With the rise in feed costs, increasing nutritional efficiency of production is, more than ever, one of the main drivers of profitability of pork production. Over the past decades, substantial effort has been placed on increasing feed efficiency. On the genetics side, this has indirectly been accomplished by selection for growth rate and leanness, which both decrease the amount of feed required to reach market weight. It is well known, however, that a large proportion (~34%) of differences in feed intake between pigs in the growing phase are not related to growth and composition but result from differences in energy required for other processes such as maintenance, activity, and digestive and metabolic efficiency. This is known as residual feed intake (RFI), which is measure of feed efficiency computed as the difference between the amount of feed a pig consumes and what it is expected to consume based on its rate of growth and backfat. So pigs with negative RFI are more efficient. Selection on RFI as been the basis of the development of two unique selection lines of Yorkshire pigs at Iowa State University over the past decade. Now in its 8th generation, pigs from the low RFI (efficient) line consume nearly 12% less feed for the same amount of growth and backfat, compared to the high RFI (inefficient) line. Over the past years, the ISU RFI lines have been an important resource for multidisciplinary research into the genetic and biological basis of differences in efficiency during the growing phase, funded by the USDA, NPB, and IPPA. Although the emphasis of the selection lines is on efficiency during the growing phase, we have also collected extensive data on sows, including individual feed intake during lactation. In recent research funded by NPB, this has led to the important finding that pigs that are selected for increased efficiency during the growing phase also tend to have greater efficiency during lactation and have slightly better reproductive performance in terms of litter size and litter weight at birth and weaning. Lactation feed intake is an important trait in swine husbandry to maximize the productivity of the sow. Decreased feed intake during lactation results in reduction in body reserves and reduce milk output, which impacts the growth of litter and there by affects the profitability.
Recent developments in genomics have given us important tools to investigate the genetic basis of traits of interest and to develop tools, in the form of genetic markers and gene tests, that can be used to select for traits such as feed efficiency, which are difficult to improve by conventional means. Capitalizing on this, and with funds from NPB, we recently used the 60k PigChip on 720 pigs from the two lines to successfully identify genomic regions associated with RFI and component traits during the growing phase, using Genome-Wide Association Studies (GWAS). The main objective of this research was to apply this same GWAS to identify genomic regions and markers that are associated with feed efficiency during lactation and reproductive performance. The present study is the first attempt to study the genetic architecture of lactation efficiency traits using a genome wide association analysis. For this purpose, combined genotypes of over 48,000 genetic markers from across the genome on 520 sows with lactation feed efficiency and reproduction traits from first and/or second parity were used to identify regions of the genome that are associated with these important traits. Multiple regions were found for most traits, with several regions affecting multiple traits. Data on parity 1 and parity 2 were analyzed separately; the amount of overlap between regions was limited, suggesting that different genes control reproduction and efficiency in first versus later parities. Several of the identified regions were consistent with regions that were found in previous research and for most regions important candidate genes that could harbor the causative mutations were identified. Although these results are promising and provide avenues for further research, these results need to be validated in other populations before they can be recommended as markers to be used for selection. To this end, we will be able to use data from a parallel GWAS project on sow feed efficiency in two commercial breeding lines that we are collaborating on with the University of Alberta and Genesus Inc.