A genomic inference of the White Plymouth Rock genealogy

Abstract

Crossing of populations has been, and still is, a central component in domestication and breed and variety formation. It is a way for breeders to utilize heterosis and to introduce new genetic variation into existing plant and livestock populations. During the mid-19th century, several chicken breeds that had been introduced to America from Europe and Asia became the founders for those formed in the USA. Historical records about the genealogy of these populations are often unclear and inconsistent. Here, we used genomics in an attempt to describe the ancestry of the White Plymouth Rock (WPR) chicken. In total, 150 chickens from the WPR and 8 other stocks that historical records suggested contributed to its formation were whole-genome re-sequenced. The admixture analyses of the autosomal and sex chromosomes showed that the WPR was likely founded as a cross between a paternal lineage that was primarily Dominique, and a maternal lineage where Black Java and Cochin contributed in essentially equal proportions. These results were consistent and provided quantification with the historical records that they were the main contributors to the WPR. The genomic analyses also revealed genome-wide contributions (<10% each) by Brahma, Langshan, and Black Minorca. When viewed on an individual chromosomal basis, contributions varied considerably among stocks.

Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history

“…This likely reflects large changes in the genome resulting from intensive breeding. The modern heavy US breeds shared common ancestors with breeds from Asia, which was as expected based on historical records and more recent analyses (Dana et al, 2011 ; Ekarius, 2007 ; Guo et al, 2019 ) describing that the Asian chicken breeds have been used to improve the local breeds in the United States. Liyang (a descendent of the Shanghai chicken) is related to multiple Asian and Western breeds further supporting the expected role of this heavy breed, or closely related ancestors of it, in the cross‐breeding (admixture) that were central for producing western meat‐type chickens (Figure 3d ).…”

“…The clustering of BM with WL is also consistent with BM being used in modern efforts to increase the size of the Leghorn breed (Roberts, 2009 ). The HWS and LWS are, however, meat‐type birds bred from the heavy White Plymouth Rock but the clustering might in part be due to the finding in an earlier study that the BM was one of the ancestors contributing to the WPR founder population of the HWS/LWS (Guo et al, 2019 ).…”

“…The current study uses both publicly available (Guo et al, 2016 , 2019 ; Li et al, 2017 ; Ulfah et al, 2016 ; Wang et al, 2015 ) and newly generated whole‐genome sequencing data (Figure 1a,b ). The new sequence data ( n = 341 individuals from 12 breeds) were generated from libraries prepared using the NeoPrep Library Prep System (Illumina) and sequenced to, on average, 8× genome coverage by paired end (2×150 bp) sequencing on the IIlumina Hiseq X Ten system at CLOUD HEALTH.…”

“…Earlier genomics‐based population genetics studies in livestock and nonmodel organisms have explored population differences, inferred demographic histories, and quantified admixture to provide deeper insights to the origin, evolution, and domestication of a range of species (Beichman et al, 2018 ; Guo et al, 2019 ; Lawal et al, 2020 ; Wang et al, 2020 ). Large‐scale sequencing and statistical analyses of the data are no longer the major barrier for such analyses, but rather the collection of suitable samples.…”

Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage

“…All 59 high (HWS) and low (LWS) founders of the AIL (n HWS = 29 and n LWS = 30) were wholegenome re-sequenced to ~30X coverage (Guo et al 2019). The obtained reads were then mapped to the newest reference genome (GalGal6a, Genome Reference Consortium 2018) using BWA (version 0.7.17 (Li 2013)).…”