Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens

Abstract An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM: a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM, which can be used as a potential molecular breeding marker.

Download Full-text

PSIII-16 Genome-wide association mapping and functional analysis of body weight, feed intake and walking ability in turkeys

Journal of Animal Science ◽

10.1093/jas/skaa278.429 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 234-235

Author(s):

Emhimad Abdalla ◽

Bayode Makanjuola ◽

Benjamin Wood ◽

Christine F Baes ◽

Ryley J Vanderhout

Keyword(s):

Gene Ontology ◽

Body Weight ◽

Feed Intake ◽

Growth Traits ◽

Gene Set Enrichment Analysis ◽

Genome Wide Association ◽

Chromosome 1 ◽

Walking Ability ◽

Genome Wide ◽

The Impact

Abstract The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Over the last few years, genome-wide association studies (GWAS) became the de facto approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with growth traits, feed intake and walking ability in a breeding turkey line. This was followed by studying the functional evidence that may support the impact of those regions on the economic traits in turkeys. A total of 31,950 phenotypic records for body weight, feed intake and walking ability with genomic (56,393 SNP) data were provided by Hybrid Turkeys, Kitchener, Canada. The analysis was carried out using a mixed linear model with hatch-week-year and sex fitted as fixed effects and the accumulated effect of all markers captured by the genomic relationship matrix fitted as random polygenic effects. Significant markers were observed on several chromosomes across the turkey genome. For example, COL8A1 and RBPMS2 genes were identified on chromosome 1 and 12, respectively, and associated with body weight. Furthermore, a gene-set enrichment analysis was performed for each trait. These functional and positional analyses uncovered a number of gene ontology functional terms, Reactome pathways and Medical Subject Headings that showed significant enrichment of genes associated with the studied traits. Many of the observed gene ontology functional terms (e.g., skeletal muscle tissue growth, regulation of digestive system process, and adult walking behavior) are known to be related to body growth, feed intake and walking ability. The results of this study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program.

Download Full-text

SNP in pre-miR-1666 decreases mature miRNA expression and is associated with chicken performance

Genome ◽

10.1139/gen-2015-0001 ◽

2015 ◽

Vol 58 (2) ◽

pp. 81-90 ◽

Cited By ~ 6

Author(s):

Shan-He Wang ◽

Shun-Hong Wang ◽

Hong Li ◽

Gui-Rong Sun ◽

Shi-Jie Lyu ◽

...

Keyword(s):

Target Gene ◽

Growth Traits ◽

Target Selection ◽

Biological Processes ◽

Muscle Weight ◽

Resource Population ◽

Mirna Genes ◽

Muscle Tissues ◽

Chicken Carcass ◽

Selection Of

Polymorphisms in miRNA genes could potentially alter various biological processes by influencing the processing and (or) target selection of miRNAs. The rs14120863 (C > G) mutation, which we characterized in a Gushi–Anka F2 resource population, resides in the precursor region of miR-1666. Association analysis with chicken carcass and growth traits showed that the SNP was significantly associated with carcass weight, evisceration weight, breast muscle weight, leg muscle weight, and body weight at 8 weeks of age, as well as some body size indexes including shank girth, chest breadth, breast bone length, and body slanting length, in the Gushi–Anka F2 resource population. Quantitative RT–PCR results showed that miR-1666 expression levels in muscle tissues differed within various genotypes. Experiment in DF1 cells further confirmed that the SNP in miR-1666 could significantly alter mature miRNA production. Subsequently, using dual-luciferase report assay, we verified that miR-1666 could perform its function through targeting of the CBFB gene. In conclusion, the SNP in the precursor of miR-1666 could significantly reduce mature miR-1666 production. It may further affect the function of miR-1666 through the target gene CBFB, hence it is associated with chicken growth traits.

Download Full-text

Genomic prediction for growth using a low-density SNP panel in dromedary camels

Scientific Reports ◽

10.1038/s41598-021-87296-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Morteza Bitaraf Sani ◽

Javad Zare Harofte ◽

Mohammad Hossein Banabazi ◽

Saeid Esmaeilkhanian ◽

Ali Shafei Naderi ◽

...

Keyword(s):

Body Weight ◽

Birth Weight ◽

Sample Size ◽

Genetic Improvement ◽

Growth Traits ◽

P Value ◽

Dromedary Camels ◽

Genome Wide ◽

A Genome ◽

Daily Gain

AbstractFor thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.

Download Full-text

Detection of 15-bp Deletion Mutation within PLAG1 Gene and Its Effects on Growth Traits in Goats

Animals ◽

10.3390/ani11072064 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2064

Author(s):

Zhenyu Wei ◽

Ke Wang ◽

Hui Wu ◽

Zhen Wang ◽

Chuanying Pan ◽

...

Keyword(s):

Body Weight ◽

Growth Traits ◽

Body Height ◽

The Body ◽

Chest Circumference ◽

Dairy Goat ◽

Cashmere Goat ◽

Indel Mutation ◽

Body Stature ◽

Body Index

Stature and weight are important growth and development traits for animals, which also significantly affect the productivity of livestock. Polymorphic adenoma gene 1 (PLAG1) is located in the growth-related quantitative trait nucleotides (QTN), and its variation has been determined to significantly affect the body stature of bovines. This study found that novel 15-bp InDel could significantly influence important growth traits in goats. The frequencies of genotypes of the 15-bp mutation and relationship with core growth traits such as body weight, body height, height at hip cross, chest circumference, hip width and body index were explored in 1581 individuals among 4 Chinese native goat breeds. The most frequent genotypes of Shaanbei white Cashmere goat (SWCG), Inner Mongolia White Cashmere goat (IMCG) and Guanzhong Dairy goat (GZDG) were II genotypes (insertion/insertion), and the frequency of ID genotype (insertion/deletion) was found to be slightly higher than that of II genotype in Hainan Black goat (HNBG), showing that the frequency of the I allele was higher than that of the D allele. In adult goats, there were significant differences between 15-bp variation and body weight, chest circumference and body height traits in SWCG (p < 0.05). Furthermore, the locus was also found to be significantly correlated with the body index of HNBG (p = 0.044) and hip width in GZDG (p = 0.002). In regard to lambs, there were significant differences in height at the hip cross of SWCG (p = 0.036) and hip width in IMWC (p = 0.005). The corresponding results suggest that the 15-bp InDel mutation of PLAG1 is associated with the regulation of important growth characteristics of both adult and lamb of goats, which may serve as efficient molecular markers for goat breeding.

Download Full-text

Identification of Quantitative Trait Loci Influencing Traits Related to Energy Balance in Selection and Inbred Lines of Mice

Genetics ◽

10.1093/genetics/152.2.699 ◽

1999 ◽

Vol 152 (2) ◽

pp. 699-711 ◽

Cited By ~ 1

Author(s):

D E Moody ◽

D Pomp ◽

M K Nielsen ◽

L D Van Vleck

Keyword(s):

Quantitative Trait Loci ◽

Energy Balance ◽

Heat Loss ◽

Quantitative Trait ◽

Subcutaneous Fat ◽

High Heat ◽

Chromosome 1 ◽

Direct Calorimetry ◽

Resource Population ◽

Trait Loci

Abstract Energy balance is a complex trait with relevance to the study of human obesity and maintenance energy requirements of livestock. The objective of this study was to identify, using unique mouse models, quantitative trait loci (QTL) influencing traits that contribute to variation in energy balance. Two F2 resource populations were created from lines of mice differing in heat loss measured by direct calorimetry as an indicator of energy expenditure. The HB F2 resource population originated from a cross between a noninbred line selected for high heat loss and an inbred line with low heat loss. Evidence for significant QTL influencing heat loss was found on chromosomes 1, 2, 3, and 7. Significant QTL influencing body weight and percentage gonadal fat, brown fat, liver, and heart were also identified. The LH F2 resource population originated from noninbred lines of mice that had undergone divergent selection for heat loss. Chromosomes 1 and 3 were evaluated. The QTL for heat loss identified on chromosome 1 in the HB population was confirmed in the LH population, although the effect was smaller. The presence of a QTL influencing 6-wk weight was also confirmed. Suggestive evidence for additional QTL influencing heat loss, percentage subcutaneous fat, and percentage heart was found for chromosome 1.

Download Full-text

Milk production and its relationship with milk composition, body and udder morphological traits in Bedouin goat reared under arid conditions

Acta Scientiarum Animal Sciences ◽

10.4025/actascianimsci.v41i1.42552 ◽

2018 ◽

Vol 41 (1) ◽

pp. 42552

Author(s):

Fatima Kouri ◽

Salima Charallah ◽

Amina Kouri ◽

Zaina Amirat ◽

Farida Khammar

Keyword(s):

Body Weight ◽

Milk Production ◽

Milk Yield ◽

Milk Fat ◽

Morphological Traits ◽

Growth Traits ◽

Average Daily Gain ◽

Arid Conditions ◽

Daily Milk Yield ◽

Daily Milk

This research aims to assess the performances of lactating Bedouin goat under arid conditions, focusing on the relationship of milk yield with body and udder morphology and growth traits. Fourteen goats and their kids were followed during early lactation (90 days post-partum). Mean daily milk yield was 0.56 kg. Milk fat, proteins, lactose, solids non-fat and minerals were respectively 34.9, 38.9, 48.8, 107 and 6.7 g L-1. Mean kids’ birth weight, adjusted body weight at 90 days of age and average daily gain were respectively 2 kg, 6.6 kg and 51.4 g day-1. Daily milk yield was correlated with goats’ body weight, withers height, rump height, udder width and udder circumference but not with linear udder score and growth performances. These results provide important data about the milk production of Bedouin goat emphasizing its correlation with body and udder morphological traits which can help to elaborate a specific breeding program for this breed.

Download Full-text

Photoperiod on growth and egg characteristics of the white leghorn chicken

GSC Biological and Pharmaceutical Sciences ◽

10.30574/gscbps.2021.15.1.0101 ◽

2021 ◽

Vol 15 (1) ◽

pp. 151-155

Author(s):

Abdul Muumin Sadick ◽

Iddrisu Mubarik ◽

Dennis Kodzo Awalime ◽

Rebecca Akumbilim ◽

Philip Larweh ◽

...

Keyword(s):

Body Weight ◽

Weight Gain ◽

Feed Intake ◽

Growth Traits ◽

Growth Parameters ◽

Skills Training ◽

Daily Weight Gain ◽

White Leghorn ◽

Initial Body Weight ◽

Final Body Weight

One hundred and twenty (120) 16 weeks old White Leghorn layer breeds were used for the study. The objective of the study was to determine effect of photoperiod on layer chicken. The research was carried out at the Poultry Section of the Animal farm of the Department of Animal Science Education, Akenten Appiah-Menka University of Skills Training and Entrepreneurial Development, Mampong. Four treatments made up of 12 hours of light, 14 hours of light, 16 hours of light and 18 hours of light were used for the study. Each treatment was replicated three times with 10 birds per replicate in a Completely Randomized Design. Birds were exposed equally to common daylight and in the evenings, lights were turned on at specified periods. Growth parameters measured were initial body weight, daily feed intake, daily weight gain and final body weight. Egg traits measured were egg weight, albumen height, yolk color and yolk weight. The data collected were analyzed using General Linear Model procedure of Statistical Analysis System. Results from the study indicated that, varied photoperiod regimes had no significant (P>0.05) effect on initial body weight, daily feed intake but had significant (P<0.05) effect on daily weight gain and final body weight of growth traits. Photoperiod had no significant (P>0.05) effect on the egg characteristics of the white Leghorn layer bird. It was concluded from the study that, increasing photoperiod had no positive effect on growth and egg characteristics of the white Leghorn layer.

Download Full-text

Estimates of (co)variance components and genetic parameters for body weights and growth efficiency traits in the New Zealand white rabbit

World Rabbit Science ◽

10.4995/wrs.2017.7057 ◽

2017 ◽

Vol 25 (4) ◽

pp. 329 ◽

Cited By ~ 1

Author(s):

M. Sakthivel ◽

D. Balasubramanyam ◽

P. Kumarasamy ◽

H. Gopi ◽

A. Raja ◽

...

Keyword(s):

Body Weight ◽

New Zealand ◽

Variance Components ◽

Environmental Effect ◽

Genetic Parameters ◽

Growth Traits ◽

Genetic Effect ◽

Growth Efficiency ◽

Body Weights ◽

Heritability Estimates

The genetic parameters of growth traits in the New Zealand White rabbits kept at Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India were estimated by partitioning the variance and covariance components. The (co)variance components of body weights at weaning (W42), post-weaning (W70) and marketing (W135) age and growth efficiency traits viz., average daily gain (ADG), relative growth rate (RGR) and Kleiber ratio (KR) estimated on a daily basis at different age intervals (42 to 70 d; 70 to 135 d and 42 to 135 d) from weaning to marketing were estimated by restricted maximum likelihood, fitting 6 animal models with various combinations of direct and maternal effects. Data were collected over a period of 15 yr (1998 to 2012). A log-likelihood ratio test was used to select the most appropriate univariate model for each trait, which was subsequently used in bivariate analysis. Heritability estimates for W42, W70 and W135 were 0.42±0.07, 0.40±0.08 and 0.27±0.07, respectively. Heritability estimates of growth efficiency traits were moderate to high (0.18 to 0.42). Of the total phenotypic variation, maternal genetic effect contributed 14 to 32% for early body weight traits (W42 and W70) and ADG1. The contribution of maternal permanent environmental effect varied from 6 to 18% for W42 and for all the growth efficiency traits except for KR2. Maternal permanent environmental effect on most of the growth efficiency traits was a carryover effect of maternal care during weaning. Direct maternal genetic correlations, for the traits in which maternal genetic effect was significant, were moderate to high in magnitude and negative in direction. Maternal effect declined as the age of the animal increased. The estimates of total heritability and maternal across year repeatability for growth traits were moderate and an optimum rate of genetic progress seems possible in the herd by mass selection. The genetic and phenotypic correlations among body weights and between growth efficiency traits were also estimated. Moderate to high heritability and higher genetic correlation in body weight traits promise good scope for genetic improvement provided measures are taken to keep the inbreeding at the lowest level.

Download Full-text

Mapping of quantitative trait loci influencing daily body weight gain (DBWG) on chromosome 6 in German Holstein population

Biotechnology in Animal Husbandry ◽

10.2298/bah0602035r ◽

2006 ◽

Vol 22 (1-2) ◽

pp. 35-46 ◽

Cited By ~ 1

Author(s):

M. Reißmann ◽

P. Reinecke ◽

U. Müller ◽

S. Abdel-Rahman

Keyword(s):

Body Weight ◽

Weight Gain ◽

Fine Mapping ◽

Marker Assisted Selection ◽

Growth Traits ◽

Body Weight Gain ◽

Chromosome 6 ◽

Production Traits ◽

Daily Body Weight ◽

Holstein Population

Twelve microsatellite markers on chromosome 6 were analyzed in German Holstein population to detect and locate QTL affecting daily body weight gain (DBWG). The results indicate promising location for QTL controlling daily body weight gain trait on chromosome 6. Where, three markers BMS2508 BM3026 and TGLA37 at three different positions in a distance 15.2 cM on BTA6 were associated with significant effects for daily body weight gain trait (DBWG). Comparison between this finding and previously identified QTL support the location of a QTL for growth traits on chromosome 6, where a significant QTL for birth and yearling weight was previously identified on chromosome 6 tightly close to marker BM3026. Finding from this study could be used in subsequent fine-mapping work and applied to marker-assisted selection (MAS) of production traits.

Download Full-text