A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative...A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.展开更多
QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL),...QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL), grain length to width ratio (LWR), chalk grain rate (CGR), chalkiness degree (CD), gelatinization temperature (GT), amylose content (AC) and gel consistency (GC) of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.展开更多
The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The...The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild‐derived strains.Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions.In this article,we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases,including type 2 diabetes and metabolic diseases,body composition,immune response,colorectal cancer,susceptibility to Aspergillus fumigatus,Klebsiella pneumoniae,Pseudomonas aeruginosa,sepsis,and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum,which were conducted at our laboratory using the CC mouse population.These traits are observed at multiple levels of the body systems,including metabolism,body weight,immune profile,susceptibility or resistance to the development and progress of infectious or chronic diseases.Herein,we present full protocols and step‐by‐step methods,implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines,mapping the gene underlying the host response to these infections and chronic diseases.The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits,including chronic and infectious diseases.展开更多
To provide a theoretical basis for further improvement of Brassica napus yield, additive dominance with additive - by - additive epistatic effects ( ADAA) genetic model and a 6 X 8 partial dial- lel cross des...To provide a theoretical basis for further improvement of Brassica napus yield, additive dominance with additive - by - additive epistatic effects ( ADAA) genetic model and a 6 X 8 partial dial- lel cross design were used to analyze the genetic effects and correlations of five yield related traits of 14 excellent Brassica napus parental lines and their 46 and F2 populations. The results showed that silique density (SD) , siliques per plant (SPP) , seeds per silique (SPS) and thousand - seed weight (TSW) exhibited not only additive and dominant effects, but also significant epistatic effects. The dominant effects of all five yield - related traits were obviously greater than their additive effects and epistatic effects. Yield per plant (YPP) showed significant genetic correlation with SD, SPP and SPS, and the main component of the genetic correlation was the dominance correlation. SPP and SPS both showed a significant negative correlation with TSW. The SD of rapeseed was genetically correlated with all three components of yield to a certain extent, and there were different components of genetic effects positively correlated with the three yield components, indicating that SD is a potential trait to reconcile the conflict between TSW and SPP as well as SPS.展开更多
The objectives of this study were to estimate genetic parameters of lactation average somatic cell scores (LSCS) and examine genetic associations between LSCS and production traits in the first three lactations of C...The objectives of this study were to estimate genetic parameters of lactation average somatic cell scores (LSCS) and examine genetic associations between LSCS and production traits in the first three lactations of Chinese Holstein cows using single-parity multi-trait animal model and multi-trait repeatability animal model. There were totally 273605 lactation records of Chinese Holstein cows with first calving from 2001 to 2012. Heritability estimates for LSCS ranged from 0.144 to 0.187. Genetic correlations between LSCS and 305 days milk, protein percentage and fat percentage were -0.079, -0.082 and -0.135, respectively. Phenotypic correlation between LSCS and 305 days milk yield was negative (-0.103 to -0.190). Genetic correlation between 305 days milk and fat percentage or protein percentage was highly negative. Genetic correlation between milk fat percentage and milk protein percentage was highly favorable. Heritabilities of production traits decreased with increase of parity, whereas heritability of LSCS increased with increase of parity.展开更多
Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role cand...Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology.Methods: Liver weight of 506 mice generated from 39 different Collaborative Cross(CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers.Results: Statistical analysis revealed a significant(P < 0.05) variation of liver weight between the CC lines, with broad sense heritability(H^2) of 0.32 and genetic coefficient of variation(CV_G) of 0.28. Subsequently, quantitative trait locus(QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb(4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13,respectively.Conclusion: To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.展开更多
基金This work was supported by Chinese National Programs for High Technology Research and Development(973 Program)(No.2004CB117306).
文摘A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.
基金supported by the National High Technology Research and Development Program of China (Grant No. 2010AA101301)the Program of Introducing International Advanced Agricultural Science and Technology in China (Grant No. 2006-G8[4]-31-1)the Program of Science-Technology Basis and Conditional Platform in China (Grant No. 505005)
文摘QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL), grain length to width ratio (LWR), chalk grain rate (CGR), chalkiness degree (CD), gelatinization temperature (GT), amylose content (AC) and gel consistency (GC) of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.
基金Hendrech and Eiran Gotwert FundWellcome, Grant/Award Number: 085906/Z/08/Z, 075491/Z/04 and 090532/Z/09/Z+6 种基金Tel-Aviv UniversityIsraeli Science foundation, Grant/Award Number: 429/09, 961/15 and 1085/18Binational Science Foundation, Grant/Award Number: 2015077German Israeli Science Foundation, Grant/Award Number: I-63-410.20-2017Israeli Cancer Research FundCancer Research Counsel-UK Cancer Biology Research Center
文摘The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild‐derived strains.Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions.In this article,we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases,including type 2 diabetes and metabolic diseases,body composition,immune response,colorectal cancer,susceptibility to Aspergillus fumigatus,Klebsiella pneumoniae,Pseudomonas aeruginosa,sepsis,and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum,which were conducted at our laboratory using the CC mouse population.These traits are observed at multiple levels of the body systems,including metabolism,body weight,immune profile,susceptibility or resistance to the development and progress of infectious or chronic diseases.Herein,we present full protocols and step‐by‐step methods,implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines,mapping the gene underlying the host response to these infections and chronic diseases.The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits,including chronic and infectious diseases.
基金This research was supported by the National Basic Research Program of China ( 973 Program, 2011CB109302);the National High - Tech R&D Pro-gram of China (863 Program, 2011AA10A104, 2012AA101107) ; Natural Science Foundation of Hu-bei Province (2015CFA103) ; Hubei Agricultural Science and Technology Innovation Center.
文摘To provide a theoretical basis for further improvement of Brassica napus yield, additive dominance with additive - by - additive epistatic effects ( ADAA) genetic model and a 6 X 8 partial dial- lel cross design were used to analyze the genetic effects and correlations of five yield related traits of 14 excellent Brassica napus parental lines and their 46 and F2 populations. The results showed that silique density (SD) , siliques per plant (SPP) , seeds per silique (SPS) and thousand - seed weight (TSW) exhibited not only additive and dominant effects, but also significant epistatic effects. The dominant effects of all five yield - related traits were obviously greater than their additive effects and epistatic effects. Yield per plant (YPP) showed significant genetic correlation with SD, SPP and SPS, and the main component of the genetic correlation was the dominance correlation. SPP and SPS both showed a significant negative correlation with TSW. The SD of rapeseed was genetically correlated with all three components of yield to a certain extent, and there were different components of genetic effects positively correlated with the three yield components, indicating that SD is a potential trait to reconcile the conflict between TSW and SPP as well as SPS.
基金fundings from the National Natural Science Foundation of China (31200927)the National Modern Agricultural Industry Technology Fund for Scientists in Sheep Industry System, China (CARS-39-04B)+1 种基金the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (2011BAD28B02, 2012BAD12B06)the Chinese Academy of Agricultural Sciences Foundation (2012cj-2)
文摘The objectives of this study were to estimate genetic parameters of lactation average somatic cell scores (LSCS) and examine genetic associations between LSCS and production traits in the first three lactations of Chinese Holstein cows using single-parity multi-trait animal model and multi-trait repeatability animal model. There were totally 273605 lactation records of Chinese Holstein cows with first calving from 2001 to 2012. Heritability estimates for LSCS ranged from 0.144 to 0.187. Genetic correlations between LSCS and 305 days milk, protein percentage and fat percentage were -0.079, -0.082 and -0.135, respectively. Phenotypic correlation between LSCS and 305 days milk yield was negative (-0.103 to -0.190). Genetic correlation between 305 days milk and fat percentage or protein percentage was highly negative. Genetic correlation between milk fat percentage and milk protein percentage was highly favorable. Heritabilities of production traits decreased with increase of parity, whereas heritability of LSCS increased with increase of parity.
基金Israeli Centers of Research ExcellenceWellcome Trust,Grant/Award Number:085906/Z/08/Z,075491/Z/04,090532/Z/09/Z+1 种基金Edmond J.Safra Center for Bioinformatics at Tel-Aviv UniversityTel-Aviv University
文摘Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology.Methods: Liver weight of 506 mice generated from 39 different Collaborative Cross(CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers.Results: Statistical analysis revealed a significant(P < 0.05) variation of liver weight between the CC lines, with broad sense heritability(H^2) of 0.32 and genetic coefficient of variation(CV_G) of 0.28. Subsequently, quantitative trait locus(QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb(4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13,respectively.Conclusion: To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.