Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
| Autor: | Chenglong Luo, Xuemin Cao, Yiqiang Zhao, Hao Qu, Jiangli Ren, Dingming Shu, Yuzhe Wang, Xiaoxiang Hu, Chunyuan Zhang, Ning Li, Zhuolin Huang, Lina Bu |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium Candidate gene lcsh:QH426-470 chicken Population Genome-wide association study Quantitative trait locus Biology haplotype association study selective sweep 03 medical and health sciences 0302 clinical medicine Genetics advanced intercross line education Genetics (clinical) Original Research Genetic association Bone growth education.field_of_study QTL fine-mapping genome-wide association study bone growth ancestral inference Genetic architecture lcsh:Genetics 030104 developmental biology Evolutionary biology 030220 oncology & carcinogenesis Molecular Medicine |
| Zdroj: | Frontiers in Genetics Frontiers in Genetics, Vol 11 (2020) |
| ISSN: | 1664-8021 |
| DOI: | 10.3389/fgene.2020.00894 |
| Popis: | The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth. |
| Databáze: | OpenAIRE |
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