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.     

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant ( P  <   0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.     

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.     

Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa

A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines.     

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.     

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.     

Genetic mapping of quantitative trait loci affecting carcass and meat quality traits in Beijing ducks (Anas platyrhynchos)

Quantitative trait loci (QTL) for carcass and meat quality traits were detected in a sample of 224 progeny from four males in line VI and 12 females in line V of Beijing ducks. These lines were selected for high body weight at 42 days of age (line VI) or high egg production at 360 days of age (line V). Traits were weights of the carcass, head, neck, shanks, wings, legs, thighs, breast, heart, liver, crop, gizzard, abdominal fat (AFW) and skin fat, as well as fat thickness in the tail, and pH value, shear force, drip loss (DL) (%) and cooking loss (CL) (%) of the breast. Using a half-sib analysis with a multiple QTL model, linkage between the carcass and meat quality traits and 95 microsatellite markers was investigated. Eight genome-wide significant QTL for weight of crop, skin fat, liver, neck, shanks, wings, DL were detected on linkage groups CAU4 and CAU6. One genome-wide suggestive QTL and one chromosome-wide significant QTL for weight of breast were found on CAU1 and CAU4 respectively. Fifteen chromosome-wide suggestive QTL influencing weight of AFW, breast, crop, heart, carcass, thighs, liver, shanks, gizzard, fat thickness in tail, DL (%) and CL (%) were mapped on CAU2, CAU4, CAU5, CAU6, CAU7, CAU10 and CAU13. In addition, two linked QTL for weight of liver and DL (%) were located on CAU2 and CAU7 respectively. The detection of QTL in ducks is a step towards identification of genes influencing these traits and their use for genetic improvement in this species.     

Detection of quantitative trait loci for carcass composition traits in pigs

A quantitative trait locus (QTL) analysis of carcass composition data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained.     

Quantitative trait loci mapping in dairy cattle: review and meta-analysis

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).     

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.     

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.     

Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake

In this study, quantitative trait loci (QTL) for chemical and physical body composition, growth and feed intake in pigs were identified in a three-generation full-sib population, developed by crossing Pietrain sires with a commercial dam line. Phenotypic data from 315 F₂ animals were available for protein and lipid deposition measured in live animals by the deuterium dilution technique at 30-, 60-, 90-, 120- and 140-kg body weight. At 140-kg body weight, carcass characteristics were measured by the AutoFOM grading system and after dissection. Three hundred and eighty-six animals from 49 families were genotyped for 51 molecular markers covering chromosomes SSC2, SSC4, SSC8, SSC9, SSC10 and SSC14. Novel QTL for protein (lipid) content at 60-kg body weight and protein (lipid) accretion from 120 to 140 kg were detected on SSC9 near several previously detected QTL for lean and fat tissue in neck, shoulder and ham cuts. Another QTL for lipid accretion was found on SSC8, closely associated with a QTL for intramuscular fat content. QTL for daily feed intake were detected on SSC2 and SSC10. The favourable allele of a QTL for food conversion ratio (FCR) on SSC2 was associated with alleles for increased lean tissue and decreased fat tissue. Because no QTL for growth rate were found in the region, the QTL for FCR is most likely due to a change in body composition. These QTL provide insights into the genomic regulation of chemical or physical body composition and its association with feed intake, feed efficiency and growth.     

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 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.     

Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross

A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%.     

Quantitative trait loci for porcine white blood cells and platelet-related traits in a White Duroc × Erhualian F2 resource population

White blood cell count and platelets are implicated as risk factors for common complex diseases. Genetic factors substantially affect these traits in humans and mice. However, little is known about the genetic architecture of these traits in pigs. To identify quantitative trait loci (QTL) for leucocyte- and platelet-related traits in pigs, the total leucocyte number and differential leucocyte counts including the fraction of basophils, eosinophils, lymphocytes, monocytes, neutrophils, and a series of platelet parameters including platelet count, mean platelet volume, platelet distribution width and plateletcrit were measured in 1033 F₂ animals on 240 days from a White Duroc × Erhualian intercross resource population. A total of 183 informative microsatellites distributed across 19 pig chromosomes (SSC) were genotyped across the entire resource population. Thirty-three QTL were identified for the examined traits, including eight genome-wide significant QTL for white blood cells and differential leucocyte counts on SSC2, 7, 8, 12 and 15 and six significant QTL for platelet-related traits on SSC2, 8, 13 and X. Erhualian or White Duroc alleles were not systematically associated with increased phenotypic values. These results not only confirmed many QTL identified previously in the mouse and swine, but also revealed a number of novel QTL for the traits recorded. Moreover, it is the first time that QTL for platelet-related traits in pigs have been reported.     

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.     

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.     

Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa

Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway.