 15 and 16 that explained 13.2-19.8% of the phenotypic variation. In addition, 3 major QTL for protein content were detected in chromosome 10, 11 and 16 that explained 40.8~53.2% of the phenotypic variation. A major QTLs was found to be associated with both seed protein and oil content. A major QTL were mapped to soybean chromosomes 16, which were designated qHPO16. These loci have not been previously reported. Our results reveal a signi cant genetic relationship between seed protein and oil fi content traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved seed protein and oil content.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.939-948
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• 2003

The objective of this study was to identify the quantitative traits loci(QTL) for economically important traits such as growth, carcass and meat quality on pig chromosome 6. A three generation resource population was constructed from cross between Korean native boars and Landrace sows. A total of 240 F$_2$ animals were produced using intercross between 10 boars and 31 sows of F$_1$ animals. Phenotypic data including body weight at 3 weeks, backfat thickness, muscle pH, shear force and crude protein level were collected from F$_2$ animals. Animals including grandparents(F$_0$), parents(F$_1$) and offspring(F$_2$) were genotyped for 29 microsatellite markers and PCR-RFLP marker on chromosome 6. The linkage analysis was performed using CRI-MAP software version 2.4(Green et al., 1990) with FIXED option to obtain the map distances. The total length of SSC6 linkage map estimated in this study was 169.3cM. The average distance between adjacent markers was 6.05cM. For mapping of QTL, we used F$_2$ QTL Analysis Servlet of QTL express, a web-based QTL mapping tool(http://qtl.cap.ed.ac.uk). Five QTLs were detected at 5% chromosome-wide level for body weight of 3 weeks of age, shear force, meat pH at 24 hours after slaughtering, backfat thickness and crude protein level on SSC6.