• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.454-462
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• 2018

Yield and grade are the key factors that affect production value of peanut. The objective of this study was to identify QTLs for pod yield, hundred-seed weight, and total sound mature kernel (TSMK). A total of 90 recombinant inbred lines, derived from Tamrun OL07 and a breeding line Tx964117, were used as a mapping population and planted in Brownfield and Stephenville, Texas. A genetic map was developed using 1,211 SNP markers based on double digest restriction-site associated DNA sequencing (ddRAD-seq). A total of 10 QTLs were identified above the permutation threshold, three for yield, three for hundred-seed weight and four for TSMK, with LOD score values of 3.7 - 6.9 and phenotypic variance explained of 12.2% - 35.9%. Among those, there were several QTLs that were detected in more than one field experiment. The commonly detected QTLs in this study may be used as potential targets for future breeding program to incorporate yield and grade related traits through molecular breeding.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.223-223
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• 2022

Saengcheonggukjang, known as Natto in Japan, is a Korean fermented soybean food that has various bioactive compounds for antioxidant and antidiabetic activity. The development of soybean (Glycine max L.) cultivars for saengcheonggukjang production relies on the selection of seed traits that influence the quality and sensory properties. One of the important traits for cultivars is seed characteristics such as seed hardness and size. In order to select the lines for breeding good quality saengcheonggukjang varieties, several simple sequence repeat (SSR) markers and quantitative trait loci (QTLs) related to seed quality of Korean cultivars, Pungsannamulkong, Socheongja, Pungwon, Heawon, and Hoseo, were analyzed. Based on the many studies to detect stable QTLs for seed traits, we tested several QTLs related to seed size and water absorbability using SSR markers on Korean cultivars. The results showed that two regions for water absorbability of Pungsannamulkong and one region for seed size traits of Haewon and Hoseo were identified in this study. These results could have applications to soybean breeding for seed size and hardness and it is necessary to narrow it down through further study.

• 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 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.3
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• pp.172-181
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• 2020

Koshihikari has been one of the most popular rice cultivars with good eating quality since the 1960s despite its susceptibility to blast disease and lodging. To map the genes controlling blast resistance and to develop promising blast-resistant breeding lines inheriting Koshihikari's high eating quality, a recombinant inbred line (RIL) population was developed from a cross between Koshihikari and a blast resistance donor with early maturity, Baegilmi. A total of 394 Koshihikari × Baegilmi RILs (KBRIL), and the two parents, were evaluated for blast resistance and major agronomic traits including heading date, culm length, panicle length, and tiller number. A linkage map encompassing 1,272.7 cM was constructed from a subset of the KBRIL (n = 142) using 130 single nucleotide polymorphisms. Two quantitative trait loci (QTL) for blast resistance, qBL1.1 harboring Pish/Pi35 and qBL2.1 harboring Pib, were mapped onto chromosomes 1 and 2, respectively. qBL1.1 was detected in both of the experimental sites, Namwon and Jeonju, while qBL2.1 was only detected in Namwon. qBL1.1 and qBL2.1 did not affect agronomic traits, including heading date, culm length, panicle length, and tiller number. From the 394 KBRILs, lines that were phenotypically similar to Koshihikari were selected according to heading date and culm length and were further divided into the following two groups based on blast resistance: Koshishikari-type blast resistant lines (KR, n = 15) and Koshishikari-type blast susceptible lines (KS, n = 15). Although no significant differences were observed in the major agronomic traits between the two groups, the KR group produced a greater mean head rice ratio than the KS group. The present study provides useful materials for developing blast-resistant cultivars that inherit both Koshihikari's high eating quality and Baegilmi's blast resistance.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1555-1561
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• 2016

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [$L^*$], redness [$a^*$], and yellowness [$b^*$]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects $b^*$ value (logarithm of odds [LOD] = 47.5, $p=1.60{\times}10^{-49}$) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences $a^*$ value (LOD = 14.2, $p=6.14{\times}10^{-16}$). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and $a^*$ ($P_{MGA}=1.69{\times}10^{-28}$; $P_{QTDT}=2.40{\times}10^{-25}$). The strongest associations were between BCDO2 g.9367 A>C and $b^*$ ($P_{MGA}=3.56{\times}10^{-66}$; $P_{QTDT}=1.68{\times}10^{-65}$). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.4
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• pp.480-488
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• 2018

Objective: Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. Methods: We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. Results: After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. Conclusion: This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.4
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• pp.413-419
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• 2011

This study was conducted to determine the physicochemical properties of a giant embryo rice 'P47JB-4-B-5-B' derived from the cross between 'P47', a mutant of 'Hwayoung' induced by T-DNA insertion, and 'Junam'. The grain appearance and chemical components of the embryo were analyzed and compared with a donor cultivar, 'Hwayoung'. The proportion of embryo weight to grain weight of 'P47 JB-4-B-5-B' was 2.2 times heavier (6.7%) than that (3.1%) of 'Hwayoung'. Total free amino acid content (75.81 mg/100 g) of 'P47JB-4-B-5-B' was 2.1 times higher than that of 'Hwayoung'. The GABA content in brown rice was 14.06 mg/100 g in 'P47JB-4-B-5-B' and 6.8 mg/100 g in 'Hwayoung'. Especially, the GABA content in brown rice of 'P47JB-4-B-5-B' remarkably increased (about 33 times from 1.48 mg to 44.81 mg/100 g) 2 days after germination. Continuous frequency distributions and transgressive segregation in embryo length and width were observed in the $F_2$ population of the cross between 'P47' and 'Cheongcheong', indicating that the giant embryo was controlled by quantitative trait loci. However, embryo length and width demonstrated high broad sense heritability, implying that giant embryonic traits could be selected in earlier generations in comparison with other quantitative traits.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.235-235
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• 2022

Genome selection is a promising tool for plant and animal breeding, which uses genome-wide molecular marker data to capture large and small effect quantitative trait loci and predict the genetic value of selection candidates. Genomic selection has been shown previously to have higher prediction accuracies than conventional marker-assisted selection (MAS) for quantitative traits. In this study, the prediction accuracy of 10 agricultural traits in the wheat core group with 567 points was compared. We used a cross-validation approach to train and validate prediction accuracy to evaluate the effects of training population size and training model.As for the prediction accuracy according to the model, the prediction accuracy of 0.4 or more was evaluated except for the SVN model among the 6 models (GBLUP, LASSO, BayseA, RKHS, SVN, RF) used in most all traits. For traits such as days to heading and days to maturity, the prediction accuracy was very high, over 0.8. As for the prediction accuracy according to the training group, the prediction accuracy increased as the number of training groups increased in all traits. It was confirmed that the prediction accuracy was different in the training population according to the genetic composition regardless of the number. All training models were verified through 5-fold cross-validation. To verify the prediction ability of the training population of the wheat core collection, we compared the actual phenotype and genomic estimated breeding value using 35 breeding population. In fact, out of 10 individuals with the fastest days to heading, 5 individuals were selected through genomic selection, and 6 individuals were selected through genomic selection out of the 10 individuals with the slowest days to heading. Therefore, we confirmed the possibility of selecting individuals according to traits with only the genotype for a shorter period of time through genomic selection.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.4
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• pp.411-418
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• 2023

Genome wide association studies (GWAS) identify genetic loci associated with quantitative traits in genomic selection. Although several studies have compared performance of various algorithms, no study compares them in olive flounder Paralichthys olivaceus. This study compared the GWAS results of four mixed linear model (MLM) algorithms and one Fixed and random model Circulating Probability Unification (FarmCPU) algorithm in olive flounder. Considering gender and genetic association matrices as fixed and random effects, the MLM had stable performance without inflation for λ_GC (genomic inflation factor) of -log₁₀P. The FarmCPU algorithm had some appropriate λ_GC of -log₁₀P, and an upward tail was identified in quantile-quantile plots. Therefore, the models were suitable for detecting genetic variants associated with olive flounder growth traits. Moreover, significant genotypes appeared several times at chromosome 22, around which quantitative trait loci are expected to exist. Finally, in both models, some of the most genetic variants were found in genes related to growth traits, confirming their reliability. These results will be helpful when applied to the genomic selection of olive flounder growth traits in the future.