P5011 Fine mapping the QTL for growth traits in outbred chicken advanced intercross lines by improved ddGBS

Wang, Y.; Cao, Xianglin; Gu, X. R.; Hu, Xingwang

doi:10.2527/jas2016.94supplement4120a

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“…Although information of QTN at the nucleotide level is largely unknown, cruder measures derived from classical quantitative trait locus (QTL) mapping, regional heritability mapping (e.g. [ 37 – 42 ]) or functional genome annotation [ 43 ] are available and could be used to crudely identify regions of the genome that may be suitable for introducing recombination hotspots. We believe that much of the benefit of shifting recombination hotspots would likely be obtained with crude knowledge of regions of the genome that harbour QTN rather than very refined knowledge of the precise location and effect of each QTN.…”

Section: Discussionmentioning

confidence: 99%

The potential of shifting recombination hotspots to increase genetic gain in livestock breeding

et al. 2017

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BackgroundThis study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs.MethodsWe simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance.ResultsOur results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain.DiscussionShifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended on the distribution of QTN in the genome, the number of recombination hotspots and whether QTN were initially inside or outside recombination hotspots.ConclusionsOur findings show future scope for targeted modification of recombination hotspots e.g. through changes in zinc-finger motifs of the PRDM9 protein to increase genetic gain in production species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0330-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%