Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2 population

A whole-genome scan was performed on 660 F₂ animals including 250 barrows and 410 gilts in a White Duroc × Erhualian intercross population to detect quantitative trait loci (QTL) for fatty acid composition in the longissimus dorsi muscle and abdominal fat. A total of 153 QTL including 63 genome-wide significant QTL and 90 suggestive effects were identified for the traits measured. Significant effects were mainly evident on pig chromosomes (SSC) 4, 7, 8 and X. No association was detected on SSC3 and 11. In general, the QTL detected in this study showed distinct effects on fatty acid composition in the longissimus muscle and abdominal fat. The QTL for fatty acid composition in abdominal fat did not correspond to those identified previously in backfat and the majority of QTL for the muscle fatty acid composition were mapped to chromosomal regions different from previous studies. Two regions on SSC4 and SSC7 showed significant pleiotropic effects on monounsaturated (MUFA) and polyunsaturated fatty acid (PUFA) in both longissimus muscle and abdominal fat. Another two QTL with significant multi-faceted effects on MUFA and PUFA in the longissimus muscle were found each on SSC8 and SSCX. Chinese Erhualian alleles were associated with increased ratios of MUFA to saturated fatty acid at most of the QTL detected, showing beneficial effect in terms of human health.     

Quantitative trait loci for litter size and prenatal loss in a White Duroc × Chinese Erhualian resource population

To detect quantitative trait loci (QTL) for litter size related traits, the total number of born piglets (TNB), the number of born alive piglets (NBA), the number of stillborn piglets (NSB) and the number of mummies (NM) at the first parity were recorded in 299 F₂ sows in a White Duroc × Chinese Erhualian intercross resource population. A whole genome scan was performed with 183 microsatellites distributed across 19 porcine chromosomes in the resource population, and the QTL analysis was performed with a least-squares method. A 5% genome-wide significant QTL was detected at 88 cM on pig chromosome (SSC) 15 for NBA, which also showed suggestive effect on TNB. In addition, four suggestive QTL were detected on SSC 6, 7, 8 and 15 for TNB, NBA or NSB. Two of the five QTL detected showed accordance with previous reports. No QTL was found for NM.     

A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Chinese Erhualian pigs have larger and floppier ears compared with White Duroc pigs (small, half- or fully-pricked ears). To identify quantitative trait loci (QTL) for ear weight and area as well as erectness, a genome-wide scan with 194 microsatellites was performed in a White Duroc × Chinese Erhualian resource population (>1000 F₂ animals). Twenty-three genome-wide significant QTL and 12 suggestive QTL were identified. All QTL for ear erectness and size detected in two previous studies, bar two on SSC6 and 9, were confirmed here. The 1% genome-wide significant QTL at 70 cM on SSC5 and at 58 cM on SSC7 have profound and pleiotropic effects on the three ear traits, with Erhualian alleles increasing weight and area but decreasing erectness. Notably, the 95% confidence interval of the QTL for weight and area on SSC7 spanned only 3 cM. New QTL reaching 1% genome-wide significance were found on SSC8 (at 37 cM) for all three ear traits, on SSC4 and 16 for weight and area, and on SSCX for area. Unexpectedly, Erhualian alleles at these loci were associated with lighter and smaller or erect ear. Some new suggestive QTL were also found on other chromosome regions. Almost all the QTL for weight and area had essentially additive effects, while the QTL for erectness on SSC2, 5 and 7 showed not only additive effects but also partial dominance effects of Erhualian alleles. The two most significant QTL on SSC7 and SSC5 could be promising targets for fine mapping and identification of the causative mutations.     

Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc × Chinese Erhualian resource population

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F₂ animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.     

Quantitative trait loci for performance traits in a broiler × layer cross

An F₂ resource population, derived from a broiler × layer cross, was used to map quantitative trait loci (QTL) for body weights at days 1, 35 and 41, weight gain, feed intake, feed efficiency from 35 to 41 days and intestinal length. Up to 577 F₂ chickens were genotyped with 103 genetic markers covering 21 linkage groups. A preliminary QTL mapping report using this same population focused exclusively on GGA1. Regression methods were applied to line-cross and half-sib models for QTL interval mapping. Under the line-cross model, eight QTL were detected for body weight at 35 days (GGA2, 3 and 4), body weight at 41 days (GGA2, 3, 4 and 10) and intestine length (GGA4). Under the half-sib model, using sire as common parent, five QTL were detected for body weight at day 1 (GGA3 and 18), body weight at 35 days (GGA2 and 3) and body weight at 41 days (GGA3). When dam was used as common parent, seven QTL were mapped for body weight at day 1 (GGA2), body weight at day 35 (GGA2, 3 and 4) and body weight at day 41 (GGA2, 3 and 4). Growth differences in chicken lines appear to be controlled by a chronological change in a limited number of chromosomal regions.     

Quantitative trait loci for red blood cell traits in swine

Haematological traits are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of erythroid traits is sparse, especially in swine. To identify QTL for erythroid traits in the pig, haematocrit (HCT), haemoglobin (HB), erythrocyte counts (RBC) and mean corpuscular haemoglobin content (MCHC) were measured in 139 F₂ pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana . The pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Forty-three single QTL controlling erythroid traits were identified on 16 chromosomes. Twelve of the QTL were significant at the genome-wide level while 31 were significant at a chromosome-wide level. Because erythroid traits varied with health and disease status, QTL influencing the erythroid phenotypes showed specific health/disease patterns. Regions on SSC5, 7, 8, 12 and 13 contained QTL for baseline erythroid traits, while the other QTL regions affected distinct stages of the disease model. Single QTL explained 9–17% of the phenotypic variance in the F₂ animals. Related traits were partly under common genetic influence. Our analysis confirms that erythroid trait variation differs between Meishan and Pietrain breeds and that this variation is associated with multiple chromosomal regions.     

Quantitative trait loci with effects on feed efficiency traits in Hereford × composite double backcross populations

Two half-sib families of backcross progeny were produced by mating F₁ Line 1 Hereford (L1) × composite gene combination (CGC) bulls with L1 and CGC cows. Feed intake and periodic weights were measured for 218 backcross progeny. These progenies were genotyped using 232 microsatellite markers that spanned the 29 BTA. Progeny from L1 and CGC females was analysed separately using composite interval mapping to find quantitative trait loci (QTL) affecting daily dry matter intake (DMI), average daily gain (ADG), feed conversion (FCR) and residual feed intake (RFI). Results from both backcrosses were pooled to find additional QTL. In the backcross to L1, QTL were detected for RFI and DMI on BTA11, FCR on BTA16, and ADG on BTA9. In the backcross to CGC, QTL were detected for RFI on BTA10, FCR on BTA12 and 16 and ADG on BTA15 and 17. After pooling, QTL were detected for RFI on BTA 2, 6, 7, 10, 11, 13 and 16; for FCR on BTA 9, 12, 16, 17 and 21; for ADG on BTA 9, 14, 15, 17; and for DMI on BTA 2, 5, 6, 9, 10, 11, 20 and 23.     

Quantitative trait loci for white blood cell numbers in swine

Differential white blood cell counts are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of leucocyte numbers and relationships is sparse, especially in swine. Total leucocyte numbers (Leu) and the differential leucocyte counts, i.e. the fractions of lymphocytes (Lym), polymorphonuclear leucocytes [neutrophils (Neu), eosinophils (Eos) and basophils (Bas)] and monocytes (Mon) were measured in 139 F₂ pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana for genome-wide quantitative trait loci (QTL) analysis. After infection, the pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Nine genome-wide significant and 29 putative, single QTL controlling leucocyte traits were identified on 15 chromosomes. Because leucocyte traits varied with health and disease status, QTL influencing the leucocyte phenotypes showed specific health/disease patterns. Regions on SSC1, 8 and 12 contained QTL for baseline leucocyte traits. Other QTL regions reached control on leucocyte traits only at distinct stages of the disease model. Two-thirds of the QTL have not been described before. Single QTL explained up to 19% of the phenotypic variance in the F₂ animals. Related traits were partly under common genetic influence. Our analysis confirms that leucocyte trait variation is associated with multiple chromosomal regions.     

Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar x Large White intercross

Here, we analysed quantitative trait loci (QTL) for fatty acid composition, one of the factors affecting fat quality, in a Japanese wild boar x Large White cross. We found 25 significant effects for 17 traits at 13 positions at the 5% genome-wise level, of which 16 effects for 12 traits at 10 positions were significant at the 1% level. QTL for saturated fatty acids (SFA) in back fat were mapped to swine (Sus scrofa) chromosomes (SSC) 1p, 9 and 15. QTL for unsaturated fatty acids in back fat were mapped to SSC1p, 1q, 4, 5, 9, 15 and 17. Using a regression model that fits back fat thickness as a covariate, two of the QTL for linoleic acid content on SSC4 and SSC17 were not significant, but one QTL for total SFA composition was detected on SSC5 with correction for back fat thickness. Wild boar alleles at six of seven QTL tended to increase SFAs and to decrease unsaturated fatty acids. QTL for fatty acid composition in perirenal fat were mapped on SSC2, 3, 4, 5, 6, 14, 16 and X. QTL for melting point (in back fat samples) were mapped on SSC1, 2 and 15. Wild boar alleles in QTL on SSC1 and SSC15 were associated with elevated melting points whereas those on SSC2 were associated with lower melting point measurements.     

Mapping of quantitative trait loci affecting eggshell quality on chromosome 9 in an F2 intercross between two chicken lines divergently selected for eggshell strength

Broken and cracked eggshells are major causes of significant economic losses to the egg production industry. The quantitative trait loci (QTL) on chromosome 9 influencing the quality of eggshells were identified by analysing an intercross between two parent lines developed from the same founder population by a two-way selection for eggshell strength with non-destructive deformation conducted over 14 generations. Chromosome-wide highly significant ( P  <   0.01) QTL associated with egg weight (EW), short length of egg (SLE), long length of egg (LLE) and eggshell weight were mapped to the distal region of chromosome 9. Among the QTL affecting EW, SLE and LLE, ovocalyxin-32 was identified as a potential candidate gene influencing eggshell traits. Marker-assisted selection based on these QTL could be used to develop strategies for reducing the breakage and cracking of eggs in commercial layer houses.     

Quantitative trait loci with additive effects on growth and carcass traits in a Wagyu-Limousin F2 population

A whole-genome scan for carcass traits [average daily gain during the pre-weaning, growth and finishing periods; birth weight; hot carcass weight and longissimus muscle area (LMA)] was performed on 328 F(2) progeny produced from Wagyu x Limousin-cross parents derived from eight founder Wagyu bulls. Nine significant (P 相似文献   

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits

A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F₂ population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome‐wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome‐wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken.     

Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein × Jersey crossbred population

We herein report results from a daughter design genome-scan study aiming to identify quantitative trait loci (QTL) associated with birth weight, direct gestation length and passive immune transfer in a backcross (Holstein × Jersey) × Holstein population. Two-hundred and seventy-six calves, offspring of seven crossbred sires, were genotyped for 161 microsatellite markers distributed along the 29 bovine autosomes. The genome scan was performed through interval mapping using an animal model in order to identify QTL accounting for phenotypic differences between individual animals. Based on significant chi-squared values, we identified putative QTL on BTA7 and BTA14 for gestation length, on BTA2, BTA6 and BTA14 for birth weight and on BTA20 for passive immune transfer. In total, these QTL accounted for 12%, 18% and 1% of the phenotypic variance in gestation length, birth weight and passive immune transfer respectively. We also report results from a supplementary and independent influential grand-daughter Holstein family. In this family, findings on BTA7 and BTA14 for direct gestation length were in agreement with results in the crossbred population. Two other regions on BTA6 and BTA21 putatively underlying QTL for direct gestation length variability were discovered with this analysis.     

A linkage map of the porcine genome from a large-scale White Duroc × Erhualian resource population and evaluation of factors affecting recombination rates

A porcine genome linkage map composed of 194 microsatellite markers was constructed with a large-scale White Duroc × Erhualian resource population. The marker order on this linkage map was consistent with the USDA-MARC reference map except for two markers on SSC3, two markers on SSC13 and two markers on SSCX. The length of the sex-averaged map (2344.9 cM) was nearly the same as that of the USDA-MARC and NIAI map. Highly significant heterogeneity in recombination rates between sexes was observed. Except for SSC1 and SSC13, the female autosomes had higher average recombination rates than the male autosomes. Moreover, recombination rates in the pseudoautosomal region were greater in males than in females. These observations are consistent with those of previous reports. The recombination rates on each paternal and maternal chromosome of F₂ animals were calculated. Recombination rates were not significantly affected by the age (in days) or parity of the F₁ animals. However, recombination rates on paternal chromosomes were affected by the mating season of the F₁ animals. This could represent an effect of environmental temperature on spermatogenesis.     

Quantitative trait loci affecting eggshell traits in an F(2) population

Good eggshell quality is important for both table egg quality and chicken reproductive performance. Weak eggshells cause economic losses in all production steps. Poor eggshell quality also poses increased risk for Salmonella infections. Eggshell quality has been a difficult trait to improve by traditional breeding, as it can be measured only for females and it is difficult and expensive to measure. Breeding for improved shell quality may therefore benefit from the use of marker-assisted selection. In an effort to find markers linked to eggshell quality, we have used an F(2) population of 668 females to map quantitative trait loci (QTL) affecting eggshell traits (eggshell deformation, breaking force, weight). By using 160 microsatellite markers on 27 chromosomes, we found 11 genome-wide and 15 suggestive QTL for shell traits measured at different times during production. Loci affecting the deformation were found on chromosomes 1, 2, 6, 10, 14 and Z. Loci affecting the breaking force were detected on chromosomes 2, 3, 10, 12 and Z. Loci affecting the shell weight were detected on chromosomes 6, 12, 24 and Z. Each QTL explains between 1.5% and 4.6% of the phenotypic variance, adding up to 10-15% of total phenotypic variance explained for the different traits. No epistatic effects were observed between loci affecting eggshell traits. Because the effects for quality are mainly additive, these results provide a basis for further characterization of the loci to identify closely linked markers to be used in marker-assisted selection.     

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.     

Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens

We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F₂ hens derived from an intercross between the Oh‐Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main‐effect QTL for AFE on chromosome 1 and four main‐effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome‐wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26–34 weeks of hen age) and the remaining one was discovered at the late stage (54–58 weeks). The alleles at the two EPR QTL derived from the Oh‐Shamo breed unexpectedly increased the trait values, irrespective of the Oh‐Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh‐Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main‐effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4–8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.     

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.     

Mapping of quantitative trait loci for clinical–chemical traits in swine

Clinical–chemical traits are diagnostic parameters essential for characterization of health and disease in veterinary practice. The traits show significant variability and are under genetic control, but little is known about the fundamental genetic architecture of this variability, especially in swine. We have identified QTL for alkaline phosphatase (ALP), lactate (LAC), bilirubin (BIL), creatinine (CRE) and ionized sodium (Na⁺), potassium (K⁺) and calcium (Ca⁺⁺) from the serum of 139 F₂ pigs from a Meishan/Pietrain family before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. After infection, the pigs passed through three stages representing acute disease, subclinical disease and chronic disease. Forty-two QTL influencing clinical–chemical traits during these different stages were identified on 15 chromosomes. Eleven of the QTL were significant on a genome-wide level; 31 QTL were chromosome-wide significant. QTL showed specific health/disease patterns with respect to the baseline values of the traits as well as the values obtained through the different stages of disease. QTL influencing different traits at different times were found primarily on chromosomes 1, 3, 7 and 14. The most prominent QTL for the investigated clinical–chemical traits mapped to SSC3 and 7. Baseline traits of ALP, LAC, BIL, Ca⁺⁺ and K⁺ were influenced by QTL regions on SSC3, 6, 7, 8 and 13. Single QTL explained up to 21.7% of F₂ phenotypic variance. Our analysis confirms that variation of clinical–chemical traits is associated with multiple chromosomal regions.     

Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population

A whole-genome scan was conducted on 328 F(2) progeny in a Wagyu x Limousin cross to identify quantitative trait loci (QTL) affecting palatability and fatty acid composition of beef at an age-constant endpoint. We have identified seven QTL on five chromosomes involved in lipid metabolism and tenderness. None of the genes encoding major enzymes involved in fatty acid metabolism, such as fatty acid synthase (FASN), acetyl-CoA carboxylase alpha (ACACA), solute carrier family 2 (facilitated glucose transporter) member 4 (SLC2A4), stearoyl-CoA desaturase (SCD) and genes encoding the subunits of fatty acid elongase, was located in these QTL regions. The present study may lead to a better-tasting and healthier product for consumers through improved selection for palatability and lipid content of beef.