Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.     

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive,dominant and epistatic effects

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.     

Identification of a 3.7-Mb region for a marbling QTL on bovine chromosome 4 by identical-by-descent and association analysis

QTL mapping for growth and carcass traits was performed using a paternal half-sib family composed of 325 Japanese Black cattle offspring. Nine QTL were detected at the 1% chromosome-wise significance level at a false discovery rate of less than 0.1. These included two QTL for marbling on BTA 4 and 18, two QTL for carcass weight on BTA 14 and 24, two QTL for longissimus muscle area on BTA 1 and 4, two QTL for subcutaneous fat thickness on BTA 1 and 15 and one QTL for rib thickness on BTA 6. Although the marbling QTL on BTA 4 has been replicated with significant linkages in two Japanese Black cattle sires, the three Q (more marbling) haplotypes, each inherited maternally, were apparently different. To compare the three Q haplotypes in more detail, high-density microsatellite markers for the overlapping regions were developed within the 95% CIs (65 markers in 44–78 cM). A detailed haplotype comparison indicated that a small region (<3.7 Mb) around 46 cM was shared between the Qs of the two sires, whose dams were related. An association of this region with marbling was shown by a regression analysis using the local population, in which the two sires were produced and this was confirmed by an association study using a population collected throughout Japan. These results strongly suggest that the marbling QTL on BTA 4 is located in the 3.7-Mb region at around 46 cM.     

Identification of quantitative trait loci for growth and carcass composition in cattle

A genomic screening to detect quantitative trait loci (QTL) affecting growth, carcass composition and meat quality traits was pursued. Two hundred nineteen microsatellite markers were genotyped on 176 of 620 (28%) progeny from a Brahman x Angus sire mated to mostly MARC III dams. Selective genotyping, based on retail product yield (%) and fat yield (%), was used to select individuals to be genotyped. Traits included in the study were birth weight (kg), hot carcass weight (kg), retail product yield, fat yield, marbling score (400 = slight00 and 500 = small00), USDA yield grade, and estimated kidney, heart and pelvic fat (%). The QTL were classified as significant when the expected number of false positives (ENFP) was less than 0.05 (F-statistic greater than 17.3), and suggestive when the ENFP was <1 (F-statistic between 10.2 and 17.3). A significant QTL (F = 19; ENFP = 0.02) was detected for marbling score at centimorgan (cM) 54 on chromosome 2. Suggestive QTL were detected for fat yield at 50 cM, for retail product yield at 53 cM, and for USDA yield grade at 63 cM on chromosome 1, for marbling score at 56 cM, for retail product yield at 70 cM, and for estimated kidney, heart and pelvic fat at 79 cM on chromosome 3, for marbling score at 44 cM, for hot carcass weight at 49 cM, and for estimated kidney, heart and pelvic fat at 62 cM on chromosome 16, and for fat yield at 35 cM on chromosome 17. Two suggestive QTL for birth weight were identified, one at 12 cM on chromosome 20 and the other at 56 cM on chromosome 21. An additional suggestive QTL was detected for retail product yield, for fat yield, and for USDA yield grade at 26 cM on chromosome 26. Results presented here represent the initial search for quantitative trait loci in this family. Validation of detected QTL in other populations will be necessary.     

Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.     

FTO gene variants are associated with growth and carcass traits in cattle

An important aim in animal breeding is the improvement of growth and meat quality traits. Previous studies have demonstrated that genetic variants in the fat mass and obesity associated (FTO) gene have a relatively large effect on human obesity as well as on body composition in rodents and, more recently, in livestock. Here, we examined the effects of the FTO gene variants on growth and carcass traits in the Slovenian population of Simmental (SS) and Brown (SB) cattle. To validate and identify new polymorphisms, we used sequencing, PCR‐RFLP analysis and TaqMan assays in the SS breed and FTO gene variants data from the Illumina BovineSNP50 v1 array for the SB breed. Sequencing of the eight samples of progeny‐tested SS sires detected 108 single nucleotide polymorphisms (SNPs) in the bovine FTO gene. Statistical analyses between growth and carcass traits and 34 FTO polymorphisms revealed significant association of FTO variants with lean meat percentage in both breeds. Additionally, FTO SNPs analyzed in SS cattle were associated with fat percentage, bone weight and live weight at slaughter. The FTO gene can thus be regarded as a candidate gene for the marker‐assisted selection programs in our and possibly other populations of cattle. Future studies in cattle might reveal novel roles for the FTO gene in shaping carcass traits in livestock species as well as body composition control in other mammals.     

Factors influencing the priority of access to food and their effects on the carcass traits for Japanese Black (Wagyu) cattle

The factors influencing the priority of access to food and the effects of the priority of access to food on their carcass traits were analyzed for Japanese Black (Wagyu) cattle in a semi-intensive fattening production system. The records of 96 clinically healthy steers and heifers were analyzed. The calves at ∼3 to 4 months of age were allocated to pens with four animals per pen; all four animals in the same pen were of the same sex and of similar body size. The ranking of the animals’ priority of access to food (1^st, 2^nd, 3^rd and 4^th), which was determined by the farm manager, was used as an indicator of social dominance in the present study. Four models including sire line, maternal grandsire line and the difference in the animals’ birth dates as fixed effects were used to analyze factors influencing the priority of access to food. Ranking was represented by ordinal scores (highest=4, lowest=1) in Model 1, and the binary scores were assigned in Model 2 (highest=1; 2^nd, 3^rd and 4^th=0), Model 3 (1^st and 2^nd=1; 3^rd and 4^th=0) and Model 4 (1^st, 2^nd and 3^rd=1; lowest=0). The results showed that the difference in the animals’ birth dates had a significant effect on the establishment of the priority of access to food in Model 3 (P<0.05), suggesting that animals born earlier may become more dominant in the pen. The maternal grandsire line tended to affect the social rank score in Models 2 and 3 (P<0.10). Our results indicated that the maternal grandsire line may affect the temperament of calves through their mothers’ genetic performance and thereby more aggressive calves may be more dominant and have higher priority of access to food. On the other hand, there was a significant effect of the priority of access to food on beef marbling score (BMS; P<0.05), and the priority of access to food also tended to influence the carcass weight (P=0.09). The highest BMS was observed for animals with the first rank of the priority of access to food (P<0.05), and the higher-ranking animals had the tendency to be heavier carcass than the lower-ranking animals. Our findings emphasized the importance of information about the priority of access to food determined by farmers’ own observation on implementing best management practices in small-scaled semi-intensive beef cattle production systems.     

Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

Meat quality traits are the most economically important traits affecting the beef industry in Korea. We performed a whole genome quantitative trait locus (QTL) mapping study of carcass data in Hanwoo Korean cattle. Two hundred sixty-six Hanwoo steers from 65 sires were genotyped using a 10K Affymetrix SNP chip. The average SNP interval across the bovine genome was 1.5Mb. Associations between each individual SNP and four carcass traits [carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling (MAR)] were assessed using a linear mixed model of each trait. Combined linkage and linkage disequilibrium analysis (LDLA) detected six potential QTL on BTA04, 06, 13, 16, 17, and 23 at the chromosome-wise level (P<0.05). Two MAR QTL were detected at 52.2 cM of BTA06 and 46.04 cM of BTA17. We identified three genes (ARAP2, LOC539460, and LOC511424) in the QTL region of BTA06 and seven genes (RPS14, SCARB1, LOC782103, BRI3BP, AACS, DHX37, and UBC) in the QTL region of BTA17. One significant QTL for CWT was detected at 100 cM on BTA04 and the corresponding QTL region spanned 1.7 cM from 99.7 to 101.4 cM. For EMA QTL, one significant QTL was detected at 3.9 cM of BTA23 and the most likely QTL interval was 1.4 cM, placing 15 candidate genes in the marker bracket. Finally, two QTL for BFT were identified at 68 cM on BTA13 and 24 cM on BTA16. The LPIN3 gene, which is functionally associated with lipodystrophy in humans, is located in the BFT QTL on BTA13. Thus, two potential candidate genes, acetoacetyl-CoA synthetase (AACS) and lipin (LPIN), were detected in QTL regions on BTA17 for MAR and BTA13 for BFT, respectively. In conclusion, LDLA analysis can be used to detect chromosome regions harboring QTL and candidate genes with a low density SNP panel, yielding relatively narrow confidence intervals regarding location.     

Genetic parameters for fatty acid composition and feed efficiency traits in Japanese Black cattle

We estimated the genetic parameters related to feed intake (FI), feed efficiency traits (including feed conversion ratio (FCR) and residual feed intake (RFI) of digestible crude protein (DCP) and total digestible nutrients (TDN)), beef marbling score (BMS), melting point of fat (MP) and fatty acid composition. Fat and meat (Musculus trapezius) samples were taken from the carcasses of 863 Japanese Black steers derived from 65 sires, for determination of the MP and fatty acid composition of the total lipid in intramuscular adipose tissue. Genetic parameters were estimated using uni- and bivariate animal models. In addition, pedigree information for 4841 animals was used. Heritability estimates for BMS, MP, individual fatty acids, monounsaturated fatty acids (MUFA), the ratio of saturated fatty acids to MUFA (MUS) and the ratio of elongation (ELONG) were generally high. The FI values of TDN and DCP were also high, but FCRs and RFIs of those were low (0.09 to 0.22). Genetic correlation of BMS with MP was -0.34 (favorable) and with C18:1, MUFA, MUS and ELONG values were 0.40, 0.28, 0.29 and 0.37, respectively (favorable). Genetic correlations of MP with C18:1, MUFA, MUS and ELONG were negative (also favorable) and high (-0.85, -0.98, -1.00 (-0.996) and -0.66, respectively). The correlation estimates for feed efficiency traits of DCP were quite similar to those of TDN. Genetic correlations of BMS with FCRs and RFIs of TDN and DCP were all positive (unfavorable; 0.21 to 0.51), and in particular, the correlations with RFIs of those were high. The correlations of C18:1, MUFA, MUS and ELONG with RFIs of TDN and DCP were positive (unfavorable) but low (0.06 to 0.17), whereas the corresponding correlations with FCRs of those were all negative (favorable; -0.38 to -0.10). These results suggest that the quantity and quality of beef fat can be simultaneously improved and that the quality of beef fat (fatty acid composition) can be improved directly or indirectly with MP. Furthermore, selecting MP or fatty acid traits does not significantly affect feed efficiency.     

Non-additive genetic variation in growth,carcass and fertility traits of beef cattle

Background

A better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of individuals. Genome-wide panels of single nucleotide polymorphisms (SNPs) have been mainly used to map additive effects for quantitative traits, but they can also be used to investigate non-additive effects. We estimated dominance and epistatic effects of SNPs on various traits in beef cattle and the variance explained by dominance, and quantified the increase in accuracy of phenotype prediction by including dominance deviations in its estimation.

Methods

Genotype data (729 068 real or imputed SNPs) and phenotypes on up to 16 traits of 10 191 individuals from Bos taurus, Bos indicus and composite breeds were used. A genome-wide association study was performed by fitting the additive and dominance effects of single SNPs. The dominance variance was estimated by fitting a dominance relationship matrix constructed from the 729 068 SNPs. The accuracy of predicted phenotypic values was evaluated by best linear unbiased prediction using the additive and dominance relationship matrices. Epistatic interactions (additive × additive) were tested between each of the 28 SNPs that are known to have additive effects on multiple traits, and each of the other remaining 729 067 SNPs.

Results

The number of significant dominance effects was greater than expected by chance and most of them were in the direction that is presumed to increase fitness and in the opposite direction to inbreeding depression. Estimates of dominance variance explained by SNPs varied widely between traits, but had large standard errors. The median dominance variance across the 16 traits was equal to 5% of the phenotypic variance. Including a dominance deviation in the prediction did not significantly increase its accuracy for any of the phenotypes. The number of additive × additive epistatic effects that were statistically significant was greater than expected by chance.

Conclusions

Significant dominance and epistatic effects occur for growth, carcass and fertility traits in beef cattle but they are difficult to estimate precisely and including them in phenotype prediction does not increase its accuracy.     

Identification of QTL for production traits in chickens

If the poultry industry hopes to continue to flourish, the identification of potential quantitative trait loci (QTL) for production-related traits must be pursued This remains true despite the sequencing of the chicken genome. In view of this need, a scan of the chicken genome using 72 microsatellite markers was carried out on a meat-type x egg-type resource population measured for production and egg quality traits. Using a Bayesian analysis, potential QTL for a number of traits were identified on several chromosomes. Evidence of eight QTL regions associated with a total of eight traits (specific gravity, albumin height, Haugh score, shell shape, total number of eggs, final body weight, gain, and feed efficiency) was found. Two of these regions, one spanning the area of 263/287 cM on GAA01 and the other spanning the area of 23/28 cM on GAA02, were associated with multiple QTL.     

Genetic dissection of floral traits in anemone-type chrysanthemum by QTL mapping

Brassica oleracea comprises several important subspecies, including cabbage, broccoli, cauliflower, Chinese kale, and kohlrabi. The petal color of Chinese kale is mostly white and sometimes yellow. To explore the genetic basis of petal color variation in Chinese kale, F₂ and BC₁ (backcross) populations were constructed from the cross of two inbred lines, 2114 (yellow petal) and 2116 (white petal). Genetic analysis of the F₂ and BC₁ populations demonstrated that yellow petal color was controlled by a single recessive nuclear gene, termed cpc-2. Insertion-deletion (InDel) markers, designed based on the parental resequencing data, were used to map cpc-2. The fine mapping results indicated that the cpc-2 gene was located in a 569-kb interval on chromosome C03 flanked by InDel markers ZB636 and ZB692, with genetic distances of 0.3 cM and 0.6 cM, respectively. By analyzing the nucleotide variations and annotations of the genes in this interval, a CCD4 family gene was predicted to be a candidate for cpc-2 and renamed BoCCD4.2. In addition, insertion of the CACTA-like transposable element (TE3) interrupted the function of the BoCCD4 gene, which may have resulted in the loss of function of BoCCD4 and the petal color transition from white to yellow. The TE3 insertion in the BoCCD4 gene was also present in 63 cabbage inbred lines among 159 accessions, which revealed that the TE3-type null allele of BoCCD4 formed before the divergence of the two subspecies cabbage and Chinese kale and that Chinese kale evolved much earlier than cabbage. This study lays the foundation for cloning BoCCD4.2 and revealing the molecular mechanism underlying petal color formation in Chinese kale.

     

Association between a single nucleotide polymorphism in the bovine chemerin gene and carcass traits in Qinchuan cattle

Qinchuan is a red or yellow draft and beef breed in China. In order to identify a predictor of carcass traits on the basis of associations between carcass traits and gene polymorphism, variation in the bovine chemerin gene was investigated using PCR-single-strand conformational polymorphism and DNA sequencing. An SNP of A868G located in exon 2 of the Bos taurus chemerin gene was detected in 716 samples of six breeds (Jiaxian red, Luxi, Nan yang, Qinchuan, Simmental and Luxi crossbred steers, and Xia'nan), all in China, and three genotypes (AA, AG and GG) were found. Based on the χ(2) test, the AA/AG/GG genotype frequencies of all six breeds were found to be in Hardy-Weinberg equilibrium. A possible association of A868G with some carcass traits was investigated in 106 Qinchuan cattle. Animals with the AG genotype were found to have significantly lower mean loin eye area and meat tenderness compared to those with the AA and GG genotypes. However, there was no significant association between any individual haplotype and backfat thickness, water holding capacity or marbling score. We suggest that A868G could be used as a molecular marker in marker-assisted selection for carcass traits.     

Heritability estimates for carcass traits of cattle: a review

We present estimates of heritability for carcass traits of cattle published in the scientific literature. Seventy-two papers published from 1962 to 2004, which reported estimates of heritability for carcass traits, were reviewed. The unweighted means of estimates of heritability for 14 carcass traits by slaughter end point (age, weight, and fat depth) were calculated. Among the three end points, carcass weight, backfat thickness, longissimus muscle area, and marbling score were the carcass traits with the most estimates of heritability (56 相似文献   

QTL mapping for nitrogen-use efficiency and nitrogen-deficiency tolerance traits in rice

Plant and Soil - The improvement of nitrogen-deficiency tolerance (NDT) and nitrogen-use efficiency (NUE) traits is an important objective of many rice breeding programs. A better understanding of...     

QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat

In bread wheat, single-locus and two-locus QTL analyses were conducted for seven yield and yield contributing traits using two different mapping populations (P I and P II). Single-locus QTL analyses involved composite interval mapping (CIM) for individual traits and multiple-trait composite interval mapping (MCIM) for correlated yield traits to detect the pleiotropic QTLs. Two-locus analyses were conducted to detect main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL × environment interactions (QE and QQE). Only a solitary QTL for spikelets per spike was common between the above two populations. HomoeoQTLs were also detected, suggesting the presence of triplicate QTLs in bread wheat. Relatively fewer QTLs were detected in P I than in P II. This may be partly due to low density of marker loci on P I framework map (173) than in P II (521) and partly due to more divergent parents used for developing P II. Six QTLs were important which were pleiotropic/coincident involving more than one trait and were also consistent over environments. These QTLs could be utilized efficiently for marker assisted selection (MAS).     

Polymorphism of bovine Y-STR UMN0929 and its correlation with carcass traits in five Chinese beef cattle populations

The correlations between Y chromosome polymorphisms and the carcass traits were studied in five Chinese beef cattle populations by PCR, single strand conformation polymorphism and Y-STR sequence analysis. Nine alleles and their frequencies were identified on Y-STR UMN0929 region in Qinchuan (n = 116), Luxi (n = 112), Jinnan (n = 104) pure breeds, Simmental × Qinchuan crossbred (n = 80) and Angus × Qinchuan crossbred (n = 96). The most popular A-176 and B-178 alleles were presented in all 5 cattle populations in the range of 12% (Jinnan) to 66% (Simmental × Qinchuan). The allele I-194 presented Luxi and Angus × Qinchuan. In Qinchun cattle, G-190 and E-186 alleles had bigger effect on BPI (4.23 ± 0.32 and 4.22 ± 0.48 kg/cm, P < 0.01) and CW (325.40 ± 49.42 and 316.73 ± 45.29 kg, P < 0.01), respectively. In Luxi cattle, I-194 allele affected higher BPI (4.08 ± 0.35 kg/cm, P < 0.01) and CW (302.07 ± 17.55 kg, P < 0.01), respectively. In Jinnan cattle breed, H-192 had higher BPI (4.32 ± 0.50 kg/cm, P < 0.05) and CW (327.87 ± 59.37 kg, P < 0.05), respectively. In Simmental × Qinchuan cross breed, C-180 allele affected largely on BPI (5.16 ± 0.25 kg/cm, P < 0.05) and CW (393.16 ± 25.92 kg, P < 0.05). In Angus × Qinchuan cross breed, I-194 had higher BPI (4.43 ± 0.33 kg, P < 0.05) and CW (346.63 ± 29.77 kg, P < 0.05). Correlations between alleles and other carcass traits (net meat weight, top grade weight, slaughter rate, net meat rate, loin-eye muscle area, carcass length, meet tenderness and shear force) were also analyzed using mixed-effect model. Cattle Y-STR UMN0929 loci alleles and its correlation with carcass traits in beef cattle populations could be implemented into the cattle breeding program for choosing beef cattle with better carcass traits.     

Genetic diversity of MYH 3 gene associated with growth and carcass traits in Chinese Qinchuan cattle

MYH₃, whose function is to convert chemical energy to mechanical energy through ATP hydrolysis, is mainly expressed in skeletal muscle at various stages and is indispensable in the procedure of development of skeletal muscle and heart. In the study, genetic variations and genotypes of MYH ₃ gene in a total of 365 Qinchuan cattles were analyzed by polymerase chain reaction-restriction fragment length polymorphism, as well as verified the effect on growth and carcass traits. After PCR products were digested by restriction enzymes, eight SNPs were identified and individuals were genotyped. It showed that the SNPs at nucleotides were all in low linkage disequilibrium, therefore no dominated haplotype was found in the population. The result of statistic analysis indicated seven SNPs were significantly associated with growth and carcass traits (P < 0.05, N = 365) except locus G13791A. To sum up, the result of the study proved that polymorphisms in MYH3 gene are associated with the growth performance of Chinese Qinchuan cattle, so the variations of the gene could be used as possible molecular assisted-makers in the beef cattle breeding program and management.     

On the use of mathematically-derived traits in QTL mapping

Mathematically-derived traits from two or more component traits, either by addition, subtraction, multiplication, or division, have been frequently used in genetics and breeding. When used in quantitative trait locus (QTL) mapping, derived traits sometimes show discrepancy with QTL identified for the component traits. We used three QTL distributions and three genetic effects models, and an actual maize mapping population, to investigate the efficiency of using derived traits in QTL mapping, and to understand the genetic and biological basis of derived-only QTL, i.e., QTL identified for a derived trait but not for any component trait. Results indicated that the detection power of the four putative QTL was consistently greater than 90% for component traits in simulated populations, each consisting of 200 recombinant inbred lines. Lower detection power and higher false discovery rate (FDR) were observed when derived traits were used. In an actual maize population, simulations were designed based on the observed QTL distributions and effects. When derived traits were used, QTL detected for both component and derived traits had comparable power, but those detected for component traits but not for derived traits had low detection power. The FDR from subtraction and division in the maize population were higher than the FDR from addition and multiplication. The use of derived traits increased the gene number, caused higher-order gene interactions than observed in component traits, and possibly complicated the linkage relationship between QTL as well. The increased complexity of the genetic architecture with derived traits may be responsible for the reduced detection power and the increased FDR. Derived-only QTL identified in practical genetic populations can be explained either as minor QTL that are not significant in QTL mapping of component traits, or as false positives.