27We present a novel way to select for highly polygenic traits. For millennia, 28 humans have used observable phenotypes to selectively breed stronger or more 29 productive livestock and crops. Selection on genotype, using single-nucleotide 30 polymorphisms (SNPs) and quantitative trait loci (QTLs), is also now applied broadly in 31 livestock breeding programs; however, selection on protein or mRNA expression 32 markers have not been proved useful yet. Here we demonstrate the utility of protein 33 markers to select for disease-resistant behaviour in the European honey bees (Apis 34 mellifera L.). Robust, mechanistically-linked protein expression markers, by integrating 35 cis and trans effects from many genomic loci, may overcome limitations of genomic 36 markers to allow for selection. After three generations of selection, the resulting stock 37 performed as well or better than bees selected using phenotype-based assessment of 38 this trait, when challenged with disease. This is the first demonstration of the efficacy of 39 protein markers for selective breeding in any agricultural species, plant or animal. 40 41 Significance statement 42The honey bee has been in the news a lot recently, largely because of world-43 wide die-offs due to the parasitic Varroa mite, which is becoming resistant to the 44 chemical controls the bee industry uses. In this study, we show that robust expression 45 biomarkers of a disease-resistance trait can be used, in an out-bred population, to select 46 for that trait. After three generations of selection, the resulting stock performed as well or 47 better than bees selected using the phenotypic best method for assessing this trait when 48 challenged with disease. This is the first demonstration of an expression marker for 49 selective breeding in any agricultural species, plant or animal. This also represents a 50 completely novel way to select for highly polygenic traits. 51Bees do, however, have some effective disease-resistance traits, which also 67 happen to be highly polygenic: one example is the social immunity function known as 68 hygienic behaviour. Bees exhibiting hygienic behaviour are more efficient at removing 69 dead, diseased, or dying brood from the hive 9, 10 , enabling them to resist or at least co-70 exist with pathogens such as American Fouldbrood (Paenibacillus larvae) or parasites 71 such as Varroa mites (V. destructor) that would otherwise kill the colony. A closely 72 related but distinct trait known as Varroa-sensitive hygiene enables bees to detect and 73 disrupt the life cycle of reproductive female Varroa mites 11 . Both hygienic behaviour and 74Varroa-sensitive hygiene are heritable 12, 13 and can therefore be selectively bred for; 75 likewise, QTLs and SNPs have been linked to each behaviour 14, 15
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