Evaluation of a Fine-mapping Method Exploiting Linkage Disequilibrium in Livestock Populations: Simulation Study

Kim, JongJoo,Farnir, Frederic Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.12

A simulation study was conducted to evaluate a fine-mapping method exploiting population-wide linkage disequilibrium. Data were simulated according to the pedigree structure based on a large paternal half-sib family population with a total of 1,034 or 2,068 progeny. Twenty autosomes of 100 cM were generated with 5 cM or 1 cM marker intervals for all founder individuals in the pedigree, and marker alleles and a number of quantitative trait loci (QTL) explaining a total of 70% phenotypic variance were generated and randomly assigned across the whole chromosomes, assuming linkage equilibrium between the markers. The founder chromosomes were then descended through the pedigree to the current offspring generation, including recombinants that were generated by recombination between adjacent markers. Power to detect QTL was high for the QTL with at least moderate size, which was more pronounced with larger sample size and denser marker map. However, sample size contributed much more significantly to power to detect QTL than map density to the precise estimate of QTL position. No QTL was detected on the test chromosomes in which QTL was not assigned, which did not allow detection of false positive QTL. For the multiple QTL that were closely located, the estimates of the QTL positions were biased, except when the QTL were located on the right marker positions. Our fine mapping simulation results indicate that construction of dense maps and large sample size is needed to increase power to detect QTL and mapping precision for QTL position.

돼지 염색체 6번의 연관지도 및 양적형질 유전자좌위 탐색

이혜영,최봉환,김태헌,박응우,윤두학,이학교,전광주,정일정,홍기창 한국동물자원과학회 2003 한국축산학회지 Vol.45 No.6

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 ?, 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 Servelt 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 ? at 24 hours after slaughtering, backfat thickness and crude protein level on SSC6.

Time-related Mapping of Quantitative Trait Loci Controlling Dry Matter Accumulation and Partitioning in Rice

Shao Bo Li,Zhi Hong Zhang,Shao Qing Li,Yang Sheng Li,You Lin Zhu,Ying Guo Zhu 한국유전학회 2008 Genes & Genomics Vol.30 No.4

Grain yield is a result of dry matter accumulation and partitioning in rice (Oryza sativa L.). To characterize the genetic basis of dynamics of traits representing dry matter accumulation and partitioning as well as their relationships with each other, composite interval mapping of quantitative trait loci (QTL) was conducted based on time-related phenotypic data obtained from a population of 258 recombinant inbred lines (F12), which was derived from a cross between Lemont (japonica var.) and Teqing (indica var.). A total of twenty-three QTL were identified for leaf weight, stem weight and panicle weight at four measuring stages after heading. However, these three dynamic traits were observed to be controlled by different QTL (genes) at different growth stages. An extreme example was that at least three types of QTL (genes) might be involved in the development of panicle weight. Growth duration, which is closely related to dry matter accumulation and partitioning, was also identified to be significantly affected by four QTL. The close correlations among the studied four traits were explained to some extent by six co-located QTL. Nevertheless, it would be of great importance to distinguish the pleiotropic or linked effects of the co-located QTL. In addition, the chromosome regions or QTL identified in this study were compared with those previously reported for the same or related traits with the same RIL population.

Identification of a novel QTL for grain number per panicle employing NGS-based QTL-seq approach in rice (Oryza sativa L.)

Bommisetty Reddyyamini,Chakravartty Navajeet,Hariprasad K. R.,Rameshbabu P.,Sudhakar P.,Bodanapu Reddaiah,Naik Jeevula Bhukya,Reddy B. V. Bhaskar,Lekkala Sivrama Prasad,Gupta Saurabh,Tanti Bhaben,Lach 한국식물생명공학회 2023 Plant biotechnology reports Vol.17 No.2

The grain number is one of the highly complex and crucial traits determining the grain yield in rice. To identify grain number QTLs in rice, we employed the QTL-seq approach in the 297 F2 population derived from the cross between BPT5204 and NLR33892. In this investigation, five regions viz., qGN1, qGN3, qGN7, qGN9, and qGN12 on chromosomes 1,3,7,9, and 12, respectively, were identified as QTLs governing grain number per panicle in rice. To verify the QTLs identified in the present study, traditional QTL mapping was carried out using InDel markers and previously reported SSRs in the QTL region. From qGN12 QTL, RM6953 showed a significant association with the number of grains per panicle with a phenotypic variance of 24.58, 22.10, and 17.20% in F2, F2:3, and BC1F2 populations, respectively, at < 0.0001 P value, indicating major QTL. From genome resequencing data, a missense variance was observed in the exonic region of LOC_Os12g39330 gene controlling AP2 domain-containing protein which plays an important role in seed development in rice. Hence, this QTL can be a potential target for map-based cloning and marker-assisted transfer to enhance the grain number in rice.

Effects of quantitative trait loci determining testicular weight in DDD/Sgn inbred mice are strongly influenced by circulating testosterone levels

Jun-ichi Suto,Misaki Kojima 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.12

Objective: Testicular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice. Methods: Quantitative trait loci (QTL) mapping of testis weight was performed with or without considering the influence of plasma testosterone level in reciprocal F2 intercross populations between DDD and C57BL/6J (B6) mice, thereby assessing the influence of testosterone on the effect of testis weight QTL. Candidate genes for testis weight QTL were investigated by next-generation sequencing analysis. Results: Four significant QTL were identified on chromosomes 1, 8, 14, and 17. The DDD-derived allele was associated with increased testis weight. The F2 mice were then divided into two groups according to the plasma testosterone level (F2 mice with relatively “low” and “high” testosterone levels), and QTL scans were again performed. Although QTL on chromosome 1 was shared in both F2 mice, QTL on chromosomes 8 and 17 were identified specifically in F2 mice with relatively high testosterone levels. By whole-exome sequencing analysis, we identified one DDD-specific missense mutation Pro29Ser in alpha tubulin acetyltransferase 1 (Atat1). Conclusion: Most of the testis weight QTL expressed stronger phenotypic effect when they were placed on circumstance with high testosterone level. High testosterone influenced the QTL by enhancing the effect of DDD-derived allele and diminishing the effects of B6-derived allele. Since Pro29Ser was not identified in other inbred mouse strains, and since Pro29 in Atat1 has been strongly conserved among mammalian species, Atat1 is a plausible candidate for testis weight QTL on chromosome 17.

Potential of the Quantitative Trait Loci Mapping Using Crossbred Population

Yang, Shulin,Zhu, Zhengmao,Li, Kui Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.12

In the process of crossbreeding, the linkage disequilibria between the quantitative trait loci (QTL) and their linked markers were reduced gradually with increasing generations. To study the potential of QTL mapping using the crossbred population, we presented a mixed effect model that treated the mean allelic value of the different founder populations as the fixed effect and the allelic deviation from the population mean as random effect. It was assumed that there were fifty QTLs having effect on the trait variation, the population mean and variance were divided to each QTL in founder generation in our model. Only the additive effect was considered in this model for simulation. Six schemes (S1-S6) of crossbreeding were studied. The selection index was used to evaluate the synthetic breeding value of two traits of the individual in the scheme of S2, S4 and S6, and the individuals with high selection index were chosen as the parents of the next generation. Random selection was used in the scheme of S1, S3 and S5. In this study, we premised a QTL explained 40% of the genetic variance was located in a region of 20 cM by the linkage analysis previously. The log likelihood ratio (log LR) was calculated to determine the presence of a QTL at the particular chromosomal position in each of the generations from the fourth to twentieth. The profiles of log LR and the number of the highest log LR located in the region of 5, 10 and 20 cM were compared between different generations and schemes. The profiles and the correct number reduced gradually with the generations increasing in the schemes of S2, S4 and S6, but both of them increased in the schemes of S1, S3 and S5. From the results, we concluded that the crossbreeding population undergoing random selection was suitable for improving the resolution of QTL mapping. Even experiencing index selection, there was still enough variation existing within the crossbred population before the fourteenth generation that could be used to refine the location of QTL in the chromosome region.

테다소나무 7-1037 클론의 단일 반형매 풍매가계 6년생 생장에 대한 QTL mapping과 QTL 대립유전자 치환의 평균효과

김용율 ( Yong Yul Kim ),이봉춘 ( Bong Choon Lee ),( David M. O`Malley ) 한국산림과학회 2006 한국산림과학회지 Vol.95 No.4

Composite Interval Mapping에 의한 사시나무 전형매 차대의 2년생 생장 형질과 관련된 QTL(Quantitative Trait Loci)의 동정

김용률 ( Yong Yul Kim ),강범용 ( Bum Yong Kang ),최형순 ( Hyung Soon Choi ),홍용표 ( Yong Pyo Hong ),여진기 ( Jin Kie Yeo ),구영본 ( Yeong Bon Koo ) 한국산림과학회 2004 한국산림과학회지 Vol.93 No.3

We studied QTL(quantitative trait loci) influencing 2-year growths such as height increment, diameter at root collar, stem dry weight, root dry weight and total biomass of full-sib progenies between two selection clones, Odae 19 and Bonghyun 4 in Populus davidiana. Using 215 AFLP(amplified fragment length polymorphism) markers, we constructed 16 framework maps covering 545 cM with the average marker density of 12.8cM. CIM(composite interval mapping) showed that two Q_(Pd-Hti)(21.8 cM in map 8) and Q_(Pd-Root)(Pd-Root)(0.01 -4 cM in map 12), were predominantly associated with the traits. Q_(Pd-Hti) significantly accounted for 11.1 % of total phenotypic variation for height increment. Q_(Pd-Root), had a significant pleiotropic effect on diameter at root collar, root dry weight, primary root dry weight and total biomass dry weight explaining 11.6~12.3 % of their phenotypic variations. The two QTLs had no interaction between them, which indicates that they independently control the height increment and the other traits, respectively. Using the single marker analysis, we also identified two independent QTLs, named as QrGM59 and QrGM127, with relatively small effect on height increment, stem dry weight, fine root dry weight and total biomass dry weight. Q,.GM59 was significantly related with height increment explaining 5.3% of phenotypic variation and had no interaction with Q_(rGM59), Q_(rGM127) showed a weak interaction with Q_(Pd-Root) for stem dry weight and total biomass dry weight, and it accounted for 6.2% and 5.4% of the individual phenotypic variation, respectively. The dominant alleles at the four QTLs were inherited from the mother tree, clone Odae 19 which had already showed the best survival rate and good growth at poor planting site in the previous clone stability test. The results in this study indicate that the above- and below-ground growth of P. davidiana could be independently controlled by few genes, and that the QTL markers will be successfully used for selecting clones with good growth in both traits.

Mapping of the Porcine Calpastatin Gene and Association Study of Its Variance with Economic Traits in Pigs

Choi, B.H.,Lee, J.S.,Jang, G.W.,Lee, H.Y.,Lee, J.W.,Lee, K.T.,Chung, H.Y.,Park, H.S.,Oh, S.J.,Sun, S.S.,Myung, K.H.,Cheong, I.C.,Kim, T.H. Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.8

The objectives of this study were to confirm a location of the calpastatin (CAST) gene in chromosome 2 and to detect associations of genetic variations with economic traits in the porcine CAST gene as a candidate gene for growth and meat quality traits in pigs. Calpastatin is a specific endogenous inhibitor of calpains. The calpain protease system is ubiquitous, and is involved in numerous growth and metabolic processes. Three single nucleotide variations were identified within a 1.6 kb fragment of the porcine CAST gene and these polymorphisms were used for genetic linkage mapping. Linkage and QTL mapping were performed with the National Livestock Research Institute (NLRI) reference families using eight microsatellites and SNP makers in the CAST gene. The porcine CAST gene was mapped adjacent to the markers, SW395 and SW1695 on SSC2 with LOD scores of 15.32 and 8.50, respectively. According to the QTL mapping, a significant association was detected at 82 cM between SW395 and CAST-Hinf I for weight at the age of 30 weeks. In addition, an association study was performed with the $F_2$ animals of NLRI reference families for Hinf I, Msp I and Rsa I polymorphisms in the CAST gene. Two polymorphisms, CAST-Rsa I and CAST-Hinf I, showed significant correlation for growth traits at p<0.01 and p<0.05, respectively.

High-Resolution Bin Maps Provide Insights for QTL Mapping of Yield-Related Traits with Milyang23/Gihobyeo Recombinant Inbred Lines

이예지,Nam-In Hyung,김태호 한국육종학회 2020 Plant Breeding and Biotechnology Vol.8 No.3

High-throughput genotyping has substantially advanced the quality and accuracy of single nucleotide polymorphism (SNP) discovery and provided an effective way to interpret phenotypic variations in a mapping population. High-resolution quantitative trait locus (QTL) mapping is important for understanding agricultural traits. However, constructing a high-resolution map without sufficient markers to detect QTLs/genes of agronomically important traits is laborious and time consuming. In this study, 160 recombinant inbred lines (RILs) derived from a cross between Milyang23 and Gihobyeo were re-sequenced, and their SNPs were used for high-resolution QTL mapping of yield-related traits. A total of 1,850,671 high-quality SNPs from RILs were detected, and 3,563 bins were used as genetic markers to construct a high-resolution genetic map using the sliding window approach. The total genetic distance was 1,278.62 cM. Using the QTL analysis, we identified 35 QTLs controlling six yield traits, namely, culm length, panicle length, panicle number per plant, primary branch number per panicle, grain number per plant, and 100-grain weight. In addition, we detected major QTLs associated with culm length and grain number, and compared their physical distances using a conventional genetic map. These results showed that rapid, high-resolution QTL mapping using high-quality SNPs as bin markers is a powerful tool for finemapping and cloning important QTLs/genes.