A genome-wide scan for quantitative trait loci affecting serum glucose and lipids in a White Duroc × Erhualian intercross F2 population

Serum glucose and lipid levels are associated with diabetes mellitus and cardiovascular disease. The purpose of this study was to identify quantitative trait loci (QTL) for serum glucose and lipids in a White Duroc × Erhualian resource population. Serum glucose, glycosylated serum proteins (GSP), and serum lipid levels were measured in a total of 760 F₂ animals at 240 days. Strong positive correlations were observed between total cholesterol (TC) and low-density-lipoprotein cholesterol (LDL-C)/high-density-lipoprotein cholesterol (HDL-C). A whole-genome scan was performed with 194 microsatellites covering the pig genome across the entire resource population, revealing 2 QTL for serum glucose and 15 QTL for serum lipids. Of them, three 1% genome-wide significant QTL were identified for LDL-C, TC, and triglycerides (TG) in an adjacent region (67–73 cM) on chromosome 2 (SSC2), and the QTL for LDL-C showed the largest effect with a 95% confidence interval of 5 cM. Another 1% genome-wide significant QTL was found for LDL-C at 87 cM on SSC8. Other QTL showed 5% genome-wide significant or suggestive effects on SSC4, 5, 7, 9, 11, 14, and 15. In total, five significant QTL for serum lipids and a suggestive QTL for GSP on SSC4 were identified for the first time in pigs. Most of the identified QTL are homologous to the previously reported QTL for serum lipids in humans and mice. As correlated traits, QTL for TC and LDL-C were always located in the same genomic regions. The results shed new light on studies of human atherosclerosis and cardiovascular-related diseases. R. Chen, J. Ren, and W. Li contributed equally to this work.     

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F2 sows from a White Duroc × Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r = -0.13, P < 0.05). Three QTL were detected on pig chromosome (SSC)2, 8 and 12 for gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13.     

Mapping and fine mapping of quantitative trait loci for the number of vertebrae in a White Duroc × Chinese Erhualian intercross resource population

The number of vertebrae is associated with body size and meat production in pigs. To identify quantitative trait loci (QTL) for the number of vertebrae, phenotypic values were measured in 1029 individuals from a White Duroc × Chinese Erhualian intercross F₂ population. A whole genome scan was performed with 194 microsatellite markers in the F₂ population. Four genome‐wide significant QTL and eight chromosome‐wide significant QTL for the number of vertebrae were identified on pig chromosomes (SSC) 1, 2, 6, 7, 10 and 12. The most significant QTL was detected on SSC7 with a confidence interval of 1 cM, explaining 42.32% of the phenotypic variance in the thoracic vertebral number. The significant QTL on SSC1, 2 and 7 confirmed previous reports. A panel of 276 animals representing seven Western and Chinese breeds was genotyped with 34 microsatellite markers in the SSC7 QTL region. No obvious selective sweep effect was observed in the tested breeds, indicating that intensive selection for enlarged body size in Western commercial breeds did not wipe out the genetic variability in the QTL region. The Q alleles for increased vertebral number originated from both Chinese Erhualian and White Duroc founder animals. A haplotype block of approximately 900 kb was found to be shared by all Q‐bearing chromosomes of F₁ sires except for one distinct Q chromosome. The critical region harbours the newly reported VRTN gene associated with vertebral number. Further investigations are required to confirm whether VRTN or two other positional candidate genes, PROX2 and FOS, cause the QTL effect.     

Detection of quantitative trait loci for porcine susceptibility to enterotoxigenic Escherichia coli F41 in a White Duroc × Chinese Erhualian resource population

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in neonatal and postweaning pigs. F41 is one of ETEC fimbriae that adhere to the small intestinal epithelium and lead to development of diarrhoea. The genetic architecture of susceptibility to ETEC F41 remains elusive in pigs. In this study, we determined the in vitro adhesion phenotypes of ETEC F41 in a total of 835 F2 animals from a White Duroc × Erhualian intercross, and performed a genome scan using both F2 and half-sib analyses with 183 microsatellite markers to detect quantitative trait loci (QTL) for porcine susceptibility to ETEC F41. The two analyses consistently revealed a 1% genome-wide significant QTL on pig chromosome 4. Moreover, we determined F41 adhesion phenotypes in 14 purebred Erhualian and 14 White Duroc pigs. The results showed that both the founder breeds are segregating for the F41 adhesion phenotype, while less percentage of Erhualian pigs were adhesive to ETEC F41 compared to White Duroc pigs.     

Detection of quantitative trait loci for growth- and fatness-related traits in a large-scale White Duroc × Erhualian intercross pig population

Growth and fatness are economically important traits in pigs. In this study, a genome scan was performed to detect quantitative trait loci (QTL) for 14 growth and fatness traits related to body weight, backfat thickness and fat weight in a large-scale White Duroc × Erhualian F(2) intercross. A total of 76 genome-wide significant QTL were mapped to 16 chromosomes. The most significant QTL was found on pig chromosome (SSC) 7 for fatness with unexpectedly small confidence intervals of ～2 cM, providing an excellent starting point to identify causal variants. Common QTL for both fatness and growth traits were found on SSC4, 5, 7 and 8, and shared QTL for fat deposition were detected on SSC1, 2 and X. Time-series analysis of QTL for body weight at six growth stages revealed the continuously significant effects of the QTL on SSC4 at the fattening period and the temporal-specific expression of the QTL on SSC7 at the foetus and fattening stages. For fatness traits, Chinese Erhualian alleles were associated with increased fat deposition except that at the major QTL on SSC7. For growth traits, most of White Duroc alleles enhanced growth rates except for those at three significant QTL on SSC6, 7 and 9. The results confirmed many previously reported QTL and also detected novel QTL, revealing the complexity of the genetic basis of growth and fatness in pigs.     

A genome-wide scan for quantitative trait loci affecting limb bone lengths and areal bone mineral density of the distal femur in a White Duroc × Erhualian F<Subscript>2</Subscript> population

Background

Limb bone lengths and bone mineral density (BMD) have been used to assess the bone growth and the risk of bone fractures in pigs, respectively. It has been suggested that limb bone lengths and BMD are under genetic control. However, the knowledge about the genetic basis of the limb bone lengths and mineralisatinon is limited in pigs. The aim of this study was to identify quantitative trait loci (QTL) affecting limb bone lengths and BMD of the distal femur in a White Duroc × Erhualian resource population.

Results

Limb bone lengths and femoral bone mineral density (fBMD) were measured in a total of 1021 and 116 F₂ animals, respectively. There were strong positive correlations among the lengths of limb bones and medium positive correlations between the lengths of limb bones and fBMD. A whole-genome scan involving 183 microsatellite markers across the pig genome revealed 35 QTL for the limb bone lengths and 2 for femoral BMD. The most significant QTL for the lengths of five limb bones were mapped on two chromosomes affecting all 5 limb bones traits. One was detected around 57 cM on pig chromosome (SSC) 7 with the largest F-value of more than 26 and 95% confidence intervals of less than 5 cM, providing a crucial start point to identify the causal genes for these traits. The Erhualian alleles were associated with longer limb bones. The other was located on SSCX with a peak at 50–53 cM, whereas alleles from the White Duroc breed increased the bone length. Many QTL identified are homologous to the human genomic regions containing QTL for bone-related traits and a list of interesting candidate genes.

Conclusion

This study detected the QTL for the lengths of scapula, ulna, humerus and tibia and fBMD in the pig for the first time. Moreover, several new QTL for the pig femoral length were found. As correlated traits, QTL for the lengths of five limb bones were mainly located in the same genomic regions. The most promising QTL for the lengths of five limb bones on SSC7 merits further investigation.

     

Genome-wide identification of QTL for age at puberty in gilts using a large intercross F2 population between White Duroc × Erhualian

Puberty is a fundamental development process experienced by all reproductively competent adults, yet the specific factors regulating age at puberty remain elusive in pigs. In this study, we performed a genome scan to identify quantitative trait loci (QTL) affecting age at puberty in gilts using a White Duroc × Erhualian intercross. A total of 183 microsatellites covering 19 porcine chromosomes were genotyped in 454 F₂ gilts and their parents and grandparents in the White Duroc × Erhualian intercross. A linear regression method was used to map QTL for age at puberty via QTLexpress. One 1% genome-wise significant QTL and one 0.1% genome-wise significant QTL were detected at 114 cM (centimorgan) on SSC1 and at 54 cM on SSC7, respectively. Moreover, two suggestive QTL were found on SSC8 and SSC17, respectively. This study confirmed the QTL for age at puberty previously identified on SSC1, 7 and 8, and reports for the first time a QTL for age at puberty in gilts on SSC17. Interestingly, the Chinese Erhualian alleles were not systematically favourable for younger age at puberty.     

Mapping of quantitative trait loci for mycoplasma and tetanus antibodies and interferon-gamma in a porcine F2 Duroc × Pietrain resource population

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in pigs. For this purpose, a Duroc × Pietrain F₂ resource population (DUPI) with 319 offspring was used to map QTL for the immune traits blood antibodies and interferon-gamma using 122 microsatellites covering all autosomes. Antibodies response to Mycoplasma hyopneumoniae and tetanus toxoid vaccine and the interferon-gamma (IFNG) serum concentration were measured at three different time points and were used as phenotypes. The differences of antibodies and interferon concentration between different time points were also used for the linkage mapping. Line-cross and imprinting QTL analysis, including two-QTL, were performed using QTL Express. A total of 30 QTL (12, 6, and 12 for mycoplasma, tetanus antibody, and IFNG, respectively) were identified at the 5% chromosome-wide-level significant, of which 28 were detected by line-cross and 2 by imprinting model. In addition, two QTL were identified on chromosome 5 using the two-QTL approach where both loci were in repulsion phase. Most QTL were detected on pig chromosomes 2, 5, 11, and 18. Antibodies were increased over time and immune traits were found to be affected by sex, litter size, parity, and month of birth. The results demonstrated that antibody and IFNG concentration are influenced by multiple chromosomal areas. The flanking markers of the QTL identified for IFNG on SSC5 did incorporate the position of the porcine IFNG gene. The detected QTL will allow further research in these QTL regions for candidate genes and their utilization in selection to improve the immune response and disease resistance in pig.     

Quantitative trait loci for porcine baseline erythroid traits at three growth ages in a White Duroc × Erhualian F<Subscript>2</Subscript> resource population

Baseline erythroid indices are increasingly involved as risk factors for common complex diseases in humans. However, little is known about the genetic architecture of baseline erythroid traits in pigs. In this study, hematocrit (Hct), hemoglobin (Hgb), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell (RBC), and red cell distribution width (RDW) were measured in 1420 (day 18), 1410 (day 46), and 1033 (day 240) F(2) pigs from a White Duroc x Erhualian intercross resource population. The entire resource population was genotyped for 183 microsatellite loci across the pig genome, and the quantitative trait loci (QTL) analysis was performed for all erythroid-related traits measured with QTL Express based on a least-squares method. A total of 101 QTL, including 46 genome-wide significant QTL and 55 chromosome-wide significant QTL, regulating erythroid traits were found on all pig chromosomes (SSC) except for SSC15 and SSC18. The genome-wide significant QTL were mainly localized on SSC1, 7, 8, 10, and X. These results confirmed most of QTL previously identified in the swine. More importantly, this study detected age-specific QTL for baseline erythroid traits in pigs for the first time. Notably, the QTL for MCV and MCH on day 18 on SSC8 with small intervals of 3 and 4 cM, respectively, provided a good starting point for identifying causal genes underlying MCV and MCH in the future.     

Microsatellite mapping of quantitative trait loci affecting meat quality, stress hormones and production traits in Duroc × Large White F2 pigs

An F2 cross between Duroc and Large White pigs was carried out in order to detect quantitative trait loci (QTL) for 11 meat quality traits (L*, a* and b* Minolta coordinates and water-holding capacity (WHC) of two ham muscles, ultimate pH of two ham and one loin muscles), 13 production traits (birth weight, average daily gain during post-weaning and fattening periods, carcass fat depths at three locations, estimated lean meat content, carcass length and weights of five carcass cuts) and three stress hormone-level traits (cortisol, adrenaline and noradrenaline). Animals from the three generations of the experimental design (including 456 F2 pigs) were genotyped for 91 microsatellite markers covering all the autosomes. A total of 56 QTL were detected: 49 reached the chromosome-wide level (suggestive QTL with a maximal probability of 0.05) and seven were significant at the genome-wide level (with a probability varying from 6 × 10(-4) to 3 × 10(-3)). Twenty suggestive QTL were identified for ultimate pH, colour measurements and WHC on chromosome (SSC) 5, 6, 7, 8, 9, 11, 13, 14, 15 and 17. For production traits, 33 QTL were detected on all autosomes except SSC6, 8 and 9. Seven of these QTL, located on SSC2, 3, 10, 13, 16 and 17, exceeded the genome-wide significance threshold. Finally, three QTL were identified for levels of stress hormones: a QTL for cortisol level on SSC7 in the cortisol-binding globulin gene region, a QTL for adrenaline level on SSC10 and a QTL for noradrenaline level on SSC13. Among all the detected QTL, seven are described for the first time: a QTL for ultimate pH measurement on SSC5, two QTL affecting birth weight on SSC2 and 10, two QTL for growth rate on SSC15 (during fattening) and 17 (during post-weaning) and two QTL affecting the adrenaline and noradrenaline levels. For each QTL, only one to five of the six F1 sires were found to be heterozygous. It means that all QTL are segregating in at least one of the founder populations used in this study. These results suggest that both meat quality and production traits can be improved in purebred Duroc and Large White pigs through marker-assisted selection. It is of particular interest for meat quality traits, which are difficult to include in classical selection programmes.     

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

A quantitative trait locus (QTL) analysis of female reproductive data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six F1 boars and 23 F1 sows, progeny of six LW boars and six MS sows, produced 573 F2 females and 530 F2 males. Six traits, i.e. teat number (TN), age at puberty (AP), ovulation rate (OR), weight at mating (WTM), number of viable embryos (NVE) and embryo survival (ES) at 30 days of gestation were analysed. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross (LC) regression and a half-full sib (HFS) maximum likelihood test. Genome-wide (GW) highly significant (P < 0.001) QTL were detected for WTM on SSC 7 and for AP on SSC 13. They explained, respectively, 14.5% and 8.9% of the trait phenotypic variance. Other GW significant (P < 0.05) QTL were detected for TN on SSC 3, 7, 8, 16 and 17, for OR on SSC 4 and 5, and for ES on SSC 9. Two additional chromosome-wide significant (P < 0.05) QTL were detected for TN, three for WTM, four for AP, three for OR, three for NVE and two for ES. With the exception of the two above-mentioned loci, the QTL explained from 1.2% to 4.6% of trait phenotypic variance. QTL alleles were in most cases not fixed in the grand-parental populations and Meishan alleles were not systematically associated with higher reproductive performance.     

Genome-wide association study of porcine hematological parameters in a Large White × Minzhu F2 resource population

Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1 and two SNPs within the region of 26.0-26.2 Mb were found to be significantly associated with RBC and RDW, respectively. Many of the SNPs were located within previously reported QTL regions and appeared to narrow down the regions compared with previously described QTL intervals. In current research, a total of seven significant SNPs were found within six candidate genes SCUBE3, KDR, TDO, IGFBP7, ADAMTS3 and AFP. In addition, the KIT gene, which has been previously reported to relate to hematological parameters, was located within the region significantly associated with MCH and MCV and could be a candidate gene. These results of this study may lead to a better understanding of the molecular mechanisms of hematological parameters in pigs.     

Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc?×?(Landrace × Yorkshire) commercial population

Background

Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F₂ crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population.

Methods

Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F₂ and Sutai pig populations.

Results

We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes.

Conclusions

These findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0120-x) contains supplementary material, which is available to authorized users.     

Results of a whole genome scan targeting QTL for growth and carcass traits in a Piétrain × Large White intercross

We herein report the results of a whole genome scan performed in a Piétrain × Large White intercross counting 525 offspring to map QTL influencing economically important growth and carcass traits. We report experiment-wide significant lod scores (> 4.6 for meatiness and fat deposition on chromosome SSC2, and for average daily gain and carcass length on chromosome SSC7. Additional suggestive lod scores (> 3.3) for fat deposition are reported on chromosomes SSC1, SSC7 and SSC13. A significant dominance deviation was found for the QTL on SSC1, while the hypothesis of an additive QTL could not be rejected for the QTL on SSC7 and SSC13. No evidence for imprinted QTL could be found for QTL other than the one previously reported on SSC2.     

Quantitative trait loci for lodging resistance in a segregating wheat×spelt population

 Lodging can strongly affect both the grain yield and the quality of wheat. Lodging represents a quantitative trait and is difficult to assess on a phenotypic basis. Marker-assisted selection (MAS) could therefore become an important tool in breeding for lodging resistance. In this study, we mapped and characterised quantitative trait loci (QTLs) for lodging resistance, as well as morphological traits correlated with lodging, in a segregating population of 226 recombinant inbred lines derived from the cross of the lodging-resistant wheat variety Forno with the susceptible spelt variety Oberkulmer. Lodging, plant height, leaf width, leaf-growth habit, culm stiffness, culm swinging, culm thickness, days to ear emergence and days to flowering were assessed in field trials at two locations in 1996 and at one location in 1997. Additionally, at one location weight and length parameters were also assessed. Plant height and culm stiffness explained 77% of the phenotypic variance of lodging in a multiple regression model over all three environments. QTL analysis of lodging and morphological parameters was based on a genetic map containing 230 loci with 23 linkage groups (2469 cM). With the method of composite interval mapping nine QTLs for lodging resistance were detected, explaining 63% of the phenotypic variance in a simultaneous fit. Seven of these QTLs coincided with QTLs for morphological traits, reflecting the correlations between these traits and lodging. In our population the most efficient way to improve lodging resistance would be by a combination of indirect selection on plant height and culm stiffness together with MAS on the two QTLs for lodging resistance which did not coincide with QTLs for morphological traits. Received: 3 August 1998 / Accepted: 28 November 1998     

Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment

An advanced backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with eight agronomic traits in a BC₂F₂ population derived from an interspecific cross between Caiapo, an upland Oryza sativa subsp. japonica rice variety from Brazil, and an accession of Oryza rufipogon from Malaysia. Caiapo is one of the most-widely grown dryland cultivars in Latin America and may be planted as a monoculture or in a multicropping system with pastures. The objectives of this study were: (1) to determine whether trait-enhancing QTLs from O. rufipogon would be detected in 274 BC₂F₂ families grown under the drought-prone, acid soil conditions to which Caiapo was adapted, (2) to compare the performance with and without pasture competition, and (3) to compare putative QTL-containing regions identified in this study with those previously reported for populations adapted to irrigated, low-land conditions. Based on analyses of 125 SSLP and RFLP markers distributed throughout the genome and using single-point, interval, and composite interval mapping, two putative O. rufipogon derived QTLs were detected for yield, 13 for yield components, four for maturity and six for plant height.We conclude that advanced backcross QTL analysis offers a useful germplasm enhancement strategy for the genetic improvement of cultivars adapted to stress-prone environments. Although the phenotypic performance of the wild germplasm would not suggest its value as a breeding parent, it is noteworthy that 56% of the trait-enhancing QTLs identified in this study were derived from O. rufipogon. This figure is similar to the 51% of favorable QTLs derived from the same parent in crosses with a high-yielding hybrid rice cultivar evaluated under irrigated conditions in a previous study. In conclusion, parallel studies in rice using AB-QTL analysis provide increasing evidence that certain regions of the rice genome are likely to harbor genes of interest for plant improvement in multiple environments. Received: 3 September 1999 / Accepted: 16 May 2000     

Quantitative trait loci for resistance against powdery mildew in a segregating wheat×spelt population

 Powdery mildew is one of the major diseases of wheat in regions with a maritime or semi-continental climate and can strongly affect grain yield. The attempt to control powdery mildew with major resistance genes (Pm genes) has not provided a durable resistance. Breeding for quantitative resistance to powdery mildew is more promising, but is difficult to select on a phenotypic basis. In this study, we mapped and characterised quantitative trait loci (QTLs) for adult-plant powdery mildew resistance in a segregating population of 226 recombinant inbred lines derived from the cross of the Swiss wheat variety Forno with the Swiss spelt variety Oberkulmer. Forno possibly contains the Pm5 gene and showed good adult-plant resistance in the field. Oberkulmer does not have any known Pm gene and showed a moderate susceptible reaction. Powdery mildew resistance was assessed in field trials at two locations in 1995 and at three locations in 1996. The high heritability (h²=0.97) for powdery mildew resistance suggests that the environmental influence did not affect the resistance phenotype to a great extent. QTL analysis was based on a genetic map containing 182 loci with 23 linkage groups (2469 cM). With the method of composite interval mapping 18 QTLs for powdery mildew resistance were detected, explaining 77% of the phenotypic variance in a simultaneous fit. Two QTLs with major effects were consistent over all five environments. One of them corresponds to the Pm5 locus derived from Forno on chromosome 7B. The other QTL on 5A, was derived from the spelt variety Oberkulmer and did not correspond to any known Pm gene. In addition, five QTLs were consistent over three environments, and six QTLs over two environments. The QTL at the Pm5 locus showed a large effect, although virulent races for Pm5 were present in the mixture of isolates. Molecular markers linked with QTLs for adult-plant resistance offer the possibility of simultaneous marker-assisted selection for major and minor genes. Received: 22 September 1998 / Accepted: 26 October 1998     

Association of B3GNT5 Polymorphisms with Susceptibility to ETEC F4ab/ac in the White Duroc?×?Erhualian Intercross and 15 Outbred Pig Breeds

The B3GNT5 gene is a candidate for the F4ab/ac receptor conferring susceptibility to enterotoxigenic Escherichia coli (ETEC) F4ab/ac in pigs. In this study, we screened mutations in the complete coding region of the porcine B3GNT5 gene and identified four SNPs in the 3' untranslated regions. We genotyped the four SNPs across a large-scale White Duroc × Chinese Erhualian F2 resource population (total F2 = 755) and 292 purebred piglets representing 15 Chinese and Western breeds. We found that the g.1476G→A locus and haplotypes [A;T;G;T] and [A;G;G;T] had significant association with susceptibility to ETEC F4ac in the resource population. None of the B3GNT5 polymorphisms and haplotypes was associated with susceptibility to ETEC F4ab/ac in outbred piglets. This result, together with other reports, supports the conclusion that B3GNT5 is not the responsible gene encoding the ETEC F4ab/ac receptors.     

Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

Background

Quantitative trait loci (QTL) analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig.

Methods

Five hundred and eighty five F₂ pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP) spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F₂ animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program.

Results

A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance.

Conclusions

Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.