Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross

Moura, Ana Silvia Alves Meira Tavares; Ledur, Mônica Corrêa; Boschiero, Clarissa; Nones, Kátia; Pinto, L. F. B.; Jaenisch, F. R. F.; Burt, David W.; Coutinho, Luiz Lehmann

doi:10.1007/s13353-015-0325-2

Cited by 6 publications

(12 citation statements)

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“…We performed the GWAS studies in a F2 experimental population generated from a cross between a white-egg type (layer, CC) line and a meat-type (broiler, TT) line 30 . These lines have a different background and previously underwent multi-trait selection for different traits for several generations, exhibiting considerable differences in growth and carcass traits 8 , 31 . According to Campos et al .…”

Section: Discussionmentioning

confidence: 99%

“…This F 2 -TCTC generation was previously used to map numerous QTLs for performance, carcass and chemical component traits 8 – 10 , 31 , 33 , 75 using microsatellite markers. For the study reported in this paper, selection of families for genotyping and GWAS was based on F1 males that appeared to be heterozygous for QTL effects reported in previous studies.…”

Section: Methodsmentioning

confidence: 99%

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Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Moreira

Boschiero

Cesar

et al. 2018

Sci Rep

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Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43–0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Moreira

Boschiero

Cesar

et al. 2018

Sci Rep

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“…Currently, QTLs have been mapped for various carcassrelated traits, including carcass weight, muscle weight, bone weight, viscera weight, and its ratio to carcass weight or body weight at slaughtering age (Sharman et al, 2007;Ankrabadu et al, 2010b;Nassar et al, 2012;Moura et al, 2016). In the present study, we focused on the TMW to PMAW ratio, which is possibly the first trial in QTL mapping for carcass-related traits.…”

Section: Discussionmentioning

confidence: 99%

Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method

et al. 2019

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In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth and carcass-related trait QTLs using 319 F 2 chickens obtained from intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcassrelated traits were also measured at this timepoint. A genetic linkage map was constructed using 545 single nucleotide polymorphism (SNP) markers that were developed using a restriction-site associated DNA sequencing method. The linkage map included the 23 autosomes and the Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant and suggestive main-effect QTLs for growth and carcass-related traits present on chromosomes 1, 2, 3, 5, 8, 19, 24, and Z. These loci explained 5.60-16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlapped with those of previously reported QTLs, whereas the targeted traits varied. Our QTLs will aid future breeding programs in improving growth and meat yield of chickens (e.g., via marker-assisted selection), particularly in the Japanese brand chicken industry.

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“…Twenty eight chickens from two different experimental lines with pedigree control and multi-trait selection by Embrapa Swine and Poultry National Research Center (Brazil) were sequenced: 14 individuals from a paternal broiler line called TT (7 females and 7 males), and 14 from a layer line called CC (7 females and 7 males). Previously, these two experimental lines were used to generate a reciprocal F 2 Resource population for QTL mapping studies [ 13 , 14 ].…”

Section: Methodsmentioning

confidence: 99%

“…In Brazil, Embrapa Swine and Poultry National Research Center maintains several chicken lines under multi-trait selection in Brazilian climatic and nutritional conditions for more than 20 years. Two of those lines, a white-egg type (layer) and a meat-type (broiler), due to considerable difference in their growth rates and carcass yields, were utilized to generate an F2 experimental population for QTL mapping studies [ 13 , 14 ]. The CC layer line used in this study is a white-egg laying hen originated from the White Leghorn, and it has been selected since 1989 mainly for reproductive traits such as egg production and fertility, besides egg quality traits [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

et al. 2018

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BackgroundMeat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.ResultsA total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.ConclusionsIn this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.

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Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross

Cited by 6 publications

References 47 publications

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

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