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Xu Z.,Guangdong Provincial Key Laboratory of Agro Animal Genomics and Molecular Breeding | Xu Z.,Wens Nanfang Poultry Breeding Co. | Ji C.,Wens Nanfang Poultry Breeding Co. | Zhang Y.,Wens Nanfang Poultry Breeding Co. | And 6 more authors.
BMC Genomics | Year: 2016

Background: Residual feed intake (RFI) is a powerful indicator for energy utilization efficiency and responds to selection. Low RFI selection enables a reduction in feed intake without affecting growth performance. However, the effective variants or major genes dedicated to phenotypic differences in RFI in quality chickens are unclear. Therefore, a genome-wide association study (GWAS) and RNA sequencing were performed on RFI to identify genetic variants and potential candidate genes associated with energy improvement. Results: A lower average daily feed intake was found in low-RFI birds compared to high-RFI birds. The heritability of RFI measured from 44 to 83 d of age was 0.35. GWAS showed that 32 of the significant single nucleotide polymorphisms (SNPs) associated with the RFI (P < 10-4) accounted for 53.01 % of the additive genetic variance. More than half of the effective SNPs were located in a 1 Mb region (16.3-17.3 Mb) of chicken (Gallus gallus) chromosome (GGA) 12. Thus, focusing on this region should enable a deeper understanding of energy utilization. RNA sequencing was performed to profile the liver transcriptomes of four male chickens selected from the high and low tails of the RFI. One hundred and sixteen unique genes were identified as differentially expressed genes (DEGs). Some of these genes were relevant to appetite, cell activities, and fat metabolism, such as CCKAR, HSP90B1, and PCK1. Some potential genes within the 500 Kb flanking region of the significant RFI-related SNPs detected in GWAS (i.e., MGP, HIST1H110, HIST1H2A4L3, OC3, NR0B2, PER2, ST6GALNAC2, and G0S2) were also identified as DEGs in chickens with divergent RFIs. Conclusions: The GWAS findings showed that the 1 Mb narrow region of GGA12 should be important because it contained genes involved in energy-consuming processes, such as lipogenesis, social behavior, and immunity. Similar results were obtained in the transcriptome sequencing experiments. In general, low-RFI birds seemed to optimize energy employment by reducing energy expenditure in cell activities, immune responses, and physical activity compared to eating. © 2016 The Author(s).


Xu Z.-Q.,South China Agricultural University | Chen J.,South China Agricultural University | Zhang Y.,Wens Nanfang Poultry Breeding Co. | Ji C.-L.,Wens Nanfang Poultry Breeding Co. | And 2 more authors.
Journal of Integrative Agriculture | Year: 2014

Marker assisted selection (MAS) for residual feed intake (RFI) is considered to be one of the powerful means to improve feed conversion efficiency, and therefore reduce production costs. To test the inner relationship among body compositions, growth traits and RFI, four models were proposed to assess the extensively explanatory variables accounting for partial variables in feed intake besides metabolic body weight and growth rate. As a result, the original model (Koch's model) had the lowest R2 (80.78%) and the highest Bayesian information criterion (1 323.3) value among the four models. Moreover, the effects on RFI caused by single nucleotide polymorphisms (SNPs) were assessed in this study. Twelve SNPs from 7 candidate genes were genotyped in 2 Chinese native strains. rs14743490 of RPLP2 gene showed suggestively significant association with initial body weight in both strains (P<0.10). rs15047274 of TAF15 was significantly associated with growth weight, final weight, and feed intake (P<0.05) in N301 strain, in contrast, it was only suggestively significant associated with feed intake (P<0.10) in N414 strain. rs15869967 was significantly associated with RFI in N414 strain but not in N301 strain. This study has identified potential genetic markers suitable for MAS in improving the above mentioned traits, but these associations need to be rectified in other larger populations in future. © 2014 Chinese Academy of Agricultural Sciences.


Zhang D.X.,South China Agricultural University | Zhang D.X.,Wens Nanfang Poultry Breeding Co. | Xu Z.Q.,South China Agricultural University | He J.,Wens Nanfang Poultry Breeding Co. | And 3 more authors.
Journal of Animal Science | Year: 2015

Somatotropic axis–related genes contribute to reproduction of ducks. Five SNP in the 5′-flanking regions of the growth hormone (GH), prolactin (PRL), and pituitary-specific transcription factor (Pit-1) genes were identified and genotyped in a female population of Muscovy ducks. Association analysis of these SNP with Muscovy duck egg production traits was performed. Results showed that SNP C-515G of GH was significantly associated with egg number in ducks at age 59 wk (E59W; P = 0.0009) and egg number in ducks at age 300 d (E300D; P = 0.0022). Single nucleotide polymorphism C-441T of GH was significantly associated with E59W (P = 0.0014). Significant associations of SNP T-884C and T-335C of PRL with the age at first egg (A1D), E59W, and E300D were detected in this population (P < 0.0001). It was concluded that these 4 SNP might be useful markers to use with the aim of increasing Muscovy duck E59W. On the basis of genetic parameter estimation, the heritability of A1D, E300D, E59W, and molting time were 0.43 ± 0.04, 0.45 ± 0.04, 0.36 ± 0.04, and 0.04 ± 0.03, respectively. Strong positive genetic correlation was noted between E59W and E300D (correlation coefficient = 0.80), whereas a negative association was noted between E59W and A1D (correlation coefficient = –0.80). Therefore, the selection for improved A1D should also increase E59W. © 2015 American Society of Animal Science. All rights reserved.


PubMed | Wens Nanfang Poultry Breeding Co. and Guangdong Provincial Key Laboratory of Agro Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics
Type: | Journal: BMC genomics | Year: 2016

Residual feed intake (RFI) is a powerful indicator for energy utilization efficiency and responds to selection. Low RFI selection enables a reduction in feed intake without affecting growth performance. However, the effective variants or major genes dedicated to phenotypic differences in RFI in quality chickens are unclear. Therefore, a genome-wide association study (GWAS) and RNA sequencing were performed on RFI to identify genetic variants and potential candidate genes associated with energy improvement.A lower average daily feed intake was found in low-RFI birds compared to high-RFI birds. The heritability of RFI measured from 44 to 83 d of age was 0.35. GWAS showed that 32 of the significant single nucleotide polymorphisms (SNPs) associated with the RFI (P<10(-4)) accounted for 53.01% of the additive genetic variance. More than half of the effective SNPs were located in a 1Mb region (16.3-17.3Mb) of chicken (Gallus gallus) chromosome (GGA) 12. Thus, focusing on this region should enable a deeper understanding of energy utilization. RNA sequencing was performed to profile the liver transcriptomes of four male chickens selected from the high and low tails of the RFI. One hundred and sixteen unique genes were identified as differentially expressed genes (DEGs). Some of these genes were relevant to appetite, cell activities, and fat metabolism, such as CCKAR, HSP90B1, and PCK1. Some potential genes within the 500 Kb flanking region of the significant RFI-related SNPs detected in GWAS (i.e., MGP, HIST1H110, HIST1H2A4L3, OC3, NR0B2, PER2, ST6GALNAC2, and G0S2) were also identified as DEGs in chickens with divergent RFIs.The GWAS findings showed that the 1Mb narrow region of GGA12 should be important because it contained genes involved in energy-consuming processes, such as lipogenesis, social behavior, and immunity. Similar results were obtained in the transcriptome sequencing experiments. In general, low-RFI birds seemed to optimize energy employment by reducing energy expenditure in cell activities, immune responses, and physical activity compared to eating.

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