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Li Y, Fang X, Lin Z. Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6089-6102. [PMID: 35724645 DOI: 10.1093/jxb/erac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.
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Affiliation(s)
- Yan Li
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Xiaojian Fang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Zhongwei Lin
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
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Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method. J Poult Sci 2019; 56:166-176. [PMID: 32055211 PMCID: PMC7005382 DOI: 10.2141/jpsa.0180066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth and carcass-related trait QTLs using 319 F2 chickens obtained from intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcass-related traits were also measured at this timepoint. A genetic linkage map was constructed using 545 single nucleotide polymorphism (SNP) markers that were developed using a restriction-site associated DNA sequencing method. The linkage map included the 23 autosomes and the Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant and suggestive main-effect QTLs for growth and carcass-related traits present on chromosomes 1, 2, 3, 5, 8, 19, 24, and Z. These loci explained 5.60–16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlapped with those of previously reported QTLs, whereas the targeted traits varied. Our QTLs will aid future breeding programs in improving growth and meat yield of chickens (e.g., via marker-assisted selection), particularly in the Japanese brand chicken industry.
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Mammadov J, Sun X, Gao Y, Ochsenfeld C, Bakker E, Ren R, Flora J, Wang X, Kumpatla S, Meyer D, Thompson S. Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.). BMC Genomics 2015; 16:916. [PMID: 26555731 PMCID: PMC4641357 DOI: 10.1186/s12864-015-2171-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gray Leaf Spot (GLS causal agents Cercospora zeae-maydis and Cercospora zeina) is one of the most important foliar diseases of maize in all areas where the crop is being cultivated. Although in the USA the situation with GLS severity is not as critical as in sub-Saharan Africa or Brazil, the evidence of climate change, increasing corn monoculture as well as the narrow genetic base of North American resistant germplasm can turn the disease into a serious threat to US corn production. The development of GLS resistant cultivars is one way to control the disease. In this study we combined the high QTL detection power of genetic linkage mapping with the high resolution power of genome-wide association study (GWAS) to precisely dissect QTL controlling GLS resistance and identify closely linked molecular markers for robust marker-assisted selection and trait introgression. RESULTS Using genetic linkage analysis with a small bi-parental mapping population, we identified four GLS resistance QTL on chromosomes 1, 6, 7, and 8, which were validated by GWAS. GWAS enabled us to dramatically increase the resolution within the confidence intervals of the above-mentioned QTL. Particularly, GWAS revealed that QTLGLSchr8, detected by genetic linkage mapping as a locus with major effect, was likely represented by two QTL with smaller effects. Conducted in parallel, GWAS of days-to-silking demonstrated the co-localization of flowering time QTL with GLS resistance QTL on chromosome 7 indicating that either QTLGLSchr7 is a flowering time QTL or it is a GLS resistance QTL that co-segregates with the latter. As a result, this genetic linkage - GWAS hybrid mapping system enabled us to identify one novel GLS resistance QTL (QTLGLSchr8a) and confirm with more refined positions four more previously mapped QTL (QTLGLSchr1, QTLGLSchr6, QTLGLSchr7, and QTLGLSchr8b). Through the novel Single Donor vs. Elite Panel method we were able to identify within QTL confidence intervals SNP markers that would be suitable for marker-assisted selection of gray leaf spot resistant genotypes containing the above-mentioned GLS resistance QTL. CONCLUSION The application of a genetic linkage - GWAS hybrid mapping system enabled us to dramatically increase the resolution within the confidence interval of GLS resistance QTL by-passing labor- and time-intensive fine mapping. This method appears to have a great potential to accelerate the pace of QTL mapping projects. It is universal and can be used in the QTL mapping projects in any crops.
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Affiliation(s)
- Jafar Mammadov
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Xiaochun Sun
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Yanxin Gao
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Cherie Ochsenfeld
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Erica Bakker
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Ruihua Ren
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Jonathan Flora
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Xiujuan Wang
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Siva Kumpatla
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - David Meyer
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Steve Thompson
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
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Jansen C, Zhang Y, Liu H, Gonzalez-Portilla PJ, Lauter N, Kumar B, Trucillo-Silva I, Martin JPS, Lee M, Simcox K, Schussler J, Dhugga K, Lübberstedt T. Genetic and agronomic assessment of cob traits in corn under low and normal nitrogen management conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1231-1242. [PMID: 25762132 DOI: 10.1007/s00122-015-2486-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/14/2015] [Indexed: 06/04/2023]
Abstract
Exploring and understanding the genetic basis of cob biomass in relation to grain yield under varying nitrogen management regimes will help breeders to develop dual-purpose maize. With rising energy demands and costs for fossil fuels, alternative energy from renewable sources such as maize cobs will become competitive. Maize cobs have beneficial characteristics for utilization as feedstock including compact tissue, high cellulose content, and low ash and nitrogen content. Nitrogen is quantitatively the most important nutrient for plant growth. However, the influence of nitrogen fertilization on maize cob production is unclear. In this study, quantitative trait loci (QTL) have been analyzed for cob morphological traits such as cob weight, volume, length, diameter and cob tissue density, and grain yield under normal and low nitrogen regimes. 213 doubled-haploid lines of the intermated B73 × Mo17 (IBM) Syn10 population have been resequenced for 8575 bins, based on SNP markers. A total of 138 QTL were found for six traits across six trials using composite interval mapping with ten cofactors and empirical comparison-wise thresholds (P = 0.001). Despite moderate to high repeatabilities across trials, few QTL were consistent across trials and overall levels of explained phenotypic variance were lower than expected some of the cob trait × trial combinations (R (2) = 7.3-43.1 %). Variation for cob traits was less affected by nitrogen conditions than by grain yield. Thus, the economics of cob usage under low nitrogen regimes is promising.
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Mao X, Li Y, Liu Y, Lange L, Li M. Testing genetic association with rare variants in admixed populations. Genet Epidemiol 2013; 37:38-47. [PMID: 23032398 PMCID: PMC3524352 DOI: 10.1002/gepi.21687] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/23/2012] [Accepted: 09/07/2012] [Indexed: 11/07/2022]
Abstract
Recent studies suggest that rare variants play an important role in the etiology of many traits. Although a number of methods have been developed for genetic association analysis of rare variants, they all assume a relatively homogeneous population under study. Such an assumption may not be valid for samples collected from admixed populations such as African Americans and Hispanic Americans as there is a great extent of local variation in ancestry in these populations. To ensure valid and more powerful rare variant association tests performed in admixed populations, we have developed a local ancestry-based weighted dosage test, which is able to take into account local ancestry of rare alleles, uncertainties in rare variant imputation when imputed data are included, and the direction of effect that rare variants exert on phenotypic outcome. We used simulated sequence data to show that our proposed test has controlled type I error rates, whereas naïve application of existing rare variants tests and tests that adjust for global ancestry lead to inflated type I error rates. We showed that our test has higher power than tests without proper adjustment of ancestry. We also applied the proposed method to a candidate gene study on low-density lipoprotein cholesterol. Our results suggest that it is important to appropriately control for potential population stratification induced by local ancestry difference in the analysis of rare variants in admixed populations.
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Affiliation(s)
- Xianyun Mao
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Yichuan Liu
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Leslie Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
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Pan Q, Ali F, Yang X, Li J, Yan J. Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize. PLoS One 2012; 7:e52777. [PMID: 23300772 PMCID: PMC3531342 DOI: 10.1371/journal.pone.0052777] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/20/2012] [Indexed: 12/30/2022] Open
Abstract
Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.
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Affiliation(s)
- Qingchun Pan
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Farhan Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Cereal Crops Research Institute (CCRI) Nowshera, Kyber Pukhtunkhwa, Pakistan
| | - Xiaohong Yang
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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9
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Li H. A quick method to calculate QTL confidence interval. J Genet 2011; 90:355-360. [PMID: 21869489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Hengde Li
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, People's Republic of China.
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10
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Wang L, Wang A, Huang X, Zhao Q, Dong G, Qian Q, Sang T, Han B. Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:327-40. [PMID: 20878143 PMCID: PMC3021254 DOI: 10.1007/s00122-010-1449-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2009] [Accepted: 09/08/2010] [Indexed: 05/06/2023]
Abstract
Mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. We conducted a quantitative trait loci (QTL) analysis of 150 rice recombinant inbred lines (RILs) derived from a cross between two cultivars, Oryza sativa ssp. indica cv. 93-11 and Oryza sativa ssp. japonica cv. Nipponbare. The RILs were genotyped through next-generation sequencing, which accurately determined the recombination breakpoints and provided a new type of genetic markers, recombination bins, for QTL analysis. We detected 49 QTL with phenotypic effect ranging from 3.2 to 46.0% for 14 agronomics traits. Five QTL of relatively large effect (14.6-46.0%) were located on small genomic regions, where strong candidate genes were found. The analysis using sequencing-based genotyping thus offers a powerful solution to map QTL with high resolution. Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice.
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Affiliation(s)
- Lu Wang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
| | - Ahong Wang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
| | - Xuehui Huang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
| | - Qiang Zhao
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006 China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006 China
| | - Tao Sang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
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Silva KM, Bastiaansen JWM, Knol EF, Merks JWM, Lopes PS, Guimarães SEF, van Arendonk JAM. Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4. Anim Genet 2010; 42:280-92. [PMID: 21198696 DOI: 10.1111/j.1365-2052.2010.02145.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.
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Affiliation(s)
- K M Silva
- Animal Science Department, Federal University of Viçosa, Viçosa, MG, 36570-000, Brazil
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Tortereau F, Gilbert H, Heuven HCM, Bidanel JP, Groenen MAM, Riquet J. Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6. Genet Sel Evol 2010; 42:42. [PMID: 21108822 PMCID: PMC2999584 DOI: 10.1186/1297-9686-42-42] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/25/2010] [Indexed: 11/16/2022] Open
Abstract
Background In pig, a number of experiments have been set up to identify QTL and a multitude of chromosomal regions harbouring genes influencing traits of interest have been identified. However, the mapping resolution remains limited in most cases and the detected QTL are rather inaccurately located. Mapping accuracy can be improved by increasing the number of phenotyped and genotyped individuals and/or the number of informative markers. An alternative approach to overcome the limited power of individual studies is to combine data from two or more independent designs. Methods In the present study we report a combined analysis of two independent design (a French and a Dutch F2 experimental designs), with 2000 F2 individuals. The purpose was to further map QTL for growth and fatness on pig chromosomes 2, 4 and 6. Using QTL-map software, uni- and multiple-QTL detection analyses were applied separately on the two pedigrees and then on the combination of the two pedigrees. Results Joint analyses of the combined pedigree provided (1) greater significance of shared QTL, (2) exclusion of false suggestive QTL and (3) greater mapping precision for shared QTL. Conclusions Combining two Meishan x European breeds F2 pedigrees improved the mapping of QTL compared to analysing pedigrees separately. Our work was facilitated by the access to raw phenotypic data and DNA of animals from both pedigrees and the combination of the two designs with the addition of new markers allowed us to fine map QTL without phenotyping additional animals.
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Affiliation(s)
- Flavie Tortereau
- INRA, UMR 0444 Génétique Cellulaire, F-31326 Castanet-Tolosan, France
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Gray-McGuire C, Guda K, Adrianto I, Lin CP, Natale L, Potter JD, Newcomb P, Poole EM, Ulrich CM, Lindor N, Goode EL, Fridley BL, Jenkins R, Le Marchand L, Casey G, Haile R, Hopper J, Jenkins M, Young J, Buchanan D, Gallinger S, Adams M, Lewis S, Willis J, Elston R, Markowitz SD, Wiesner GL. Confirmation of linkage to and localization of familial colon cancer risk haplotype on chromosome 9q22. Cancer Res 2010; 70:5409-18. [PMID: 20551049 DOI: 10.1158/0008-5472.can-10-0188] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genetic risk factors are important contributors to the development of colorectal cancer. Following the definition of a linkage signal at 9q22-31, we fine mapped this region in an independent collection of colon cancer families. We used a custom array of single-nucleotide polymorphisms (SNP) densely spaced across the candidate region, performing both single-SNP and moving-window association analyses to identify a colon neoplasia risk haplotype. Through this approach, we isolated the association effect to a five-SNP haplotype centered at 98.15 Mb on chromosome 9q. This haplotype is in strong linkage disequilibrium with the haplotype block containing HABP4 and may be a surrogate for the effect of this CD30 Ki-1 antigen. It is also in close proximity to GALNT12, also recently shown to be altered in colon tumors. We used a predictive modeling algorithm to show the contribution of this risk haplotype and surrounding candidate genes in distinguishing between colon cancer cases and healthy controls. The ability to replicate this finding, the strength of the haplotype association (odds ratio, 3.68), and the accuracy of our prediction model (approximately 60%) all strongly support the presence of a locus for familial colon cancer on chromosome 9q.
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Affiliation(s)
- Courtney Gray-McGuire
- Department of Arthritis and Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
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Druka A, Druka I, Centeno AG, Li H, Sun Z, Thomas WTB, Bonar N, Steffenson BJ, Ullrich SE, Kleinhofs A, Wise RP, Close TJ, Potokina E, Luo Z, Wagner C, Schweizer GF, Marshall DF, Kearsey MJ, Williams RW, Waugh R. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genet 2008; 9:73. [PMID: 19017390 PMCID: PMC2630324 DOI: 10.1186/1471-2156-9-73] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 11/18/2008] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. DESCRIPTION Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. CONCLUSION By integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.
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Affiliation(s)
- Arnis Druka
- Scottish Crop Research Institute, Invergowrie, Dundee, UK.
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Ball RD. Quantifying evidence for candidate gene polymorphisms: Bayesian analysis combining sequence-specific and quantitative trait loci colocation information. Genetics 2007; 177:2399-416. [PMID: 18073437 PMCID: PMC2219489 DOI: 10.1534/genetics.106.069955] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 10/15/2007] [Indexed: 11/18/2022] Open
Abstract
We calculate posterior probabilities for candidate genes as a function of genomic location. Posterior probabilities for quantitative trait loci (QTL) presence in a small interval are calculated using a Bayesian model-selection approach based on the Bayesian information criterion (BIC) and used to combine QTL colocation information with sequence-specific evidence, e.g., from differential expression and/or association studies. Our method takes into account uncertainty in estimation of number and locations of QTL and estimated map position. Posterior probabilities for QTL presence were calculated for simulated data with n = 100, 300, and 1200 QTL progeny and compared with interval mapping and composite-interval mapping. Candidate genes that mapped to QTL regions had substantially larger posterior probabilities. Among candidates with a given Bayes factor, those that map near a QTL are more promising for further investigation with association studies and functional testing or for use in marker-aided selection. The BIC is shown to correspond very closely to Bayes factors for linear models with a nearly noninformative Zellner prior for the simulated QTL data with n > or = 100. It is shown how to modify the BIC to use a subjective prior for the QTL effects.
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Affiliation(s)
- Roderick D Ball
- Scion (New Zealand Forest Research Institute Limited), Rotorua, New Zealand.
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16
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Abstract
The arrival of highly dense genetic maps at low cost has geared the focus of linkage analysis studies toward developing methods for placing putative trait loci in narrow regions with high confidence. This shift has led to a new analytic scheme that expands the traditional two-stage protocol of preliminary genome scan followed by fine mapping through inserting a new stage in between the two. The goal of this new "intermediate" fine mapping stage is to isolate disease loci to narrow intervals with high confidence so that association studies can be more focused, efficient, and cost-effective. In this paper, we compared and contrasted five methods that can be used for performing this intermediate step. These methods are: the lod support approach, the generalized estimating equations (GEE) method, the confidence set inference (CSI) procedure, and two bootstrap methods. We compared these methods in terms of the coverage probability and precision of localization of the resulting intervals. Results from a simulation study considering several two-locus models demonstrated that the two bootstrap methods yield intervals with approximately correct coverage. On the other hand, the 1-lod support intervals, and those produced by the GEE method, tend to significantly undercover the trait locus, while the regions obtained by the CSI incline to overcover the gene position. When the observed coverage of the confidence intervals produced by all the methods was held to be the same, those obtained through the CSI procedure displayed a higher ability to localize loci, especially when these loci have a minor contribution to the trait and when the amount of data available for the analysis is relatively small. However, with very large sample sizes, lod support intervals emerged as a winner. Application of the methods to the data from the Arthritis Research Campaign National Repository led to intervals containing the position of a known trait locus for all methods, with the greatest precision achieved by the CSI.
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Vales MI, Schön CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1260-70. [PMID: 16179997 DOI: 10.1007/s00122-005-0043-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/06/2005] [Indexed: 05/04/2023]
Abstract
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
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Affiliation(s)
- M I Vales
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA.
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18
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Vales MI, Schön CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1260-1270. [PMID: 16179997 DOI: 10.1007/s00122-524005-0043-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/06/2005] [Indexed: 05/24/2023]
Abstract
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
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Affiliation(s)
- M I Vales
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA.
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19
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Forbes SN, Valenzuela RK, Keim P, Service PM. Quantitative trait loci affecting life span in replicated populations of Drosophila melanogaster. I. Composite interval mapping. Genetics 2005; 168:301-11. [PMID: 15454544 PMCID: PMC1448087 DOI: 10.1534/genetics.103.023218] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Composite interval mapping was used to identify life-span QTL in F2 progeny of three crosses between different pairs of inbred lines. Each inbred line was derived from a different outbred population that had undergone long-term selection for either long or short life span. Microsatellite loci were used as genetic markers, and confidence intervals for QTL location were estimated by bootstrapping. A minimum of 10 QTL were detected, nine of which were located on the two major autosomes. Five QTL were present in at least two crosses and five were present in both sexes. Observation of the same QTL in more than one cross was consistent with the hypothesis that genetic variation for life span is maintained by balancing selection. For all QTL except one, allelic effects were in the direction predicted on the basis of outbred source population. Alleles that conferred longer life were always at least partially dominant.
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Affiliation(s)
- Scott N Forbes
- Department of Biological Sciences, Northern Arizona University, Flagstaff 86011, USA
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20
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Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, Melchinger AE. Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 2005; 167:485-98. [PMID: 15166171 PMCID: PMC1470842 DOI: 10.1534/genetics.167.1.485] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given.
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Affiliation(s)
- Chris C Schön
- State Plant Breeding Institute, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
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21
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Bennewitz J, Reinsch N, Guiard V, Fritz S, Thomsen H, Looft C, Kühn C, Schwerin M, Weimann C, Erhardt G, Reinhardt F, Reents R, Boichard D, Kalm E. Multiple quantitative trait loci mapping with cofactors and application of alternative variants of the false discovery rate in an enlarged granddaughter design. Genetics 2004; 168:1019-27. [PMID: 15514072 PMCID: PMC1448815 DOI: 10.1534/genetics.104.030296] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The experimental power of a granddaughter design to detect quantitative trait loci (QTL) in dairy cattle is often limited by the availability of progeny-tested sires, by the ignoring of already identified QTL in the statistical analysis, and by the application of stringent experimentwise significance levels. This study describes an experiment that addressed these points. A large granddaughter design was set up that included sires from two countries (Germany and France), resulting in almost 2000 sires. The animals were genotyped for markers on nine different chromosomes. The QTL analysis was done for six traits separately using a multimarker regression that included putative QTL on other chromosomes as cofactors in the model. Different variants of the false discovery rate (FDR) were applied. Two of them accounted for the proportion of truly null hypotheses, which were estimated to be 0.28 and 0.3, respectively, and were therefore tailored to the experiment. A total of 25 QTL could be mapped when cofactors were included in the model-7 more than without cofactors. Controlling the FDR at 0.05 revealed 31 QTL for the two FDR methods that accounted for the proportion of truly null hypotheses. The relatively high power of this study can be attributed to the size of the experiment, to the QTL analysis with cofactors, and to the application of an appropriate FDR.
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Affiliation(s)
- Jörn Bennewitz
- Institute of Animal Breeding and Husbandry, University of Kiel, D-24098 Kiel, Germany.
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22
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Abstract
Several recent studies have used quantitative complementation tests to identify relatively short chromosome regions that contain genes that influence life span and to screen for candidate life-span genes in flies. The methodology and logic of quantitative complementation tests are described. Arguments are presented that suggest that these tests may be misleading because there is a substantial, but unknown, likelihood of false positive results. The arguments are supported by the published results of quantitative complementation tests.
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Affiliation(s)
- Philip M Service
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.
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Ron M, Feldmesser E, Golik M, Tager-Cohen I, Kliger D, Reiss V, Domochovsky R, Alus O, Seroussi E, Ezra E, Weller JI. A Complete Genome Scan of the Israeli Holstein Population for Quantitative Trait Loci by a Daughter Design. J Dairy Sci 2004; 87:476-90. [PMID: 14762091 DOI: 10.3168/jds.s0022-0302(04)73187-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Eleven Israeli Holstein families including 5221 cows were analyzed by a daughter design for eight economic traits: milk, fat and protein production, fat and protein percentage, somatic cell score (SCS), herd-life, and female fertility. The cows were genotyped for 73 microsatellites with maximum spacing between markers of 53 cM. There were 86,304 informative genotypes. Preliminary analysis was by ANOVA of each trait, with the marker effect nested within sire. Significance was determined by controlling the false discovery rate at 0.4, after excluding markers with genome-wide significance for at least a single trait, and traits without any significant effects at this level. Thus, four markers on chromosomes 6 and 14 and female fertility were excluded. There remained 40 significant marker-trait combinations, and it is expected that 24 of these are true effects. To perform interval mapping for the families with significant contrasts, 21 additional markers were genotyped on chromosomes 2, 7, and 27. The bootstrap confidence intervals for gene effect did not include zero for protein percent on chromosome 2 and fat yield, protein yield, and SCS on chromosome 7. Quantitative trait locus heterozygosity was 33%, which is consistent with the hypothesis that only two alleles are segregating with unequal allele frequency.
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Affiliation(s)
- M Ron
- Institute of Animal Sciences, ARO, The Volcani Center, Bet Dagan 50250, Israel
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Bennewitz J, Reinsch N, Paul S, Looft C, Kaupe B, Weimann C, Erhardt G, Thaller G, Kühn C, Schwerin M, Thomsen H, Reinhardt F, Reents R, Kalm E. The DGAT1 K232A mutation is not solely responsible for the milk production quantitative trait locus on the bovine chromosome 14. J Dairy Sci 2004; 87:431-42. [PMID: 14762086 DOI: 10.3168/jds.s0022-0302(04)73182-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The gene, acyl-CoA:diacylglycerol acyltransferase1 (DGAT1), was recently identified as the one underlying the quantitative trait locus (QTL) for milk production traits in the centromeric region of the bovine chromosome 14. Until now, 2 alleles, the lysine variant (increasing fat yield, fat and protein percentage) and the alanine variant (increasing protein and milk yield), were postulated at DGAT1. This study investigated whether the diallelic DGAT1 polymorphism is responsible for all the genetic variation at the centromeric region of this chromosome for milk, fat, and protein yield and fat and protein percentage. A statistical model was applied to a granddaughter design to analyze 16 German Holstein families. The model included the diallelic DGAT1 effect and the QTL transition probability estimated for each chromosomal position by a multiple marker approach. Because the regression coefficient of this probability was corrected for the diallelic DGAT1 polymorphism, it represented a putative conditional QTL effect. The effect of the DGAT1 gene was always highly significant. The conditional QTL effect was significant genomewise for fat percentage at the proximal end of the chromosome and for protein percentage at a more distal chromosomal region. Additional chromosomewise significance was found for fat and protein yield. Our results suggest an additional source of genetic variance on this chromosome for these traits; either one or more additional alleles segregating at DGAT1 that were not previously detected, a second quantitative trait locus affecting these traits, or both.
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Affiliation(s)
- J Bennewitz
- Institut für Tierzucht und Tierhaltung, Christian-Albrechts-Universität, D-24098 Kiel, Germany.
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Bennewitz J, Reinsch N, Kalm E. Comparison of several bootstrap methods for bias reduction of QTL effect estimates. J Anim Breed Genet 2003. [DOI: 10.1046/j.0931-2668.2003.00410.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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