Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of the RB1 gene in chicken

Abstract

Previously, a quantitative trait locus (QTL) that affects body weight (BW) at 4-12 weeks of age and carcass weight at 12 weeks of age had been mapped on chicken chromosome 1. After including more markers and individuals, the confidence interval was narrowed down to approximately 5.5 Mbps and located this QTL near a microsatellite marker (ADL328). This QTL is the same as the QTL for 12 bone traits, including metatarsus length and metatarsus circumference at 4, 6, 8, 10 and 12 weeks of age and keel length and metatarsus claw weight at 12 weeks of age, that was identified using the same population. In the current study, 1010 individuals from the Northeast Agricultural University F(2) resource population were used and 14 single-nucleotide polymorphism (SNPs) around ADL328 were developed to construct haplotypes, and an association analysis was performed to fine-map the QTL. The haplotypes were constructed on the basis of a sliding 'window', with three SNP markers included in each 'window'. The association analysis results indicated that the haplotypes in 'windows' 6-12 were significantly associated with BW and bone traits and suggested that the QTL for BW and bone traits was located between SNP8 and SNP14 or was in linkage disequilibrium with this region. The interval from SNP8 to SNP14 was approximately 400 kbps. This region contained five RefSeq genes (RB1, P2RY5, FNDC3A, MLNR and CAB39L) on the University of California Santa Cruz website. The RB1 gene was selected as a candidate gene and five SNPs were identified in the gene. The association results indicated that the RB1 gene was a major gene for BW and bone traits. The SNPs g.39692 G>A and g.77260 A>G in RB1 gene might be two quantitative trait nucleotides for BW and bone traits.

Allelic Variation in Cinnamyl Alcohol Dehydrogenase (LoCAD) Associated with Wood Properties of Larix olgensis

“…Linkage disequilibrium: LD was measured as the squared correlation of allele frequencies R 2 , which was affected by both recombination and differences in allele frequencies between sites [33]. The R 2 value between each pair of 29 common SNPs (minor allele frequencies > 0.10) in LoCAD was calculated using Haploview software (http://www.broad.mit.edu/mpg/haploview.html).…”

“…Intuitively, haplotypes (a block of linked ordered markers) may be more powerful than individual markers [35,36]. In this study, haplotypes were constructed based on a sliding "window" that consisted of three markers; the "window" was allowed to slide one marker at a time ( Figure S3, Table S2) [33]. The haplotypes of each "window" were constructed using the HAPLOTYPE procedure in SAS 9.1.3 software (Chapel Hill, NC, USA).…”

Comparative Study on Various Growth Performances of Korean Oge and White Leghorn Chickens

“…were found on chromosome 1 for 12 on bone traits, and the retinoblastoma 1 (RB1) gene has strong relation with bone traits (Zhang et al, 2011). Examination of growth performances on chest width and chest grith helps for the understanding and selection of breeds for the meat production and weight.…”

Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers

“…According to Zhang et al (2011), QTL mapping is a major approach to detecting genetic variability of economically important traits. Zhang et al (2010) studied bone traits and identified 12 QTL between LEI0079 and ROS0025 markers on GGA1.…”

“…The use of advanced techniques for genome studies can be an effective alternative in order to decrease skeletal problems in heavy broilers. Quantitative trait loci (QTL) mapping is one of the major approaches in molecular genetic studies for detecting genetic variability of economically important traits (Zhang et al, 2011). Mapping studies have identified regions in the chicken genome that contribute to characterization of genetic variation, thus allowing mapping of candidate genes.…”