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Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods.
British Poultry Science ( IF 1.6 ) Pub Date : 2020-02-26 , DOI: 10.1080/00071668.2020.1724879
A H Khaltabadi Farahani 1 , H Mohammadi 2 , M H Moradi 1 , H A Ghasemi 1
Affiliation  

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.



中文翻译:

使用贝叶斯方法通过基于单倍型的全基因组关联研究来鉴定卵重的潜在基因组区域。

1.从理论上讲,单倍型基因组可能是SNP基因型的更合适替代品,因为与全基因组关联研究中的单个SNP基因型相比,它们通常更容易捕获多等位基因QTL效应。这项研究的目的是使用GenSel软件通过适合固定长度单倍型的贝叶斯方法(BayesA,BayesB和BayesN)来鉴定与蛋重性状有关的基因组区域。

2.将600K Affymetrix芯片上常见的294,705个SNP的基因型分阶段用于1,063只产蛋母鸡。记录的特征包括第28、36、56、66、72和80周龄的第一卵重(FEW)和平均卵重。

2.从BayesB拟合1Mb单倍型导致了解释鸡蛋重量性状的遗传变异比例最高。根据性状,每个标记解释的遗传变异范围为27%至76%。

3.与卵重性状相关的单倍型窗口仅解释了遗传变异的一小部分。

4. GGA1上最上面的一个1 MB窗口解释了FEW总遗传变异的约4.05%。确定了候选基因,包括PRKAR2B,HMGA2,LEMD3,GRIP1,EHBP1,MAP3K7MYH的卵重性状。

5.鉴定了可能与卵重性状相关的几个基因组区域,其中一些与已知基因和先前报道的产卵性状的QTL区域重叠。

更新日期:2020-02-26
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