Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially ...Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.展开更多
为评估不同SNP标记密度对凡纳滨对虾AHPND抗性基因组预测准确性的影响,本实验对26个全同胞家系进行Vp_(AHPND)侵染,收集686尾个体的存活时间数据,对其中242尾个体利用液相芯片“黄海芯1号”(55.0 K SNP)进行基因分型,基于A、G和H亲缘关...为评估不同SNP标记密度对凡纳滨对虾AHPND抗性基因组预测准确性的影响,本实验对26个全同胞家系进行Vp_(AHPND)侵染,收集686尾个体的存活时间数据,对其中242尾个体利用液相芯片“黄海芯1号”(55.0 K SNP)进行基因分型,基于A、G和H亲缘关系矩阵估计Vp_(AHPND)侵染后存活时间的遗传参数;采用随机和等距抽取方式,基于55.0K SNP构建了8个低密度SNP面板(40.0、30.0、20.0、10.0、5.0、1.0、0.5和0.1 K),利用GBLUP和ssGBLUP等方法预测Vp_(AHPND)侵染后存活时间的基因组育种值,利用交叉验证方法计算其预测准确性,并与BLUP方法进行对比分析。遗传参数估计结果显示,Vp_(AHPND)侵染后存活时间表现为高遗传力水平,估计值为0.68~0.79。在55.0 K SNP密度下,针对242尾基因分型个体数据集(G242),利用BLUP、GBLUP和ssGBLUP方法获得的预测准确性分别为0.424、0.450和0.452,GBLUP和ssGBLUP比BLUP分别提升了6.13%和6.60%;针对686尾表型测定个体数据集(P686),利用BLUP和ssGBLUP方法获得的预测准确性分别为0.510和0.535,后者比前者提升了4.90%。对于8个低密度SNP面板,当SNP密度≥10.0 K时,基因组预测准确性变化幅度在G242和P686数据集中均较小(1.1%~1.8%);随着SNP密度自10.0 K不断降低,基因组预测准确性在2个数据集中也不断降低,其中5.0 K密度降幅为0.6%~2.6%、1.0 K密度降幅为5.8%~11.0%、0.5 K密度降幅为11.4%~17.2%、0.1 K密度降幅为38.8%~41.6%。10.0 K与55.0 K SNP密度间基因组亲缘系数、GEBV的相关系数均高于0.99,表明利用10.0 K SNP面板可以准确地预测同胞个体间的亲缘关系及其GEBV。研究表明,使用10.0 K SNP面板对Vp_(AHPND)侵染后存活时间进行基因组遗传评估可以得到与55.0 K SNP芯片近似的预测准确性,为低密度SNP分型芯片设计提供了参考。展开更多
基金the National Key R&D Program of China(No.2018YFD0901301),the Shandong Province’s Agricultural Seed Improvement Project(No.2017LZN011)the Central Public-interest Scientific Institution Basal Research Fund,CAFS(No.20603022020003)+3 种基金the China Agriculture Research System(CARS-48)the Projects of International Exchange and Cooperation in Agriculture of Ministry of Agriculture and Rural Affairs of China–Science,Technology and Innovation Cooperation Cooperation in Aquaculture with Tropical Countriesthe Introduction of International Advanced Agricultural Science and Technology Plan of China(No.2016-X39)the Major Applied Technology Innovation Project of Agriculture in Shandong Province(No.SD2019YY001).
文摘Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.
文摘为评估不同SNP标记密度对凡纳滨对虾AHPND抗性基因组预测准确性的影响,本实验对26个全同胞家系进行Vp_(AHPND)侵染,收集686尾个体的存活时间数据,对其中242尾个体利用液相芯片“黄海芯1号”(55.0 K SNP)进行基因分型,基于A、G和H亲缘关系矩阵估计Vp_(AHPND)侵染后存活时间的遗传参数;采用随机和等距抽取方式,基于55.0K SNP构建了8个低密度SNP面板(40.0、30.0、20.0、10.0、5.0、1.0、0.5和0.1 K),利用GBLUP和ssGBLUP等方法预测Vp_(AHPND)侵染后存活时间的基因组育种值,利用交叉验证方法计算其预测准确性,并与BLUP方法进行对比分析。遗传参数估计结果显示,Vp_(AHPND)侵染后存活时间表现为高遗传力水平,估计值为0.68~0.79。在55.0 K SNP密度下,针对242尾基因分型个体数据集(G242),利用BLUP、GBLUP和ssGBLUP方法获得的预测准确性分别为0.424、0.450和0.452,GBLUP和ssGBLUP比BLUP分别提升了6.13%和6.60%;针对686尾表型测定个体数据集(P686),利用BLUP和ssGBLUP方法获得的预测准确性分别为0.510和0.535,后者比前者提升了4.90%。对于8个低密度SNP面板,当SNP密度≥10.0 K时,基因组预测准确性变化幅度在G242和P686数据集中均较小(1.1%~1.8%);随着SNP密度自10.0 K不断降低,基因组预测准确性在2个数据集中也不断降低,其中5.0 K密度降幅为0.6%~2.6%、1.0 K密度降幅为5.8%~11.0%、0.5 K密度降幅为11.4%~17.2%、0.1 K密度降幅为38.8%~41.6%。10.0 K与55.0 K SNP密度间基因组亲缘系数、GEBV的相关系数均高于0.99,表明利用10.0 K SNP面板可以准确地预测同胞个体间的亲缘关系及其GEBV。研究表明,使用10.0 K SNP面板对Vp_(AHPND)侵染后存活时间进行基因组遗传评估可以得到与55.0 K SNP芯片近似的预测准确性,为低密度SNP分型芯片设计提供了参考。
