- relationship matrix, for birth weight, body weight at and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.. - Variations in the genome, especially single nu- cleotide polymorphisms (SNPs), are known to be associ- ated with phenotypic variation [5]. - higher copy number was observed in ani- mals with lower body weight. - The significant CNV segments associated with body weight gain (GGA overlapped with previously mapped QTLs for body weight at 49 days of age (QTL . - Moreover, both significant CNV segments overlapped with 18 out of 27 previously published QTLs for growth-related traits mapped in the Embrapa F2 Chicken Resource Population ([37], Table 2). - 1 Manhattan plots for CNV segments across the 33 autosomal chromosomes associated with a birth weight, b body weight at 35 days, c body weight at 41 days and d body weight at 42 days and e body weight gain. - Likewise, Yi et al. - [42], Gorla et al.. - [7] and Sohrabi et al. - In the present study, significant CNV segments associ- ated with performance traits on chromosome 3, for body weight at 35, 41 and 42 days and body weight gain from 35 to 41 days, and on chromosome 5 for birth weight were identified. - Given that these traits are not independ- ent, and genetic correlations between performance traits have been widely reported in chickens [45], it is ex- pected that certain CNV regions may be concomitantly associated with more than one trait, especially body weight measured in different ages (Fig. - In the qPCR validation, we systematically assessed the overall agreement rate of the significant CNV segments detected in silico with qPCR results. - We identified overlaps of significant CNV segments associated with body weight at days and body weight gain with four previously mapped QTLs for weight traits and residual feed intake (RFI). - RFI is de- fined as the difference between actual feed intake and predicted feed intake based on energy requirements for body weight gain and maintenance [46]. - associated with performance traits in the TT Reference Population. - a BWG: body weight gain from 35 to 41 days. - BW35: body weight at 35 days;. - BW41: body weight at 41 days. - BW42: body weight at 42 days. - c Number of annotated genes within a 1-Mb window of each significant CNV segment associated with performance traits in the TT Reference Population, based on Ensembl Genes 101. - found genomic windows defined by significant CNV seg- ments overlapping published QTLs for growth-related traits in the Embrapa F2 Chicken Resource Population [24].. - 2 a Birth weight, b body weight at 35 days, c body weight at 41 days and d body weight at 42 days and e body weight gain distribution in each CN state for the significant CNV segment. - Each dot represents an animal in the corresponding copy number state (0-3n) on the X-axis and the observed phenotypic value on the Y-axis. - Indeed, Pértille et al. - [37] identified 88 QTLs associated with feed conversion, feed intake, birth weight, and body weight at 35 and 41 days of age in the Embrapa F2 Chicken Resource Population. - Mebratie et al. - [46] and Moreira et al. - [48] identified, respectively, 11 and 19 QTLs associated with body weight traits in a commercial broiler chicken population and in the Embrapa F2 Chicken Resource Population. - We identified 32 genes annotated within a 1-Mb window of significant CNV segments associated with birth weight, body weight at 35, 41 and 42 days and body weight gain from 35 to 41 days.. - Note that animals presenting deletions (0n/1n) in sig- nificant CNV segments were less frequent in our popu- lation, while their average body weights at birth and at 35, 41 and 42 days of age were higher compared to ani- mals with normal copy number (2n) in the same CNV segments (Fig. - In 2010, Johansson et al. - Conversely, for body weight gain, the increase in the copy number of the respective significant CNV segment was positively associated with the phenotype (Fig. - However, as expected due to its low frequency distribution in the genome, no overlap be- tween CpG islands and the significant CNV segments was identified.. - QTL #1979 Body_weight. - QTL #1980 Body_weight. - QTL #7184 Body_weight_(41_days). - QTL #7180 Body_weight_(35_days). - QTL #55904 Body_weight_(35_days). - QTL #24377 Body_weight_(35_days). - QTL #24378 Body_weight_(41_days). - QTL #24379 Body_weight_(42_days). - QTL #7167 Body_weight_(1_day). - QTL #7171 Body_weight_(35_days). - QTL #7174 Body_weight_(41_days). - QTL #1957 Body_weight. - QTL #7156 Body_weight_(35_days). - QTL #7161 Body_weight_(41_days). - QTL #1961 Body_weight. - QTL #1962 Body_weight. - QTL #6611 Body_weight_(112_days). - QTL #6612 Body_weight_(200_days). - QTL #6610 Body_weight_(8_days). - QTL #9420 Body_weight_(63_days). - QTL #11768 Body_weight_(49_days). - QTL #11772 Body_weight_(63_days). - QTL #1969 Body_weight. - QTL #1972 Body_weight. - QTLs that overlap genomic intervals covered by CNV segments associated with body weight gain (GGA and/or body weight at 35, 41 and 42 days (GGA are highlighted in bold text. - It has been reported that the effect of the KCNJ11 gene on muscle may occur due to alterations in the KATP. - Our analysis of regulatory elements suggests that changes in the copy number in the KCNJ11 Table 3 List of notated genes within a 1-Mb window of significantly associated CNV segments. - b BWG: body weight gain from 35 to 41 days, BW35: body weight at 35 days, BW41: body weight at 41 days, BW42: body weight at 42 days, BW: birth weight. - Interestingly, a novel 163-bp indel in the downstream region of this gene was significantly associated with growth traits in chickens [56]. - expression is associated with increased body weight and muscle mass [62]. - b matching proteins IDs in the network. - c matching proteins labels in the network. - We found genes nearby significant CNV segments asso- ciated with body weight at 35, 41 and 42 days (LPIN1 and TRIB2) and body weight gain (GPRC6A and NT5DC1) that may be of special importance and have potential ef- fects on chicken growth. - Body weight was recorded at 1 (birth weight and 42 (after fasting) days of age. - Over the period be- tween 35 and 41 days of age, chickens were transferred to individual cages for measuring feed intake and body weight gain, to evaluate feed conversion. - First, the CNV segments to be used in the association analyses were established. - performance traits analyzed in the TT Reference Population. - BW21: body weight at 21 days in grams. - body weight at 35 days in grams. - BW41: body weight at 41 days in grams;. - BW42: body weight at 42 days in grams. - BWG: body weight gain from 35 to 41 days in grams. - Copy number was determined in the 3 significant CNV segments using primer pairs designed to target each segment. - BW21: Body Weight at 21 days of age. - BW35: Body Weight at 35 days of age. - BW41: Body Weight at 41 days of age. - BW42: Body Weight at 42 days of age. - BWG: Body Weight Gain;. - Additional file 2 Manhattan plots for CNV segments across the 33 autosomal chromosomes associated with (a) birth weight, (b) body weight at 35 days, (c) body weight at 41 days and (d) body weight at 42 days and (e) body weight gain. - Additional file 3 QQ-plots show the relation of normal theoretical quantiles of the probability distributions between expected (X-axis) and observed (Y-axis) p -values from (a) birth weight, (b) body weight at 35 days, (c) body weight at 41 days, (d) body weight at 42 days and (e) body weight gain. - 78 publications significantly enriched in the STRING network. - Copy number variation in the genomes of domestic animals. - Global variation in copy number in the human genome. - Genome-wide detection of CNVs and association with body weight in sheep based on 600K SNP arrays. - Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy. - Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the Silkie chicken. - Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. - A high-resolution survey of deletion polymorphism in the human genome. - Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation. - Review of quantitative trait loci identified in the chicken. - Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. - Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. - ATP Sensitive Potassium Channels in the Skeletal Muscle Function:. - Involvement of the KCNJ11(Kir6.2) Gene in the Determination of Mechanical Warner Bratzer Shear Force. - channels control energy expenditure determining body weight. - A single-nucleotide polymorphism in the 3 ′ untranslated region of the LPIN1 gene and association analysis with performance traits in chicken. - An initial map of chromosomal segmental copy number variations in the chicken.
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