Abstract
The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
Highlights
Identifying key polymorphisms and dissecting the genetic architecture of complex growth traits is of considerable interest in fields like agriculture breeding and evolution
We reported a running chicken advanced intercross line (AIL) that was generated by crossing High Quality chicken Line A (HQLA) × Huiyang Bearded (HB), which was differentially bred for fast growth and slow growth prior to subsequent intercrossing
Systematic characterization of the genetic architecture of AIL makes it possible to evaluate the suitability of different genomic situations for genome wide association studies (GWASs)
Summary
Identifying key polymorphisms and dissecting the genetic architecture of complex growth traits is of considerable interest in fields like agriculture breeding and evolution. It is not enough to rely on a single generation of meiotic recombination to break up and randomize the parental genomes to finely map causal variants of complex quantitative traits (Flint et al, 2005) Improved strategies, such as the use of larger sample cohorts, the construction of advanced intercross lines (AIL) (Besnier et al, 2011; Parker et al, 2012), nested association mapping population (NAM), and multiparent advanced generation inter-cross (MAGIC) in animals and plants (Poland et al, 2011; Gatti et al, 2014; Pascual et al, 2015) can increase the precision of quantitative trait loci (QTL) mapping by introducing more recombination events and together provide a series of alternatives to the traditional association mapping of populations. We should always pay attention to the tradeoff between mapping resolution and statistical power, as the causal allele may become rare with a continuous increase of the inbreeding coefficient in the AIL (Yalcin et al, 2010; Parker et al, 2016)
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