Within-line segregation as contributors to long-term, single-trait selection responses in the Virginia chicken lines

• Populations display a remarkable capability to adapt under natural or artificial selection, even far beyond the original phenotype range, given intense single trait selection. The genetic mechanisms to facilitate this however, are still unclear. Here we use an Advanced Intercross Line, generated after 40 generations of intense bi-directional selection from a common outbred founder population, in an attempt to quantify the contribution of still segregating variants to the selection response.While the selection response of the founding lines has been extensively profiled within this population, this has been done under the assumption that the most important regions were fixed for divergent alleles between the lines. Investigating beyond this paradigm has been previously hampered due to requirements in power, marker density, and number of recombination events. Here we use a large low-coverage sequencing dataset that has been imputed to both founder-line haplotypes as well as dense marker coverage using high-quality, deep-coverage sequenced founders. Utilizing this dataset for a multi-locus GWAS approach to contrast with a more traditional cross-QTL methodology, the aim of this study is to identify novel regions that contribute to the phenotype and assess whether and how they contribute to the selection response. Out of 40 (a=890g, 23.9% of total phenotypic variance) Loci retained in the multilocus model, 24 (a=557.5g, 15% of total phenotypic variance) do not overlap known QTL. While some freely segregate between lines, 14 (a=346.6g, 9.3% of total phenotypic variance) of them are fixed in at least one founding line, and likely contribute a significant fraction of the selection response.The variance effect prediction result provides a functional view of markers. The RNASEH2B and TBXAS1 genes were considered as candidates, with previous research supporting body weight-related functions. For GALNT7, ENSGALG00000049347, TOM1, ENSGALG00000013583, ENSGALG00000039245, CHD7, and CNTNAP5 genes, the high conservation score provides a clue of being important for biological functions. However, the mechanism by which these genes regulate body weight still remains limited.

Ämnesord

LANTBRUKSVETENSKAPER  -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)

AGRICULTURAL SCIENCES  -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)

Nyckelord

Bioinformatik

Bioinformatics

Publikations- och innehållstyp

vet (ämneskategori)

ovr (ämneskategori)