The genetic basis of feed efficiency in swine divergently selected for residual feed intake

Feed efficiency is an economically important trait in the swine industry since feed accounts more than 50% of total production costs. A measure of feed efficiency, residual feed intake (RFI), is defined as the difference between observed and expected feed intake based on production and maintenance requirements. Since 2001 at Iowa State University (ISU), divergent selection for improved (Low RFI) and reduced feed efficiency (High RFI) has been conducted in Yorkshire pigs for ten generations. Using these selection lines, the over-arching objective of this dissertation was to further our knowledge of the biological and genetic basis of RFI in pigs. The main objectives were to investigate genotype-by diet interactions, identify genomic regions associated with RFI and component traits, validate insulin like growth factor I (IGF-I) as an early genetic indicator of grow-finish RFI, and to evaluate correlated responses to selection for grow-finish RFI on feed efficiency and performance of nursery pigs. To quantify genotype by diet interactions for RFI, in generation (G) 8 through G10 of the high and low RFI lines, a lower-energy, higher-fiber (LEHF) diet was fed to a subset of pigs and compared to the performance of pigs fed a standard corn and soybean-meal based diet, similar to the diet fed during selection, which was higher in energy and lower in fiber (HELF). These diets differed in metabolizable energy (3.32 vs. 2.87 Mcal/kg for the HELF vs. LEHF diet) and neutral detergent fiber (9.4 vs. 25.9% NDF). When pigs were fed the HELF, the Low RFI pigs had lower average daily feed intake (-12%), energy intake (-12%), average daily gain (-6%), and backfat depth (-12%) than High RFI pigs (P \u3c 0.05). Regardless of RFI line, performance was reduced when pigs were fed the LEHF compared to the HELF diet. For the LEHF diet compared to the HELF diet, differences between the RFI lines were smaller for average daily feed intake (-11%), energy intake (-10%), gain to feed ratio (+2%), and RFI (-6%) (P \u3c 0.05). Feed digestibility was reduced when pigs were fed the LEHF diet, with the Low RFI pigs digesting significantly (P ≤ 0.04) more dry matter (+7%), gross energy (+7%), nitrogen (+10%) and NDF (+32%) than High RFI pigs when fed the LEHF diet. However, no line differences in digestibility were observed when the HELF diet was fed. Estimates of genetic correlations of performance traits across diets were high and positive for RFI and component traits, with a 0.87 ñ 0.28 genetic correlation for RFI across diets. The observed correlated response to selection in RFI when feeding the LEHF diet was 55% less than predicted based on the genetic correlation for RFI between diets. Genotype-by-diet interactions were further investigated by estimating single nucleotide polymorphism (SNP) by diet interactions, but these were found to account for less than 0.7% of the genetic variance in any given non-overlapping 1-Megabase window for RFI and component traits. By comparing the top genomic regions associated with RFI for the HELF and LEHF diets separately, we observed that the top associations were located on Sus scrofa chromosome (SSC) 2 near IGF2 (insulin like growth factor II) when pigs were fed the HELF but on SSC 6 for the LEHF diet, which demonstrates that at least some genomic regions associated with these traits were different between diets. This agrees with the estimated genetic correlation between diets for RFI (0.87 ñ 0.28) and provides more evidence of genotype-by-diet interactions for RFI. Genomic regions associated with RFI and component traits given the HELF, LEHF and both diets combined were identified using a genome-wide association study (GWAS). Two genomic regions were associated with multiple traits, indicating pleiotropic effects, on SSC1 near MC4R (melanocortin-4 receptor) and on SSC2 near IGF2. Results showed that the genetic architecture of RFI was highly polygenic. Genomic regions were also identified by evaluating genomic regions under selection in the ISU and in an independent Large White population that was also divergently selected for RFI (INRA). Regions were identified on SSC 2 near CAST (calpastatin) and on SSC 13 near GAPBA (GA binding protein transcription factor alpha subunit), which were different than associations found using GWAS. However, findings also suggested that the differences in RFI between the ISU and INRA Low and High RFI lines may be the result of selection affecting different genes and biological pathways, as few common regions were identified to be under selective pressure in the two populations. Using IGF-I data collected in G2 through G5, and in G10 and G11, IGF-I was found to have a positive genetic correlation with grow-finish RFI (0.54 ñ 0.19 for G2-G5 and 0.51 ñ 0.48 for G10-G11), indicating IGF-I is a good early biological marker for grow-finish RFI. In nursery-aged pigs in G10, the Low RFI line was found to eat less (-20%), grow slower (-10%) and have greater feed efficiency (+12% measured as gain to feed ratio) compared to the High RFI line, showing that selection for grow-finish RFI also improved nursery feed efficiency in the Low RFI line. In conclusion, RFI is a biologically and genetically complex trait with no genes with major effects and many genes contributing small effects. Nutritional value of the diet fed during selection impacts feed efficiency and its genetic architecture. Therefore, genotype-by-diet interactions must be taken into consideration in selection programs, particularly those that desire to improve feed efficiency. Genomic selection would be a good strategy to improve feed efficiency because of the highly polygenic genetic architecture of RFI. In addition, juvenile IGF-I can be used as a genetic indicator for grow-finish RFI. Finally, correlated responses to selection for grow-finish RFI also led to improved feed efficiency of Low RFI pigs in the nursery

Juvenile IGF-I: An Early Bio-marker for Feed Efficiency in Pigs

At Iowa State University, purebred Yorkshire pigs have been divergently selected for increased and decreased feed efficiency based on residual feed intake for ten generations. In this study, juvenile IGF-I serum concentrations were measured in these divergently selected lines, with the goal of validating juvenile IGF-I as an early blood bio-marker to help select young piglets for later feed efficiency performance. Previous findings (Bunter et al., 2002, 2005, 2010) and this validation study support that lower juvenile IGF-I concentration in piglets is genetically correlated with increased grow-finish feed efficiency. IGF-I concentration is a moderately heritable trait that is more cost and time effective to measure than feed intake and feed efficiency. These characteristics make IGF-I a useful bio-marker for feed efficiency in swine

Analysis of Ten Generations of Selection for Residual Feed Intake in Yorkshire Pigs

Ten generations (G) of divergent selection for residual feed intake (RFI) was practiced in Yorkshire pigs. This study shows that feed efficiency based on RFI was moderately heritable and responded to selection. Pigs selected for increased feed efficiency from the low RFI line ate less, grew slightly slower, and were leaner than pigs from the high RFI line. Thus, the results of this study show that selection for decreased RFI can improve feed efficiency and can be included in an economic selection index in addition to growth for reducing feed cost

Effect of Low Energy, High Fiber Diets on Pigs Selected for Residual Feed Intake

The ever high feed costs in swine production contribute to the largest variable expense for today’s producers. Due to this fact, research has focused on increasing feed efficiency. In this study, residual feed intake (RFI) was utilized as a measure of feed efficiency in lines of purebred Yorkshire pigs that were selected for increased and decreased feed efficiency on a standard corn-soybean diet that was high in energy and low in fiber (control diet). The low RFI (LRFI) line was selected for increased feed efficiency while the high RFI (HRFI) line was selected for reduced feed efficiency. In generations 8 and 9, the low and high RFI lines were challenged with a low energy, high fiber diet (LEHF). This diet reflects the addition of alternative feed stuffs to swine diets in commercial settings in order to decrease feed costs. Results indicate that the difference in feed efficiency between the two lines was substantially lower when fed the LEHF diet compared to the control diet. Thus, when pigs are fed diets with substantial byproducts, it is important that pigs are also selected for efficiency under such diets

Diet by Genotype Interaction in Yorkshire Pigs Divergently Selected for Feed Efficiency

For ten generations, purebred Yorkshire pigs were divergently selected for increased and decreased feed efficiency based on residual feed intake when fed a standard corn and soybean-meal based diet. In this study, gilts and barrows bornin generations 8, 9, and 10were fed either a standard diet or an alternative diet that incorporated by-products while reducing corn and soybean-meal, resultingina lower energy, higher fiber diet. Genotypeby diet interactions were investigatedby estimating heritabilities, genetic correlations, response to selection,and genome wide associations for six traits based on thesetwo diets. Results indicate that feed efficiency is a genetically complex trait that appears to be genetically different depending on the diet fed. Thus, genetic gains made by selection on standard diets may not be fully expressed in swine production systems that use alternative diets, particularly those incorporating by-products

Effect of Low Energy, High Fiber Diets on Digestibility Traits in Pigs Selected for Residual Feed Intake

In this study, barrows and gilts from the Iowa State University Residual Feed Intake selection lines were fed two diets. The first, the Control diet, was corn and soybean-meal based, and was high in energy yet low in fiber content. The second, the Fiber diet, substituted in corn bran, wheat middlings, and soybean hulls, and resulted in a lower energy and higher fiber diet. These two diets were fed to pigs that had previously been selected for increased and decreased feed efficiency over the course of 8 generations based on residual feed intake. Fecal grab samples were collected from these pigs during the first and third finishing growth-phases with the objective of evaluating differences in dry matter, gross energy, nitrogen, and neutral detergent fiber digestibility between the two genetic lines and the two diets. This study observed beneficial increases in digestibility of fibrous feed components in pigs selected for increased feed efficiency

Phenotypic and genotypic diversity of selected Free Range Local Chickens in Tanzania

Free range local chickens are an important source of protein as meat and eggs in Tanzania. Few studies have been done to improve their productivity. To this end, this paper focuses on characterizing three common Tanzanian local chicken ecotypes. Morphologic and genetic diversity studies show that the Kuchi have relatively higher body dimension measures than Ching’wekwe and Morogoro medium and that the Ching’wekwe ecotype is genetically more related to Morogoro medium than to the Kuchi ecotype. These differences indicate variation in traits that call for further research and opportunities to improve productivity of free range local chickens

The genetic basis of feed efficiency in swine divergently selected for residual feed intake

Feed efficiency is an economically important trait in the swine industry since feed accounts more than 50% of total production costs. A measure of feed efficiency, residual feed intake (RFI), is defined as the difference between observed and expected feed intake based on production and maintenance requirements. Since 2001 at Iowa State University (ISU), divergent selection for improved (Low RFI) and reduced feed efficiency (High RFI) has been conducted in Yorkshire pigs for ten generations. Using these selection lines, the over-arching objective of this dissertation was to further our knowledge of the biological and genetic basis of RFI in pigs. The main objectives were to investigate genotype-by diet interactions, identify genomic regions associated with RFI and component traits, validate insulin like growth factor I (IGF-I) as an early genetic indicator of grow-finish RFI, and to evaluate correlated responses to selection for grow-finish RFI on feed efficiency and performance of nursery pigs. To quantify genotype by diet interactions for RFI, in generation (G) 8 through G10 of the high and low RFI lines, a lower-energy, higher-fiber (LEHF) diet was fed to a subset of pigs and compared to the performance of pigs fed a standard corn and soybean-meal based diet, similar to the diet fed during selection, which was higher in energy and lower in fiber (HELF). These diets differed in metabolizable energy (3.32 vs. 2.87 Mcal/kg for the HELF vs. LEHF diet) and neutral detergent fiber (9.4 vs. 25.9% NDF). When pigs were fed the HELF, the Low RFI pigs had lower average daily feed intake (-12%), energy intake (-12%), average daily gain (-6%), and backfat depth (-12%) than High RFI pigs (P Genomic regions associated with RFI and component traits given the HELF, LEHF and both diets combined were identified using a genome-wide association study (GWAS). Two genomic regions were associated with multiple traits, indicating pleiotropic effects, on SSC1 near MC4R (melanocortin-4 receptor) and on SSC2 near IGF2. Results showed that the genetic architecture of RFI was highly polygenic. Genomic regions were also identified by evaluating genomic regions under selection in the ISU and in an independent Large White population that was also divergently selected for RFI (INRA). Regions were identified on SSC 2 near CAST (calpastatin) and on SSC 13 near GAPBA (GA binding protein transcription factor alpha subunit), which were different than associations found using GWAS. However, findings also suggested that the differences in RFI between the ISU and INRA Low and High RFI lines may be the result of selection affecting different genes and biological pathways, as few common regions were identified to be under selective pressure in the two populations. Using IGF-I data collected in G2 through G5, and in G10 and G11, IGF-I was found to have a positive genetic correlation with grow-finish RFI (0.54 à ± 0.19 for G2-G5 and 0.51 à ± 0.48 for G10-G11), indicating IGF-I is a good early biological marker for grow-finish RFI. In nursery-aged pigs in G10, the Low RFI line was found to eat less (-20%), grow slower (-10%) and have greater feed efficiency (+12% measured as gain to feed ratio) compared to the High RFI line, showing that selection for grow-finish RFI also improved nursery feed efficiency in the Low RFI line. In conclusion, RFI is a biologically and genetically complex trait with no genes with major effects and many genes contributing small effects. Nutritional value of the diet fed during selection impacts feed efficiency and its genetic architecture. Therefore, genotype-by-diet interactions must be taken into consideration in selection programs, particularly those that desire to improve feed efficiency. Genomic selection would be a good strategy to improve feed efficiency because of the highly polygenic genetic architecture of RFI. In addition, juvenile IGF-I can be used as a genetic indicator for grow-finish RFI. Finally, correlated responses to selection for grow-finish RFI also led to improved feed efficiency of Low RFI pigs in the nursery.</p

Signatures of Selection in Two Independent Populations of Pigs Divergently Selected for Feed Efficiency

In two independent populations of pigs, divergent selection for increased and decreased feed efficiency, measured as residual feed intake (RFI), was performed over ten generations in purebred Yorkshire pigs at Iowa State University (ISU) and eight generations in French Large White pigs at the French National Institute for Agricultural Research (INRA). Over time and generations, favorable alleles for improved feed efficiency were expected to increase in frequency in the more feed efficient (Low RFI) lines, while unfavorable alleles decrease, and vice versa in the less feed efficient (High RFI) lines. When changes in allele frequency over time are more extreme than what could be caused by genetic drift, this indicates a selection signature. Genes that are important in both populations were expected to have overlapping selection signatures. In this study, two such selection signatures were identified for RFI, on chromosomes 2 and 13, with candidate genes related to protein turnover rate and mitochondrial function. These selection signatures give insight into the genetic basis of feed efficiency in pigs and markers in these regions can be used to select for more feed efficient pigs.</p

Analysis of Ten Generations of Selection for Residual Feed Intake in Yorkshire Pigs

Ten generations (G) of divergent selection for residual feed intake (RFI) was practiced in Yorkshire pigs. This study shows that feed efficiency based on RFI was moderately heritable and responded to selection. Pigs selected for increased feed efficiency from the low RFI line ate less, grew slightly slower, and were leaner than pigs from the high RFI line. Thus, the results of this study show that selection for decreased RFI can improve feed efficiency and can be included in an economic selection index in addition to growth for reducing feed cost.</p