Genome Wide Association Studies for Milk Production Traits in Chinese Holstein Population
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{"title"=>"Genome wide association studies for milk production traits in Chinese Holstein population", "type"=>"journal", "authors"=>[{"first_name"=>"Li", "last_name"=>"Jiang", "scopus_author_id"=>"56784727400"}, {"first_name"=>"Jianfeng", "last_name"=>"Liu", "scopus_author_id"=>"51665144000"}, {"first_name"=>"Dongxiao", "last_name"=>"Sun", "scopus_author_id"=>"14919704800"}, {"first_name"=>"Peipei", "last_name"=>"Ma", "scopus_author_id"=>"36911507700"}, {"first_name"=>"Xiangdong", "last_name"=>"Ding", "scopus_author_id"=>"36647183400"}, {"first_name"=>"Ying", "last_name"=>"Yu", "scopus_author_id"=>"56911305200"}, {"first_name"=>"Qin", "last_name"=>"Zhang", "scopus_author_id"=>"56180272100"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0013661", "sgr"=>"78149436393", "issn"=>"19326203", "pui"=>"359931349", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pmid"=>"21048968", "scopus"=>"2-s2.0-78149436393"}, "id"=>"5d432f05-c892-333a-af9f-13fd64baf64a", "abstract"=>"Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk production traits using current state-of-the-art SNP genotyping technology, i.e., the Illumina BovineSNP50 BeadChip. In the analyses, the five most commonly evaluated milk production traits are involved, including milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP) and milk protein percentage (PP). Estimated breeding values (EBVs) of 2,093 daughters from 14 paternal half-sib families are considered as phenotypes within the framework of a daughter design. Association tests between each trait and the 54K SNPs are achieved via two different analysis approaches, a paternal transmission disequilibrium test (TDT)-based approach (L1-TDT) and a mixed model based regression analysis (MMRA). In total, 105 SNPs were detected to be significantly associated genome-wise with one or multiple milk production traits. Of the 105 SNPs, 38 were commonly detected by both methods, while four and 63 were solely detected by L1-TDT and MMRA, respectively. The majority (86 out of 105) of the significant SNPs is located within the reported QTL regions and some are within or close to the reported candidate genes. In particular, two SNPs, ARS-BFGL-NGS-4939 and BFGL-NGS-118998, are located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively. Our findings herein not only provide confirmatory evidences for previously findings, but also explore a suite of novel SNPs associated with milk production traits, and thus form a solid basis for eventually unraveling the causal mutations for milk production traits in dairy cattle.", "link"=>"http://www.mendeley.com/research/genome-wide-association-studies-milk-production-traits-chinese-holstein-population-7", "reader_count"=>81, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>21, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>7, "Student > Master"=>13, "Other"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>21, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>7, "Student > Master"=>13, "Other"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>61, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Physics and Astronomy"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>61}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Colombia"=>1, "Egypt"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/821930"], "description"=>"a<p>Numbers of SNPs commonly detected by both methods.</p>b<p>Numbers of SNPs detected by either L1-TDT or MMRA.</p>", "links"=>[], "tags"=>["snps", "l1-tdt"], "article_id"=>492296, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Numbers_of_significant_SNPs_detected_by_L1_TDT_and_MMRA_/492296", "title"=>"Numbers of significant SNPs detected by L1-TDT and MMRA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:40:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/821994"], "description"=>"<p>Descriptive statistics of EBVs and the accuracy of five milk production traits for 2,093 daughters.</p>", "links"=>[], "tags"=>["ebvs"], "article_id"=>492367, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t001", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Descriptive_statistics_of_EBVs_and_the_accuracy_of_five_milk_production_traits_for_2_093_daughters_/492367", "title"=>"Descriptive statistics of EBVs and the accuracy of five milk production traits for 2,093 daughters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/822169"], "description"=>"<p>Note: See note to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-t004\" target=\"_blank\">Table 4</a>.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>492541, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t008", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wise_significant_p_lt_0_05_SNPs_with_protein_percentage_PP_/492541", "title"=>"Genome-wise significant (p<0.05) SNPs with protein percentage (PP).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:41:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/821964"], "description"=>"a<p>Derived from the most recent bovine genome sequence assembly (Btau_4.0) (<a href=\"http://www.ncbi.nlm.nih.gov/genome/guide/cow/\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/genome/guide/cow/</a>)</p>b<p>These SNPs are not assigned to any chromosomes.</p>", "links"=>[], "tags"=>["snps", "distances", "adjacent"], "article_id"=>492331, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributions_of_SNPs_after_quality_control_and_the_average_distances_between_adjacent_SNPs_on_each_chromosome_/492331", "title"=>"Distributions of SNPs after quality control and the average distances between adjacent SNPs on each chromosome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:40:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/822071"], "description"=>"<p>Note: See note to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-t004\" target=\"_blank\">Table 4</a>.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>492444, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wise_significant_p_lt_0_05_SNPs_with_protein_yield_PY_/492444", "title"=>"Genome-wise significant (p<0.05) SNPs with protein yield (PY).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:40:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/822135"], "description"=>"<p>Note: SNPs with a superscript “a” are detected by L1-TDT only, SNPS with a superscript “b” are detected by MMRA only, SNPs with a superscript “ab” are detected by both L1-TDT and MMRA, and SNPs in italic are located within the QTL regions reported previously. Names in parentheses are standard RRS/RS names in the NCBI database (<a href=\"http://www.ncbi.nlm.nih.gov\" target=\"_blank\">http://www.ncbi.nlm.nih.gov</a>).</p>c<p>The nearest known gene to the significant SNP.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>492505, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wise_significant_p_/492505", "title"=>"Genome-wise significant (<i>p</i><0.05) SNPs for milk yield (MY).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:41:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/821771"], "description"=>"<p>Under the null hypothesis of no association at any SNP locus, the points would be expected to follow the slope lines. Deviations from the slope lines correspond to loci that deviate from the null hypotheses.</p>", "links"=>[], "tags"=>["plots", "genome-wide", "mmra"], "article_id"=>492138, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.g002", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantile_quantile_Q_Q_plots_of_genome_wide_association_results_by_MMRA_for_five_milk_production_traits_/492138", "title"=>"Quantile-quantile (Q-Q) plots of genome-wide association results by MMRA for five milk production traits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 22:39:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/821627"], "description"=>"<p>Chromosomes 1–29 and X are shown separated by color. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-g001\" target=\"_blank\">Fig. 1-a1, 1-a2, 1-a3, 1-a4 and 1-a5</a> refer to plots generated by L1-TDT for MY, FY, PY, FP and PP, respectively. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-g001\" target=\"_blank\">Fig. 1-b1, 1-b2, 1-b3, 1-b4 and 1-b5</a> refer to plots generated by MMRA for MY, FY, PY, FP and PP, respectively. The corresponding horizontal lines indicate the genome-wise significance levels (−log<sub>10</sub>(1.28×10<sup>−6</sup>) for L1-TDT and −log<sub>10</sub>(1.24×10<sup>−6</sup>) for MMRA).</p>", "links"=>[], "tags"=>["plots", "snp", "loci", "sequential"], "article_id"=>491991, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_plots_of_log_10_p_values_for_association_of_SNP_loci_with_five_milk_production_traits_in_sequential_order_/491991", "title"=>"Genome-wide plots of −log<sub>10</sub>(<i>p</i>-values) for association of SNP loci with five milk production traits in sequential order.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 22:38:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/822037"], "description"=>"<p>Note: See note to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-t004\" target=\"_blank\">Table 4</a>.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>492408, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t007", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wise_significant_p_lt_0_05_SNPs_with_fat_percentage_FP_/492408", "title"=>"Genome-wise significant (p<0.05) SNPs with fat percentage (FP).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:40:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/822099"], "description"=>"<p>Note: See note to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013661#pone-0013661-t004\" target=\"_blank\">Table 4</a>.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>492470, "categories"=>["Genetics"], "users"=>["Li Jiang", "Jianfeng Liu", "Dongxiao Sun", "Peipei Ma", "Xiangdong Ding", "Ying Yu", "Qin Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0013661.t005", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wise_significant_p_/492470", "title"=>"Genome-wise significant (<i>p</i><0.05) SNPs with fat yield (FY).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 22:41:02"}

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