Identification of new genes and quantitative trait locis associated with growth curve parameters in F2 chicken population using genome‐wide association study

Moroudi, R. Seifi; Mahyari, Saeid Ansari; Torshizi, R Vaez; Lanjanian, Hossein; Masoudi‐Nejad, Ali

doi:10.1111/age.13038

Cited by 14 publications

(2 citation statements)

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“…Each nonlinear function has 3 or more parameters, having the potential to summarize or derivatives of production-related traits ( Ramos et al . , 2013 ; Ware and Power, 2017 ; Küçüktopcu and Cemek, 2021 ; Seifi Moroudi et al . , 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Investigation of egg production curve in ostrich using nonlinear functions

Shibak

Maghsoudi²,

Rokouei³

et al. 2023

Poultry Science

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Section: Introductionmentioning

confidence: 99%

Investigation of egg production curve in ostrich using nonlinear functions

Shibak

Maghsoudi²,

Rokouei³

et al. 2023

Poultry Science

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“…Accurately detecting sequence variation associated with traits of economic importance in the domestic chicken is a major goal of genetic research into this globally widespread dietary protein source [1]. Many groups are now genotyping chicken genomes to discover the underlying molecular basis of specific traits [2][3][4][5][6], but current methods, both sequence-and array-based, have unquantified limitations in assessing the underlying variation that connects many loci to studied traits.…”

Section: Introductionmentioning

confidence: 99%

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Rice¹,

Alberdi²,

Alfieri³

et al. 2023

Preprint

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Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Results. We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K ‘feathering’ locus using short reads, which would not be possible using a linear reference. Conclusions. We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

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