Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar × Meishan F₂ family to the chromosome X region flanked by SW2456 and SW1943 . Improved QTL resolution was possible using data for F₂ animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR , SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F -ratio values for all QTL. Maxima of F -ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F₂ phenotypic variance (VF₂) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4 , with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR . An analysis performed separately for F₂ male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF₂) near AR and two QTL for muscling traits (up to 9.9% VF₂) mapped close to ACSL4 . In the F₂ female animals, QTL affecting muscling (up to 12.1% VF₂) mapped at ACSL4 and SW2456 , and QTL for fat deposition (10% VF₂) and growth (up to 10.5% VF₂) mapped at ACSL4 .     

Identification of chromosomal regions associated with growth and carcass traits in an F3 full sib intercross line originating from a cross of chicken lines divergently selected on body weight

An F₃ resource population originating from a cross between two divergently selected lines for high (D+ line) or low (D− line) body weight at 8-weeks of age (BW55) was generated and used for Quantitative Trait Locus (QTL) mapping. From an initial cross of two founder F₀ animals from D(+) and D(−) lines, progeny were randomly intercrossed over two generations following a full sib intercross line (FSIL) design. One hundred and seventy-five genome-wide polymorphic markers were employed in the DNA pooling and selective genotyping of F₃ to identify markers with significant effects on BW55. Fifty-three markers on GGA2, 5 and 11 were then genotyped in the whole F₃ population of 503 birds, where interval mapping with GridQTL software was employed. Eighteen QTL for body weight, carcass traits and some internal organ weights were identified. On GGA2, a comparison between 2-QTL vs. 1-QTL analysis revealed two separate QTL regions for body, feet, breast muscle and carcass weight. Given co-localization of QTL for some highly correlated traits, we concluded that there were 11 distinct QTL mapped. Four QTL localized to already mapped QTL from other studies, but seven QTL have not been previously reported and are hence novel and unique to our selection line. This study provides a low resolution QTL map for various traits and establishes a genetic resource for future fine-mapping and positional cloning in the advanced FSIL generations.     

A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach

Quantitative trait loci (QTL) influencing the weight of abdominal fat (AF) and of breast muscle (BM) were detected on chicken chromosome 5 (GGA5) using two successive F₂ crosses between two divergently selected 'Fat' and 'Lean' INRA broiler lines. Based on these results, the aim of the present study was to identify the number, location and effects of these putative QTL by performing multitrait and multi-QTL analyses of the whole available data set. Data concerned 1186 F₂ offspring produced by 10 F₁ sires and 85 F₁ dams. AF and BM traits were measured on F₂ animals at slaughter, at 8 (first cross) or 9 (second cross) weeks of age. The F₀, F₁ and F₂ birds were genotyped for 11 microsatellite markers evenly spaced along GGA5. Before QTL detection, phenotypes were adjusted for the fixed effects of sex, F₂ design, hatching group within the design, and for body weight as a covariable. Univariate analyses confirmed the QTL segregation for AF and BM on GGA5 in male offspring, but not in female offspring. Analyses of male offspring data using multitrait and linked-QTL models led us to conclude the presence of two QTL on the distal part of GGA5, each controlling one trait. Linked QTL models were applied after correction of phenotypic values for the effects of these distal QTL. Several QTL for AF and BM were then discovered in the central region of GGA5, splitting one large QTL region for AF into several distinct QTL. Neither the 'Fat' nor the 'Lean' line appeared to be fixed for any QTL genotype. These results have important implications for prospective fine mapping studies and for the identification of underlying genes and causal mutations.     

A major QTL for acute ethanol sensitivity in the alcohol tolerant and non-tolerant selected rat lines

The Alcohol Tolerant and Alcohol Non-Tolerant rats (AT, ANT) were selectively bred for ethanol-induced ataxia as measured on the inclined plane. Here we report on a quantitative trait locus (QTL) study in an F₂ intercross population derived from inbred AT and ANT (IAT, IANT) and a follow-up study of congenics that were bred to examine one of the mapped QTLs. Over 1200 F₂ offspring were tested for inclined plane sensitivity, acute tolerance on the inclined plane, duration of the loss of righting reflex (LORR) and blood ethanol at regain of the righting reflex (BECRR). F₂ rats that were in the upper and lower 20% for inclined plane sensitivity were genotyped with 78 SSLP markers. Significant QTLs for inclined plane sensitivity were mapped on chromosomes 8 and 20; suggestive QTLs were mapped on chromosomes 1, 2 and 3. Highly significant QTLs for LORR duration (LOD = 12.4) and BECRR (LOD = 5.7) were mapped to the same locus on chromosome 1. Breeding and testing of reciprocal congenic lines confirmed the chromosome 1 LORR/BECRR QTL. A series of recombinant congenic sub-lines were bred to fine-map this QTL. Current results have narrowed the QTL to an interval of between 5 and 20 Mb. We expect to be able to narrow the interval to less than 5 Mb with additional genotyping and continued breeding of recombinant sub-congenic lines.     

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 associated with fatness in a broiler–layer cross

An F₂ population established by crossing a broiler male line and a layer line was used to map quantitative trait loci (QTL) affecting abdominal fat weight, abdominal fat percentage and serum cholesterol and triglyceride concentrations. Two genetic models, the line-cross and the half-sib, were applied in the QTL analysis, both using the regression interval method. Three significant QTL and four suggestive QTL were mapped in the line-cross analysis and four significant and four suggestive QTL were mapped in the half-sib analysis. A total of five QTL were mapped for abdominal fat weight, six for abdominal fat percentage and four for triglyceride concentration in both analyses. New QTL associated with serum triglyceride concentration were mapped on GGA5, GGA23 and GG27. QTL mapped between markers LEI0029 and ADL0371 on GGA3 for abdominal fat percentage and abdominal fat weight and a suggestive QTL on GGA12 for abdominal fat percentage showed significant parent-of-origin effects. Some QTL mapped here match QTL regions mapped in previous studies using different populations, suggesting good candidate regions for fine-mapping and candidate gene searches.     

Mapping of quantitative trait loci on porcine chromosome 4

A F₂ population derived from a cross between European Large White and Chinese Meishan pigs was established in order to study the genetic basis of breed differences for growth and fat traits. Chromosome 4 was chosen for initial study as previous work had revealed quantitative trait loci (QTLs) on this chromosome affected growth and fat traits in a Wild Boar × Large White cross. Individuals in the F₂ population were typed for nine markers spanning a region of approximately 124 c m . We found evidence for QTLs affecting growth between weaning and the end of test (additive effect: 43·4 g/day) and fat depth measured in the mid-back position (additive effect: 1·82 mm). There was no evidence of interactions between the QTLs and sex, grandparents or F₁ sires, suggesting that the detected QTLs were fixed for alternative alleles in the Meishan and Large White breeds. Comparison of locations suggests that these QTLs could be the same as those found in the Wild Boar × Large White cross.     

Mapping quantitative trait loci regulating chicken body composition traits

Genome scans were conducted on an F₂ resource population derived from intercross of the White Plymouth Rock with the Silkies Fowl to detect QTL affecting chicken body composition traits. The population was genotyped with 129 microsatellite markers and phenotyped for 12 body composition traits on 238 F₂ individuals from 15 full-sib families. In total, 21 genome-wide QTL were found to be responsible for 11 traits, including two newly studied traits of proventriculus weight and shank girth. Three QTL were genome-wide significant: at 499 c m on GGA1 (explained 3.6% of phenotypic variance, P  < 0.01) and 51 c m on GGA5 (explained 3.3% of phenotypic variance, P  < 0.05) for the shank & claw weight and 502 c m on GGA1 (explained 1.4% of phenotypic variance, P  < 0.05) for wing weight. The QTL on GGA1 seemed to have pleiotropic effects, also affecting gizzard weight at 490 c m , shank girth at 489 c m and intestine length at 481 c m . It is suggested that further efforts be made to understand the possible pleiotropic effects of the QTL on GGA1 and that on GGA5 for two shank-related traits.     

Serum albumin polymorphism and its relationship to economic traits in crossbred cattle

The serum albumin genotypes of 65 Jersey × Hariana (F₁), 75 Holstein Friesian × Hariana (F₁) and 47 Brown Swiss × Hariana (F₁) crossbred cows were determined by starch gel electrophoresis. Two albumin alleles Alb^F and Alb^s , but only either as Alb^F homozygotes or Alb^Fs heterozygotes, were observed amongst these animals. There were no Alb^S homozygotes or other genotypes. Highly significant relationships between albumin genotypes and both birth weights and first-lactation milk yields of these cows were observed. The Alb^F allele was associated with increased milk yield and greater birth weights.     

Accumulation and utilization of triacylglycerol and polysaccharides in Liposcelis bostrychophila (Psocoptera, Liposcelididae) selected for resistance to carbon dioxide

Abstract: Two populations of the psocid, Liposcelis bostrychophila Badonnel, were exposed to two CO₂-enriched atmospheres (35% CO₂ + 21% O₂, and 55% CO₂ + 21% O₂, balance N₂) for 30 generations. Controls were reared in normal atmospheres. The reserves of triacylglycerol and polysaccharides were evaluated in adults of the two experimental and the control populations in generations F₁₅ and F₃₀. The utilization rate of triacylglycerol and polysaccharides in the CO₂-enriched atmospheres were also determined in generation F₃₀. The results indicated that the reserves of triacylglycerol and polysaccharides increased significantly during selection for CO₂ resistance; the higher the resistance level, the greater the reserves. Exposure of these populations to controlled atmosphere was associated with a steady utilization of the reserves. By contrast, the unselected population responded to controlled atmospheres by accelerated utilization of triacylglycerol and polysaccharides. Comparison of the utilization rates during CO₂ exposure showed that triacylglycerol is the main energy source, and polysaccharides contribute to metabolic energy supply only to a small extent.     

Sex ratio bias in the F1 adult progeny of African rice gall midge, Orseolia oryzivora H. and G. (Dipt., Cecidomyiidae)

Abstract:  Against the background of conflicting reports of variable sex ratio distribution in different populations of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagne, the number and sex ratios of F₁ adult progeny produced per female from wild and screen house populations were investigated in the screen house at 27 ± 3°C, 60–70% relative humidity and 12 : 12 h (light : dark) photoperiod. Results indicated the occurrence of a single sex-biased ratio in all the F₁ adult progeny produced per female of this pest. Regardless of the source, whether from wild or screen house population, each mated female AfRGM produced a full complement of either sex only but never both. The difference between the number of eggs laid and F₁ adult progeny that emerged per female from wild and screen house populations was not significant (P > 0.05), indicating consistency in the occurrence of this phenomenon among AfRGM populations. The reason for this could not be ascertained in this study but AfRGM eggs must be fertilized for development and eclosion to occur. No F₂ adults emerged when a cohort of emergents from the same female were allowed to re-infest susceptible seedlings, indicating absence of parthenogenesis.     

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.     

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.     

Heritabilities and quantitative trait loci for blood gases and blood pH in swine

Maintaining pH and blood gases in a narrow range is essential to sustain normal biochemical reactions. Decreased oxygenation, poor tissue perfusion, disturbance to CO₂ expiration, and shortage of HCO₃⁻ can lead to metabolic acidosis. This is a common situation in swine, and originates from a broad range of medical conditions. pH and blood gases appear to be under genetic control, and populations with physiological traits closer to the pathological thresholds may be more susceptible to developing pathological conditions. However, little is known about the genetic basis of such traits. We have therefore estimated phenotypic and genetic variability and identified quantitative trait loci (QTL) for pH and blood gases in blood samples from 139 F₂ pigs from the Meishan/Pietrain family. Samples were taken before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. Twenty-seven QTL influencing pH and blood gases were identified on nine chromosomes. Five of the QTL were significant on a genome-wide level; 22 QTL were significant on a chromosome-wide level. QTL for pH-associated traits have been mapped to SSC3, 18 and X. QTL associated with CO₂ have been detected on SSC6, 7, 8 and 9, and QTL associated with O₂ on SSC2 and SSC8. QTL showed specific health/disease patterns that were related to the physiological state of the pigs from day 0, to acute disease (day 14), convalescence (day 28) and chronic disease (day 42). The results demonstrate that pH and blood gases are influenced by multiple chromosomal areas, each with relatively small effects.     

Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population

Genome-wide association studies have become possible in the chicken because of the recent availability of the complete genome sequence, a polymorphism map and high-density single nucleotide polymorphism (SNP) genotyping platforms. We used these tools to study the genetic basis of a very high level of heterosis that was previously observed for fatness in two F₂ populations established by crossing one outbred broiler (meat-type) sire with dams from two unrelated, highly inbred, light-bodied lines (Fayoumi and Leghorn). In each F₂ population, selective genotyping was carried out using phenotypically extreme males for abdominal fat percentage (AF) and about 3000 SNPs. Single-point association analysis of about 500 informative SNPs per cross showed significant association ( P  < 0.01) of 15 and 24 markers with AF in the Broiler × Fayoumi and Broiler × Leghorn crosses respectively. These SNPs were on 10 chromosomes (GGA1, 2, 3, 4, 7, 8, 10, 12, 15 and 27). Interestingly, of the 39 SNPs that were significantly associated with AF, there were about twice as many homozygous genotypes associated with higher AF that traced back to the inbred lines alleles, although the broiler line had on average higher AF. These SNPs are considered to be associated with QTL with cryptic alleles. This study reveals cryptic alleles as an important factor in heterosis for fatness observed in two chicken F₂ populations, and suggests epistasis as the common underlying mechanism for heterosis and cryptic allele expression. The results of this study also demonstrate the power of high marker-density SNP association studies in discovering QTL that were not detected by previous microsatellite-based genotyping studies.     

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.     

Geographic variation and genetic aspects of reproductive diapause in Drosophila triauraria and D. quadraria

ABSTRACT. Geographic variation and genetic aspect of reproductive diapause were studied in Drosophila triauraria Bock & Wheeler and D. quadraria Bock & Wheeler, in relation to their quantitative response to photoperiods. D. quadraria from the subtropical region had no photoperiodic diapause. In D. triauraria strains, diapause was induced under LD 10:14 or 12:12, but not under LD 14:10 or longer photoperiods. Their diapause was induced more effectively and maintained longer by LD 10:14 than by LD 12:12. The duration of diapause was longer in a northern strain, but the diapause inducing process varied little among different geographical strains. Diapause incidence was 50% or lower in F₁ hybrids between D. triauraria and D. quadraria and backcross progenies between F₁ and D. quadraria , and about 70% in backcross progenies between F₁ and D. triauraria under LD 10:14, but very low under LD 12:12. The lower incidence of diapause in these F; and backcross progenies is assumed to be due to the less efficient induction of diapause, since once diapause was induced in them, it was maintained for a long time, especially in the backcross progenies between F₁ and D. triauraria. These experiments suggest that diapause induction and maintenance are different physiological processes controlled by different genetic systems.     

Two consensus quantitative trait loci clusters controlling anthesis–silking interval, ear setting and grain yield might be related with drought tolerance in maize

Unravelling the molecular basis of drought tolerance will provide novel opportunities for improving crop yield under water-limited conditions. The present study was conducted to identify quantitative trait loci (QTLs) controlling anthesis–silking interval (ASI), ear setting percentage (ESP) and grain yield (GY). The mapping population included 234 F₂ plants derived from the cross X178 (drought tolerant) × B73 (drought susceptible). The corresponding F_2:3 progenies, along with their parents, were evaluated for the above-mentioned traits under both well-watered and water-stressed field conditions in three different trials carried out in central and southern China. Interval mapping and composite interval mapping identified 45 and 65 QTLs for the investigated traits, respectively. Two QTL clusters influencing ASI and ESP on chromosomes 1 (bin 1.03) and 9 (bins 9.03–9.05) were identified in more than two environments, showing sizeable additive effects and contribution to phenotypic variance; these two QTL clusters influenced GY only in one environment. No significant interaction was detected between the two genomic regions. A comparative analysis of these two QTL clusters with the QTLs controlling maize drought tolerance previously described in three mapping populations confirmed and extended their relevance for marker-assisted breeding to improve maize production under water-limited conditions.     

Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana

Recombinant inbred (RI) lines of Arabidopsis thaliana (Arabidopsis) have been generated from a cross between the ecotypes Landsberg erecta and Columbia. Progeny of 300 individual F₂ seedlings were taken by single seed descent to the F₈ generation. Sixty-seven loci, scored using 64 RFLP probes and one phenotypic marker, chosen at approximately 20 cM intervals from the two previously published RFLP maps, were mapped using 100 of these RI lines. More than 500 other new loci are currently being mapped using these RI lines by several other groups. These 100 RI lines thus provide the material to map new probes or phenotypic traits polymorphic between Landsberg erecta and Columbia, relative to an increasing number of molecular markers. Higher resolution mapping of distinct chromosomal regions can be achieved by analysing the segregation of particular markers on the additional 200 RI lines.     

QTL for resistance to Salmonella carrier state confirmed in both experimental and commercial chicken lines

The ability of chickens to carry Salmonella without displaying disease symptoms is responsible for Salmonella propagation in poultry stocks and for subsequent human contamination through the consumption of contaminated eggs or meat. The selection of animals more resistant to carrier state might be a way to decrease the propagation of Salmonella in poultry stocks and its transmission to humans. Five QTL controlling variation for resistance to carrier state in a chicken F₂ progeny derived from the White Leghorn inbred lines N and 6₁ had been previously identified using a selective genotyping approach. Here, a second analysis on the whole progeny was performed, which led to the confirmation of two QTL on chromosomes 2 and 16. To assess the utility of these genomic regions for selection in commercial lines, we tested them together with other QTL identified in an [N×6₁] × N backcross progeny and with the candidate genes SLC11A1 and TLR4 . We used a commercial line divergently selected for either low or high carrier-state resistance both in young chicks and in adult hens. In divergent chick lines, one QTL on chromosome 1 and one in the SLC11A1 region were significantly associated with carrier-state resistance variations; in divergent adult lines, one QTL located in the major histocompatibility complex on chromosome 16 and one in the SLC11A1 region were involved in these variations. Genetic studies conducted on experimental lines can therefore be of potential interest for marker-assisted selection in commercial lines.