Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens' comb formation. Fixation index (FST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger FST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, FST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.

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“…comparing FST values between distinct populations (Vitalis et al, 2001;Guo et al, 2016;Lillie et al, 2018).…”

Section: Genomic Regions With High Levels Of Genetic Differentiation mentioning

confidence: 99%

“…Both FST and π statistics are useful for the detection of selection signatures (Lillie et al, 2018).…”

Section: Genomic Regions With High Levels Of Genetic Differentiation mentioning

confidence: 99%

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Identifying Signatures of Selection Related to Comb Development

Liu

Zhang

et al. 2021

J. Poult. Sci.

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“…Throughout the long-term experiment, individual selection has been practiced within the respective HWS and LWS lines, and by avoiding matings among half sib or close relatives, the resulting inbreeding is moderate given the low effective population sizes (N eHWS = 32 and N eLWS = 38, respectively) [13,15,25,26]. Now, after more than 60 generations of bi-directional selection, there is an approximately 15-fold difference in body weight between them [26].…”

Section: Discussionmentioning

confidence: 99%

Haplotype Purging after Relaxation of Selection in Lines of Chickens That Had Undergone Long-Term Selection for High and Low Body Weight

Yang

Zan

Honaker

et al. 2020

Genes

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Bi-directional selection for increased and decreased 56-day body weights (BW56) has been applied to two lines of White Plymouth Rock chickens—the Virginia high (HWS) and low (LWS) body weight lines. Correlated responses have been observed, including negative effects on traits related to fitness. Here, we use high and low body weight as proxies for fitness. On a genome-wide level, relaxed lines (HWR, LWR) bred from HWS and LWS purged some genetic variants in the selected lines. Whole-genome re-sequencing was here used to identify individual loci where alleles that accumulated during directional selection were purged when selection was relaxed. In total, 11 loci with significant purging signals were identified, five in the low (LW) and six in the high (HW) body weight lineages. Associations between purged haplotypes in these loci and BW56 were tested in an advanced intercross line (AIL). Two loci with purging signals and haplotype associations to BW56 are particularly interesting for further functional characterization, one locus on chromosome 6 in the LW covering the sour-taste receptor gene PKD2L1, a functional candidate gene for the decreased appetite observed in the LWS and a locus on chromosome 20 in the HW containing a skeletal muscle hypertrophy gene, DNTTIP1.

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“…Most of these differences were due to changes at many loci, with each having small additive effects (Jacobsson et al, 2005). Lillie et al (2018) reviewed the genomic signatures of these lines, which differ in percentage of adipose tissue as well as in abdominal fat (Sutherland et al, 2018). The increased adiposity, heavier fat pads, and higher percentage carcass fat was also observed in comparisons of 1957 and 1991 broilers that were of the same age and were fed the same diet (Havenstein et al, 1994).…”

Section: Discussionmentioning

confidence: 99%

Glucose Tolerance and Plasma Non-Esterified Fatty Acid Levels in Chickens Selected for Low Body Weight, Red Junglefowl, and their Reciprocal Cross

et al. 2019

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Responses of an individual to food deprivation, such as a 16-h fast, are complex, and are influenced by environmental and genetic factors. Domestication is an ongoing process during which adaptations to changing environments occur over generations. Food deprivation by their caretakers is less for domestic chickens than for their junglefowl ancestors. Unlike domestic chicken, the junglefowl adapted over generations to periods of food deprivation, which may be reflected in differences in metabolic responses to brief periods without food. Here, we compared the blood glucose and plasma levels of non-esterified fatty acids (NEFA) among four populations when deprived of feed for 16 h. The four populations included a domestic White Rock experimental line (LWS) maintained for generations under ad libitum feeding, adult red junglefowl (RJF), and a reciprocal cross of the lines. Although there were significant differences in adult (31-week) body weight between the RJF (683 g) and LWS (1282 g), with the weight of F 1 crosses being intermediate, the amount of abdominal fat relative to body weight was similar for all populations. Patterns for blood glucose responses to a glucose bolus after a 16-h fast were similar for the initial and final points in the parental and cross populations. However, RJF reached their peak faster than LWS, with the reciprocal cross intermediate to the parental populations. Plasma NEFA concentrations were higher after the 16-h fast than in fed states, with no population differences for the fasting state. However, in the fed state, NEFA levels were lesser for LWS than for others, which was reflected further in percentage change from fed to fasted. This larger change in LWS suggests differences in mobilization of energy substrates and implies that during domestication or development of the LWS line, thresholds for responses to acute stressors may have increased.

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Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Cited by 25 publications

References 41 publications

Identifying Signatures of Selection Related to Comb Development

Identifying Signatures of Selection Related to Comb Development

Haplotype Purging after Relaxation of Selection in Lines of Chickens That Had Undergone Long-Term Selection for High and Low Body Weight

Glucose Tolerance and Plasma Non-Esterified Fatty Acid Levels in Chickens Selected for Low Body Weight, Red Junglefowl, and their Reciprocal Cross

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