QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle)

Causal mutations affecting quantitative trait variation can be good targets for marker-assisted selection for carcass traits in beef cattle. In this study, linkage and linkage disequilibrium analysis (LDLA) for four carcass traits was undertaken using 19 markers on bovine chromosome 14. The LDLA analysis detected quantitative trait loci (QTL) for carcass weight (CWT) and eye muscle area (EMA) at the same position at around 50?cM and surrounded by the markers FABP4SNP2774C>G and FABP4_??sat3237. The QTL for marbling (MAR) was identified at the midpoint of markers BMS4513 and RM137 in a 3.5-cM marker interval. The most likely position for a second QTL for CWT was found at the midpoint of tenth marker bracket (FABP4SNP2774C>G and FABP4_??sat3237). For this marker bracket, the total number of haplotypes was 34 with a most common frequency of 0.118. Effects of haplotypes on CWT varied from a ?5-kg deviation for haplotype 6 to +8?kg for haplotype 23. To determine which genes contribute to the QTL effect, gene expression analysis was performed in muscle for a wide range of phenotypes. The results demonstrate that two genes, LOC781182 (p?=?0.002) and TRPS1 (p?=?0.006) were upregulated with increasing CWT and EMA, whereas only LOC614744 (p?=?0.04) has a significant effect on intramuscular fat (IMF) content. Two genetic markers detected in FABP4 were the most likely QTL position in this QTL study, but FABP4 did not show a significant effect on both traits (CWT and EMA) in gene expression analysis. We conclude that three genes could be potential causal genes affecting carcass traits CWT, EMA, and IMF in Hanwoo.     

Test for positional candidate genes for body composition on pig chromosome 6

One QTL affecting backfat thickness (BF), intramuscular fat content (IMF) and eye muscle area (MA) was previously localized on porcine chromosome 6 in an F₂ cross between Iberian and Landrace pigs. This work was done to study the effect of two positional candidate genes on these traits: H-FABP and LEPR genes. The QTL mapping analysis was repeated with a regression method using genotypes for seven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP and LEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis. The effects of the candidate gene polymorphisms were analyzed in two ways. When an animal model was fitted, both genes showed significant effects on fatness traits, the H-FABP polymorphism showed significant effects on IMF and MA, and the LEPR polymorphism on BF and IMF. But when the candidate gene effect was included in a QTL regression analysis these associations were not observed, suggesting that they must not be the causal mutations responsible for the effects found. Differences in the results of both analyses showed the inadequacy of the animal model approach for the evaluation of positional candidate genes in populations with linkage disequilibrium, when the probabilities of the parental origin of the QTL alleles are not included in the model.     

Association of genetic variants for <Emphasis Type="Italic">FABP3</Emphasis> gene with back fat thickness and intramuscular fat content in pig

The swine fatty acid binding protein gene (FABP3) has been screened with 4 primer sets for 270 purebred Yorkshire pigs from National Institute of Animal Science. The selection of primers was based on the swine cDNA sequence (AJ416019), and primer sets (FABP3-2 and FABP3-3) amplified target segments in real time PCR to analyze expression levels at growth stages, producing 235 and 224 bp of fragments, respectively. Relative expression of the swine FABP3 gene for back and intramuscular fat was continuously increased from day 0 to 150, and decreased at day 210, showing the highest expression levels at day 150 compared with day 0. The results may be caused by requirements of high physiological activities with more gene expressions for growth around day 150. Nucleotide variations were observed at nucleotide positions 80 (A/G), 167 (A/G), 260 (A/G), 295 (A/G), 394 (T/C), and 440 (A/G), showing substitutions of amino acids at positions 80 (S to G), 167 (T to A), and 260 (S to G). FABP3 genotypes at positioned nt167 have been associated with carcass back fat thickness (BFT), and dominance genetic effects were observed for BFT with nt167 and intramuscular fat (IMF) contents with nt80. Our results concluded that the FABP3 polymorphisms can be used as genetic markers in breeding programs for IMF content as well as carcass BFT.     

Developmental changes and effect on intramuscular fat content of H-FABP and A-FABP mRNA expression in pigs

H-FABP and A-FABP genes are considered as candidates for intramuscular fat (IMF) accretion. The aim of the present study was to assess the expression of H-FABP and A-FABP genes in m. longissimus dorsi (LD) and liver tissues of Laiwu and Lulai Black pig populations of different body weight (BW). Eighty-four barrows at different BW (30, 40, 50, 60, 70, 80, 90 and 100 kg, n?=?6 per group) of Laiwu Black pig (no 100 kg group) and Lulai Black pig (no 30 kg group) were used to study the development changes of A-FABP and H-FABP mRNA expression and their relationships to IMF content. The results showed that, in both breeds, the IMF content increased continuously with growing (P?<?0.05). The expression of H-FABP and A-FABP genes also increased with growing in LD tissue (P?<?0.05), and reached a peak at 50 and 70 kg BW in Laiwu and Lulai Black pig, respectively. However, this regularity was not observed in liver tissue in both breeds. A positive correlation was just found between the A-FABP mRNA expression level in LD tissue and IMF content and BW in both breeds (P?<?0.05). In conclusion, the A-FABP gene is strongly related to the development and function of IMF accretion in pigs.     

Candidate gene expression affects intramuscular fat content and fatty acid composition in pigs

The objective of this study was to correlate the expression pattern of candidate genes with the intramuscular fat (IMF) content and fatty acid composition of the Longissimus dorsi muscle of Duroc × Shanzhu commercial crossbred pigs. Animals of both sexes were slaughtered at a body weight of about 90 kg. The IMF content and fatty acid composition of the Longissimus dorsi muscle were measured and correlated with candidate genes mRNA expression (AdPLA, ADRB3, LEPR, MC4R, PPARγ, PPARα, LPL, PEPCK, and SCD). Females presented higher IMF content (p < 0.05) than males. The total saturated fatty acid (SFA) in males was greater (p < 0.01), whereas the total monounsaturated fatty acid (MUFA) (p < 0.01) and polyunsaturated fatty acid (PUFA) (p < 0.05) were lower than in females. The expressions of AdPLA, MC4R, PEPCK, and SCD correlated with the IMF content (p < 0.05). AdPLA showed a positive association with MUFA and a negative association with SFA (p < 0.05). LEPR and MC4R were both positively and significantly associated with C18:3 and C20:0 (p < 0.05). PPARα and PPARγ were negatively correlated with SFA, and PPARγ was positively associated with MUFA (p < 0.05). LPL was positively associated with MUFA and negatively associated with SFA (p < 0.05). PEPCK was negatively correlated with PUFA (p < 0.05). SCD was positively associated with MUFA (p < 0.05). The revealed correlations may confirm that these candidate genes are important for fat deposition and fatty acid composition in pigs, and the evaluation and use of these genes may be useful for improving porcine meat quality.     

Ectopic overexpression of porcine DGAT1 increases intramuscular fat content in mouse skeletal muscle

The microsomal enzyme 1, 2-acyl CoA: diacylglyceroltransferase-1 (DGAT1) plays an important role in triglyceride storage in adipose tissue and expresses in skeletal muscle as well. The primary goal of the present study was to investigate the effect of porcine DGAT1 on intramuscular fat (IMF) content of transgenic mice produced by pronuclear microinjection with muscle specific promoter of porcine muscle creatine kinase (MCK). In normal chow-fed diet, 4 month-old male transgenic mice expressed more DGAT1, ACC1, UCP1, and FABP4 mRNAs and proteins in skeletal muscle than control mice by real-time PCR and western blot. No significant changes were detected for ACC2, CD36, ADRP, PPAR gamma and LPL. Triacylglycerol assay and soleus muscle sections showed overexpression of porcine DGAT1 in skeletal muscle increased intramyocellular triglyceride and percent of the total cell surface covered by lipid droplets. Thus, upregulation of porcine DGAT1 in skeletal muscle increases IMF content. The present study may further serve to develop transgenic pigs with higher IMF content and improved meat quality.     

Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs

Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.     

Contrasting cellularity on fat deposition in the subcutaneous adipose tissue and longissimus lumborum muscle from lean and fat pigs under dietary protein reduction

The production of pork with high amounts of intramuscular fat (IMF) without an increase in subcutaneous fat is highly desirable for the pig industry and consumers. Herein, we question the impact of dietary protein reduction (18% v. 13%) on fat deposition in the subcutaneous adipose tissue (SAT) and longissimus lumborum (LL) muscle using genetically diverse pigs for body fatness (lean v. fat). A clear effect of genotype was observed on plasma insulin (P=0.004) and leptin (P<0.001), as well as on backfat thickness (P<0.001), with the fat pigs having higher values. Accordingly, IMF was higher in the fat pigs, when compared with their lean counterparts (P=0.003), which was supported by enlarged adipocytes (P<0.001). The area of lipid droplets within the LL fibres (P=0.039) and extramyocellular lipids number (P=0.017) were increased in pigs fed reduced protein diets, regardless of genotype, which is consistent with higher levels of plasma triacylglycerols (P=0.002). The gene-expression pattern of lipogenic factors in the SAT was distinct from the LL muscle. In the SAT, PPARG expression was similar among genotypes (P>0.05), whereas in the LL muscle it was higher in the lean pigs (P=0.023), especially when fed on low protein diet (P=0.057). The CEBPA and FABP4 mRNA levels were increased in the SAT of fat pigs (P<0.001), without changes in the LL muscle (P>0.05). The influence of diet on FABP4 expression in the SAT was dependent on pig’s genetic background (P=0.005). In conclusion, fat deposition was clearly influenced by genotype and, to a lesser extent, by dietary protein level, the SAT being more sensitive than the LL muscle. One can speculate that the pathways involved in lipid metabolism are downregulated in intramuscular adipocytes when compared with SAT fat cells. This result might be a direct consequence of the relatively low proportion of adipocytes found in the LL muscle.     

Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4

Interval mapping (IM) implemented in QTL Express or GridQTL is widely used, but presents some limitations, such as restriction to a fixed model, risk of mapping two QTL when there may be only one and no discrimination of two or more QTL using both cofactors located on the same and other chromosomes. These limitations were overcome with composite interval mapping (CIM). We reported QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4 through implementation of CIM and analysis of phenotypic data using mixed models. Thirty-four microsatellite markers were used to genotype 360 F₂ chickens from crosses between males from a layer line and females from a broiler line. Sixteen QTL were mapped using CIM and 14 QTL with IM. Furthermore, of those 30 QTL, six were mapped only when CIM was used: for body weight at 35 days (first and third peaks on GGA4), body weight at 41 days (GGA1B and second peak on GGA4), and weights of back and legs (both on GGA4). Three new regions had evidence for QTL presence: one on GGA1B associated with feed intake 35–41 d at 404 cM (LEI0107-ADL0183) and two on GGA4 associated with weight of back at 163 cM (LEI0076-MCW0240) and weight gain 35–41 d, feed efficiency 35–41 d and weight of legs at 241 cM (LEI0085-MCW0174). We dissected one more linked QTL on GGA4, where three QTL for BW35 and two QTL for BW41 were mapped. Therefore, these new regions mapped here need further investigations using high-density SNP to confirm these QTL and identify candidate genes associated with those traits.     

Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

The improvement of fruit quality is an important objective in citrus breeding. Using an F₁ segregating population from a cross between citrus cultivars ‘Harehime’ (‘E647’—‘Kiyomi’ [Citrus unshiu Marcow. ‘Miyagawa Wase’ × Citrus sinensis (L.) Osbeck ‘Trovita’] × ‘Osceola’—a cultivar of clementine [Citrus clementina hort. ex Tanaka] × ‘Orland’ [Citrus paradisi Macfad. ‘Duncan’ × Citrus tangerina hort. ex Tanaka] × ‘Miyagawa Wase’) and ‘Yoshida’ ponkan (Citrus reticulata Blanco ‘Yoshida’), a SNP-based genetic linkage map was constructed and quantitative trait locus (QTL) mapping of four fruit-quality traits (fruit weight, sugar content, peel puffing, and water rot) was performed. The constructed genetic linkage map of ‘Harehime’ consisted of 442 single nucleotide polymorphisms (SNPs) on 9 linkage groups (LGs) and covered 635.8 cM of the genome, while that of ‘Yoshida’ ponkan consisted of 332 SNPs on 9 LGs and covered 892.9 cM of its genome. We identified four QTLs associated with fruit weight, one QTL associated with sugar content, three QTLs associated with peel puffing, and one QTL associated with water rot. For these QTL regions, we estimated the haplotypes of the crossed parents and verified the founding cultivars that these QTLs were originated from and their inheritance in descendant cultivars using pedigree information. QTLs identified in this study provide useful information for marker-assisted breeding of citrus in Japan.     

Polymorphisms of the porcine cathepsins,growth hormone-releasing hormone and leptin receptor genes and their association with meat quality traits in Ukrainian Large White breed

Cathepsins, growth hormone-releasing hormone (GHRH) and leptin receptor (LEPR) genes have been receiving increasing attention as potential markers for meat quality and pig performance traits. This study investigated the allele variants in four cathepsin genes (CTSB, CTSK, CTSL, CTSS), GHRH and LEPR in pure-bred Ukrainian Large White pigs and evaluated effects of the allele variants on meat quality characteristics. The study was conducted on 72 pigs. Genotyping was performed using PCR–RFLP technique. Meat quality characteristics analysed were intramuscular fat content, tenderness, total water content, ultimate pH, crude protein and ashes. A medium level of heterozygosity values was established for GHRH and LEPR genes which corresponded to very high levels of informativeness indexes. Cathepsins CTSL, CTSB and CTSK had a low level of heterozygosity, and CTSS did not segregate in this breed. Association studies established that intramuscular fat content and tenderness were affected by the allele variance in GHRH and LEPR but not by CTSB and CTSL genes. The GHRH results could be particularly relevant for the production of lean prime cuts as the A allele is associated with both, a lower meat fat content and better tenderness values, which are two attributes highly regarded by consumers. Results of this study suggest that selective breeding towards GHRH/AA genotype would be particularly useful for improving meat quality characteristics in the production systems involving lean Large White lines, which typically have less than 2 % intramuscular fat content.     

Quantitative gene expression analysis on chromosome 6 between Korean native pigs and Yorkshire breeds for fat deposition

Pig chromosome 6 (SSC6) has been reported to have QTL affecting backfat thickness (BFT) and intramuscular fat (IMF). A human-pig comparative map covering 18 autosomes with the highest resolution has been constructed and based on this map SSC6 has conserved syntenicgroups with human chromosome (HSA) 16, 19, 1, and 18. In this study, the pig Affy elements mapped to the SSC6 were analyzed, and the differentially expressed genes in three tissues (liver, backfat and loin muscle) between Yorkshire and Korean Native Pigs (KNP) were collected, in particular those genes located in the internal between markers SW1355 and SW1823 where a quantitative trait loci (QTL) affecting the intramuscular fat content (IMF) have been detected in multiple pig populations. The genes listed here may offer information for further study the candidate genes affecting these QTL on the expression level.     

Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations

Key message

A novel high-density consensus wheat genetic map was obtained based on three related RIL populations, and the important chromosomal regions affecting yield and related traits were specified.

Abstract

A prerequisite for mapping quantitative trait locus (QTL) is to build a genetic linkage map. In this study, three recombinant inbred line populations (represented by WL, WY, and WJ) sharing one common parental line were used for map construction and subsequently for QTL detection of yield-related traits. PCR-based and diversity arrays technology markers were screened in the three populations. The integrated genetic map contains 1,127 marker loci, which span 2,976.75 cM for the whole genome, 985.93 cM for the A genome, 922.16 cM for the B genome, and 1,068.65 cM for the D genome. Phenotypic values were evaluated in four environments for populations WY and WJ, but three environments for population WL. Individual and combined phenotypic values across environments were used for QTL detection. A total of 165 putative additive QTL were identified, 22 of which showed significant additive-by-environment interaction effects. A total of 65 QTL (51.5 %) were stable across environments, and 23 of these (35.4 %) were common stable QTL that were identified in at least two populations. Notably, QTkw-5B.1, QTkw-6A.2, and QTkw-7B.1 were common major stable QTL in at least two populations, exhibiting 11.28–16.06, 5.64–18.69, and 6.76–21.16 % of the phenotypic variance, respectively. Genetic relationships between kernel dimensions and kernel weight and between yield components and yield were evaluated. Moreover, QTL or regions that commonly interact across genetic backgrounds were discussed by comparing the results of the present study with those of previous similar studies. The present study provides useful information for marker-assisted selection in breeding wheat varieties with high yield.     

Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker‐assisted introgression

We investigated the effects of previously identified quantitative trait loci (QTL) in an experimental backcross (BC) between Chinese Meishan pigs and commercial Duroc pigs. We performed marker‐assisted introgression of two QTL for intramuscular fat (IMF) content (IMF population) and three QTL for reproductive traits (reproduction population) from a donor Meishan pig into a recipient Duroc pig. At the fourth BC generation of the IMF population and third BC generation of the reproduction population, carrier animals were selected for the production of animals homozygous for the QTL. Our previous studies have shown that the presence of a Meishan allele on the IMF QTL is associated with low IMF values, and the Meishan allele on the reproductive QTL is associated with large litters. In this study, the presence of a Duroc allele at the IMF QTL on SSC9 resulted in a 0.27% increase in IMF (additive effect = 0.27 ± 0.08), whereas the presence of a Meishan allele at the IMF QTL on SSC7 resulted in a 0.34% increase in IMF (additive effect = ?0.34 ± 0.09). The presence of the Meishan allele at the IMF QTL on SSC7 thus had the opposite effect to our previous studies, that is, increased IMF. In the reproduction population, we observed no differences between the genotypes of the three QTL in regard to number of corpora lutea or litter size. Marker‐assisted introgression at these QTL is thus unlikely to result in an associated increase in litter size. These results show that it is possible to introgress alleles from other breeds into a selection population using molecular markers; any unexpected results might be associated with the genetic background.     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Mapping quantitative trait loci affecting some carcass and meat traits in duck (Anas platyrhynchos)

Contrary to chicken and livestock mammals, duck genome has not been explored much. Nowadays a relatively small number of reports on molecular variability and mapping of loci in Peking ducks has been published. Therefore, the objective of this study was to detect single loci affecting body weight, carcass and meat traits in Peking ducks (Anas platyrhynchos). The study was based on an F2 cross between two parental lines A-55 and GL-30. Phenotypes of 387 birds from generation F2 including carcass and meat quality traits were collected. Linkage map, of the linkage group CAU1, consisting of 29 microsatellite markers was constructed. One highly significant (p?p?相似文献   

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.