利用全基因组高通量SNP标记定位猪乳头数和断奶体重QTL
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摘要
本研究构建了二花脸×通城、二花脸×荣昌、二花脸x巴马香和二花脸x沙子岭4个F2资源群体,利用Illumina porcine 60k DNA芯片判定了392头F2代仔猪个体及其亲本的基因型,并对乳头数表型进行了全基因组关联分析以定位猪的乳头数QTL。
结果表明：13个总乳头数QTL(7个5%基因组显著水平和6个1%基因组显著水平)分别定位于SSC1、SSC3、SSC5、SSC6、SSC7、SSC9、SSC10、SSC12、SSC13和SSC14,其中,位于SSC1、SSC3、SSC5、SSC6、SSC10和SSC12上的8个QTL与前人的定位结果相同,位于SSC7、SSC9、SSC13和SSC14上的5个QTL为新检测到的总乳头数QTL；11个左侧乳头数QTL(2个5%基因组显著水平和9个1%基因组显著水平)分别定位于SSC3、SSC4、SSC7、SSC8、SSC9、SSC10、SSC13、SSC14、SSC15和SSC18,其中,有5个QTL与总乳头数QTL一致,另外,SSC8上的QTL验证了前人的报道,其余染色体上的QTL为首次报道的左侧乳头数QTL；9个右侧乳头数QTL(1个5%基因组显著水平和8个1%基因组显著水平)分别定位于SSC1、SSC3、SSC5、SSC6、SSC7、SSC12和SSC13,其中,有7个QTL与总乳头数QTL相同,另外,SSC1上的QTL与前人的报道相同,其余染色体上的QTL为新发现的右侧乳头数QTL。
通过最显著关联的SNP标记的F值下降3来确定QTL的临界区域,并通过Ensemble和NCBI网站猪基因组数据库搜寻猪乳头数QTL区域内的位置候选基因,结果发现了RBFOX2、ARID5A、PDIA2、ACTB、DYRKIA、TUBAL3、MYOCD、NEDD9、PPRC1、CUEDC2、CYP17A1和INSIG1共12个位置候选基因,这些结果为深入鉴别控制猪乳头数的因果基因(QTG)提供了重要的参考。
本研究在四个不同的资源群体中检测到多个不同的影响乳头数的QTL,发现左右侧乳头数QTL大多位于不同染色体区域,且增加乳头数形成的QTL有利等位基因来源于不同的地方猪种始祖,这些结果一方面体现出左右乳头发育的不对称性,另一方面揭示出乳头数遗传基础的复杂性。
本研究构建了二花脸×通城、二花脸×荣昌、二花脸×巴马香和二花脸×沙子岭4个F2资源群体,利用Illumina porcine 60k DNA芯片判定了392头F2代仔猪个体及其亲本的基因型,并利用仔猪45日龄断奶体重表型进行了全基因组关联分析以定位仔猪45日龄断奶体重QTL,结果在4个F2资源群体中定位到了9个(5个5%基因组显著水平,4个1%基因组显著水平)影响仔猪45日龄断奶体重的QTL,它们分别位于SSC1、SSC2、SSC5、SSC7、SSC11和SSC14,其中在二花脸×巴马香资源群体中定位到正效应最大的QTL,位于SSC7的103.85 Mb处；在二花脸×沙子岭F2资源群体中检测到负效应最大的QTL,位于SSC14的43.77 Mb处。
前人研究将28-42日龄仔猪断奶体重QTL定位于SSC1、SSC2、SSC4、SSC7、SSC9、SSC15、SSC17和SSC18,本研究也在SSC1、SSc2和SSC7这3条染色体上检测到了仔猪断奶体重QTL,这些QTL分别位于二花脸×荣昌资源群体SSC1的291.24 Mb处、二花脸×沙子岭资源群体SSC2的40.31 Mb处、二花脸×通城资源群体SSC7的7.23Mb、二花脸×荣昌资源群体SSc7的28.13 Mb和二花脸x巴马香资源群体SSC7的103.85 Mb处,而位于二花脸×荣昌猪F2资源群体SSC7上的断奶体重QTL与前人的定位结果相同。
在Ensemble和NCBI网站的猪基因组数据库中搜寻45日龄仔猪断奶体重QTL置信区间内的位置候选基因,结果表明AGPAT1、RNF5、NOTCH4、DPF3、CYP2R1、COPB1、PDE3B、NOP2和GDF3等9个基因可作为影响仔猪断奶体重的位置候选基因。这些结果为全面揭示断奶体重的分子遗传机理和最终鉴别控制断奶体重的因果突变位点提供了有利的前期工作基础。
Four F2 resource populations of Erhualian×Tongcheng, Erhualian×Rongchang, Erhualian×Bamaxiang and Erhualian×Shaziling were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for teat number in pigs.
Results showed that thirteen QTLs for total teat number including seven at 5% and six at 1% genome-wide significance level were mapped to SSC1, SSC3, SSC5, SSC6, SSC7, SSC9, SSC10, SSC12, SSC13 and SSC14. Eight QTLs on SSC1, SSC3, SSC5, SSC6, SSC10 and SSC12 were overlaped with the previous QTLs, and 5 QTLs on SSC7, SSC9, SSC13 and SSC14 were detected only in this study. Eleven QTLs for teat number at left side including two at 5% and nine at 1% genome-wide significance level were detected on SSC3, SSC4, SSC7, SSC8, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18, and 5 Of the 11 QTLs were overlaped with the QTLs for total teat number, QTL for left teat number on SSC8 was consistent with the previous reports, and the other chromosomes including SSC3, SSC4, SSC7, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18 contained novel QTLs for this trait. Nine QTLs for teat number at right side including one at 5% and eight at 1% genome-wide significance level were detected on SSC1, SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13, and of them,7 QTLs were overlaped with the QTLs for total teat number, QTL on SSC1 confirmed previous report, and QTLs for right teat number on SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13 were detected for the first time.
The confidence intervals of QTL were defined by SNPs with lower F values of 3 compared with the most significantly associated SNP marker. Twelve positional candidate genes within the QTL confidence intervals were characterized for teat number including RBFOX2, ARID5A, PDIA2, ACTB, DYRK1A, TUBAL3, MYOCD, NEDD9, PPRC1, CUEDC2, CYP17A1 and INSIG1. These results would benefit the final characterization of the responsible genes for teat number.
This study detected multiple QTLs for teat number in 4 F2 resource populations from Chinese indigenous pig crosses. A majority of QTLs for teat number at left and right sides were found in different chromsomal regions. The favourable QTL alleles for increased teat number were originated from different Chinese founder breeds. The results reflected the genetic basis of teat asymmetry and the complex genetic architecture of teat number in pigs.
Four F2 resource populations including Erhualian x Tongcheng, Erhualian x Rongchang, Erhualian x Bamaxiang and Erhualian x Shaziling intercross were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina Porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for body weight of piglets weaned at day 45. Nine QTLs for this trait were mapped to SSC1, SSC2, SSC5, SSC7, SSC11 and SSC14, respectively, including five 5% genome-wide significant QTLs and four 1% genome-wide significant QTLs. The most significant QTL with Erhualian-derived favorable alleles was detected at 103.85 Mb on SSC7 in the Erhualian x Bamaxiang cross, and the most significant QTL with non-Erhualian originated favourable alleles was evidenced at 43.77 Mb on SSC14 in the Erhualian×Shaziling resource population.
The previous studies showed that the QTLs for body weight of piglets weaned at days 28 to 42 were mapped to SSC1, SSC2, SSC4, SSC7, SSC9, SSC15, SSC17 and SSC18. In this study, QTLs for weaned body weight were also deteced on SSC1, SSC2 and SSC7, including one QTL located at 291.24 Mb on SSC1 in the Erhualian x Rongchang resource population, one at 40.31 Mb on SSC2 in the Erhualian×Shaziling resource population, three at 7.23Mb,28.13 Mb and 103.85 Mb on SSC7 in the Erhualian x Tongcheng, Erhualian x Rongchang and Erhualian x Bamaxiang resource population, respectively, QTL on SSC7 in the Erhualian x Rongchang resource population was consistent with the previous report.
Positional candidate genes in the QTL regions were characterized from pig genome database on Ensemble and NCBI. Nine positional candidate genes were identified, including AGPAT1, RNF5, NOTCH4, DPF3, CYP2R1, COPB1, PDE3B, NOP2 and GDF3.
These findings revealed the genetic architecture of weaned body weight and could benefit the final chracterization of the causative genes and mutations for weaned body weight.
结果表明：13个总乳头数QTL(7个5%基因组显著水平和6个1%基因组显著水平)分别定位于SSC1、SSC3、SSC5、SSC6、SSC7、SSC9、SSC10、SSC12、SSC13和SSC14,其中,位于SSC1、SSC3、SSC5、SSC6、SSC10和SSC12上的8个QTL与前人的定位结果相同,位于SSC7、SSC9、SSC13和SSC14上的5个QTL为新检测到的总乳头数QTL；11个左侧乳头数QTL(2个5%基因组显著水平和9个1%基因组显著水平)分别定位于SSC3、SSC4、SSC7、SSC8、SSC9、SSC10、SSC13、SSC14、SSC15和SSC18,其中,有5个QTL与总乳头数QTL一致,另外,SSC8上的QTL验证了前人的报道,其余染色体上的QTL为首次报道的左侧乳头数QTL；9个右侧乳头数QTL(1个5%基因组显著水平和8个1%基因组显著水平)分别定位于SSC1、SSC3、SSC5、SSC6、SSC7、SSC12和SSC13,其中,有7个QTL与总乳头数QTL相同,另外,SSC1上的QTL与前人的报道相同,其余染色体上的QTL为新发现的右侧乳头数QTL。
通过最显著关联的SNP标记的F值下降3来确定QTL的临界区域,并通过Ensemble和NCBI网站猪基因组数据库搜寻猪乳头数QTL区域内的位置候选基因,结果发现了RBFOX2、ARID5A、PDIA2、ACTB、DYRKIA、TUBAL3、MYOCD、NEDD9、PPRC1、CUEDC2、CYP17A1和INSIG1共12个位置候选基因,这些结果为深入鉴别控制猪乳头数的因果基因(QTG)提供了重要的参考。
本研究在四个不同的资源群体中检测到多个不同的影响乳头数的QTL,发现左右侧乳头数QTL大多位于不同染色体区域,且增加乳头数形成的QTL有利等位基因来源于不同的地方猪种始祖,这些结果一方面体现出左右乳头发育的不对称性,另一方面揭示出乳头数遗传基础的复杂性。
本研究构建了二花脸×通城、二花脸×荣昌、二花脸×巴马香和二花脸×沙子岭4个F2资源群体,利用Illumina porcine 60k DNA芯片判定了392头F2代仔猪个体及其亲本的基因型,并利用仔猪45日龄断奶体重表型进行了全基因组关联分析以定位仔猪45日龄断奶体重QTL,结果在4个F2资源群体中定位到了9个(5个5%基因组显著水平,4个1%基因组显著水平)影响仔猪45日龄断奶体重的QTL,它们分别位于SSC1、SSC2、SSC5、SSC7、SSC11和SSC14,其中在二花脸×巴马香资源群体中定位到正效应最大的QTL,位于SSC7的103.85 Mb处；在二花脸×沙子岭F2资源群体中检测到负效应最大的QTL,位于SSC14的43.77 Mb处。
前人研究将28-42日龄仔猪断奶体重QTL定位于SSC1、SSC2、SSC4、SSC7、SSC9、SSC15、SSC17和SSC18,本研究也在SSC1、SSc2和SSC7这3条染色体上检测到了仔猪断奶体重QTL,这些QTL分别位于二花脸×荣昌资源群体SSC1的291.24 Mb处、二花脸×沙子岭资源群体SSC2的40.31 Mb处、二花脸×通城资源群体SSC7的7.23Mb、二花脸×荣昌资源群体SSc7的28.13 Mb和二花脸x巴马香资源群体SSC7的103.85 Mb处,而位于二花脸×荣昌猪F2资源群体SSC7上的断奶体重QTL与前人的定位结果相同。
在Ensemble和NCBI网站的猪基因组数据库中搜寻45日龄仔猪断奶体重QTL置信区间内的位置候选基因,结果表明AGPAT1、RNF5、NOTCH4、DPF3、CYP2R1、COPB1、PDE3B、NOP2和GDF3等9个基因可作为影响仔猪断奶体重的位置候选基因。这些结果为全面揭示断奶体重的分子遗传机理和最终鉴别控制断奶体重的因果突变位点提供了有利的前期工作基础。
Four F2 resource populations of Erhualian×Tongcheng, Erhualian×Rongchang, Erhualian×Bamaxiang and Erhualian×Shaziling were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for teat number in pigs.
Results showed that thirteen QTLs for total teat number including seven at 5% and six at 1% genome-wide significance level were mapped to SSC1, SSC3, SSC5, SSC6, SSC7, SSC9, SSC10, SSC12, SSC13 and SSC14. Eight QTLs on SSC1, SSC3, SSC5, SSC6, SSC10 and SSC12 were overlaped with the previous QTLs, and 5 QTLs on SSC7, SSC9, SSC13 and SSC14 were detected only in this study. Eleven QTLs for teat number at left side including two at 5% and nine at 1% genome-wide significance level were detected on SSC3, SSC4, SSC7, SSC8, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18, and 5 Of the 11 QTLs were overlaped with the QTLs for total teat number, QTL for left teat number on SSC8 was consistent with the previous reports, and the other chromosomes including SSC3, SSC4, SSC7, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18 contained novel QTLs for this trait. Nine QTLs for teat number at right side including one at 5% and eight at 1% genome-wide significance level were detected on SSC1, SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13, and of them,7 QTLs were overlaped with the QTLs for total teat number, QTL on SSC1 confirmed previous report, and QTLs for right teat number on SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13 were detected for the first time.
The confidence intervals of QTL were defined by SNPs with lower F values of 3 compared with the most significantly associated SNP marker. Twelve positional candidate genes within the QTL confidence intervals were characterized for teat number including RBFOX2, ARID5A, PDIA2, ACTB, DYRK1A, TUBAL3, MYOCD, NEDD9, PPRC1, CUEDC2, CYP17A1 and INSIG1. These results would benefit the final characterization of the responsible genes for teat number.
This study detected multiple QTLs for teat number in 4 F2 resource populations from Chinese indigenous pig crosses. A majority of QTLs for teat number at left and right sides were found in different chromsomal regions. The favourable QTL alleles for increased teat number were originated from different Chinese founder breeds. The results reflected the genetic basis of teat asymmetry and the complex genetic architecture of teat number in pigs.
Four F2 resource populations including Erhualian x Tongcheng, Erhualian x Rongchang, Erhualian x Bamaxiang and Erhualian x Shaziling intercross were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina Porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for body weight of piglets weaned at day 45. Nine QTLs for this trait were mapped to SSC1, SSC2, SSC5, SSC7, SSC11 and SSC14, respectively, including five 5% genome-wide significant QTLs and four 1% genome-wide significant QTLs. The most significant QTL with Erhualian-derived favorable alleles was detected at 103.85 Mb on SSC7 in the Erhualian x Bamaxiang cross, and the most significant QTL with non-Erhualian originated favourable alleles was evidenced at 43.77 Mb on SSC14 in the Erhualian×Shaziling resource population.
The previous studies showed that the QTLs for body weight of piglets weaned at days 28 to 42 were mapped to SSC1, SSC2, SSC4, SSC7, SSC9, SSC15, SSC17 and SSC18. In this study, QTLs for weaned body weight were also deteced on SSC1, SSC2 and SSC7, including one QTL located at 291.24 Mb on SSC1 in the Erhualian x Rongchang resource population, one at 40.31 Mb on SSC2 in the Erhualian×Shaziling resource population, three at 7.23Mb,28.13 Mb and 103.85 Mb on SSC7 in the Erhualian x Tongcheng, Erhualian x Rongchang and Erhualian x Bamaxiang resource population, respectively, QTL on SSC7 in the Erhualian x Rongchang resource population was consistent with the previous report.
Positional candidate genes in the QTL regions were characterized from pig genome database on Ensemble and NCBI. Nine positional candidate genes were identified, including AGPAT1, RNF5, NOTCH4, DPF3, CYP2R1, COPB1, PDE3B, NOP2 and GDF3.
These findings revealed the genetic architecture of weaned body weight and could benefit the final chracterization of the causative genes and mutations for weaned body weight.
引文
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