scholarly journals Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens

2016 ◽  
Vol 134 (2) ◽  
pp. 87-97 ◽  
Author(s):  
J.J. Stainton ◽  
B. Charlesworth ◽  
C.S. Haley ◽  
A. Kranis ◽  
K. Watson ◽  
...  
2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Wim Gorssen ◽  
Roel Meyermans ◽  
Steven Janssens ◽  
Nadine Buys

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.


2007 ◽  
Vol 31 (S1) ◽  
pp. S22-S33 ◽  
Author(s):  
Heike Bickeböller ◽  
Katrina A.B. Goddard ◽  
Robert P. Igo ◽  
Peter Kraft ◽  
Jingky P. Lozano ◽  
...  

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 450
Author(s):  
Youssef A. Attia ◽  
Mohammed A. Al-Harthi ◽  
Ali S. El-Shafey

This study looks at the influence of time and/or frequency of multienzymes application on productivity, carcass characteristics, metabolic profile, and red blood cell characteristics of broiler chickens. Two hundred and eighty, one-day-old Arbor Acres broiler male chicks were randomly distributed into seven treatment groups. Each group consisted of eight replicates of five unsexed birds. The same basal diet was fed in a crumble form to all experimental groups: group one was the unsupplemented control that did not receive multienzymes supplementation. Additionally, multienzymes in water were supplemented in six groups in a factorial arrangement, including three times of application (starter time only which included days 1–21 of age, grower time only which included days 22–37 of age, and starter and grower time which included days 1–37 of age) and two application frequencies (continuously or intermittently). In the continuous application, the multienzymes were added to water over 24 h in a day, while in the intermittent frequency multienzymes were added to water for one day followed by a day off according to the time of application. Regardless of time and frequency of application, enzymes supplementation significantly increased growth rate, feed intake, European Production Index (EPI), protein digestibility, serum albumin, and high-density lipoprotein (HDL). Intermittent multienzymes application during days 1–21 of age or days 22–37 of age resulted in significantly greater growth, better feed conversion rate (FCR), and higher EPI of broilers during the whole rearing period than those under continuous multienzymes during different growth periods. Besides, intermittent multienzymes addition during days 1–37 of age improved FCR of broiler chicks compared to constant application. The intermittent addition of multienzymes during days 1–21 of age or 22–37 days of age and days 1–37 of age caused a significant increase in dry matter (DM) digestibility than the continuous application. The intermittent addition of multienzymes during days 1–21 of age significantly increased the digestibility of crude protein (CP), ether extract (EE), and crude fiber (CF) compared to continuous application. A similar trend was shown in the digestibility of CP and EE due to intermittent use during days 22–37 of age. Intermittent enzymes addition significantly increased high density lipoprotein (HDL) of groups receiving enzymes during days 22–37 of age compared to continuous application of enzymes. In conclusion, the use of multienzymes intermittently during days 1–21 of age and 22–37 days of age significantly increased growth, improved FCR, and raised EPI. Intermittent use can replace continuous multienzyme applications which can save 68.6% of the cost, even though further research is need from the cost-saving edge.


BMC Genomics ◽  
2019 ◽  
Vol 20 (S3) ◽  
Author(s):  
Andrey A. Yurchenko ◽  
Tatiana E. Deniskova ◽  
Nikolay S. Yudin ◽  
Arsen V. Dotsev ◽  
Timur N. Khamiruev ◽  
...  

Microarrays ◽  
2013 ◽  
Vol 2 (3) ◽  
pp. 171-185 ◽  
Author(s):  
Lingyang Xu ◽  
Yali Hou ◽  
Derek Bickhart ◽  
Jiuzhou Song ◽  
George Liu

PLoS ONE ◽  
2009 ◽  
Vol 4 (8) ◽  
pp. e6711 ◽  
Author(s):  
Elisha D. O. Roberson ◽  
Jonathan Pevsner

2019 ◽  
Author(s):  
María I. Cádiz ◽  
María E. López ◽  
Diego Díaz-Domínguez ◽  
Giovanna Cáceres ◽  
Grazyella M. Yoshida ◽  
...  

AbstractNile tilapia (Oreochromis niloticus Linnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, using two complementary methods based in extended haplotype homozygosity (EHH)._Whole-genome sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia from two countries (Brazil and Costa Rica) was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control pipelines, a total of ~1.3M high-quality SNPs were inferred and used as input for the Integrated Haplotype Score (|iHS|) and standardized log-ratio of integrated EHH between pairs of populations (Rsb) methods. We detected 16, 174 and 96 candidate genes subjected to selection in strain A, B, and C, respectively. These candidate genes represent putative genomic landmarks that could contain functions of biological and commercial interest.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
A. Urnikyte ◽  
A. Flores-Bello ◽  
M. Mondal ◽  
A. Molyte ◽  
D. Comas ◽  
...  

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