Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysi...Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations.展开更多
Mature wild-type yellow catfish( Pelteobagrus fulvidraco Richardson) individuals with excellent traits have been screened from the Yangtze River as broodstock to establish the germplasm bank of pure-line yellow catfis...Mature wild-type yellow catfish( Pelteobagrus fulvidraco Richardson) individuals with excellent traits have been screened from the Yangtze River as broodstock to establish the germplasm bank of pure-line yellow catfish by artificial gynogenesis technique and hormonal sex reversal method. Based on pure lines of yellow catfish,super-males and physiological females of yellow catfish were selected by GMT technique,hormonal sex reversal method and test-crossing to establish the germplasm bank of YY physiological females( YY♀). The propagation system of male yellow catfish( XY♂) was established based on the combination of super-males( YY♂) and pure-line female( XX♀) for large-scale production of pure-line yellow catfish males,which effectively overcome the disadvantages in the production of common fingerlings and male fingerlings using low-grade fish with slow growth and small size at the bottom of the fish grader as broodfish,such as progeny germplasm degeneration,loss of growth vigor and reduction of breeding benefits. The technical route of breeding pure-line YY physiological females( YY♀) and YY super-males( YY♂) laid the foundation for large-scale production of environmentally friendly yellow catfish males with pure germplasm and strong stress resistance,and provided an efficient,stable,healthy,environmentally friendly,energy-saving and income-increasing approach for sustainable development of yellow catfish breeding industry.展开更多
为探讨甘芪品系高抗麻口病特性在蛋白质水平上的抗病机制,利用iBAQ(intensity-basedabsolute-protein-quantification)非标记定量蛋白质组学技术分析鉴定具有高抗麻口病特性的甘芪纯系群体(HQ_(1)、HQ_(6)、HQ_(19))与高感麻口病黄芪(CK...为探讨甘芪品系高抗麻口病特性在蛋白质水平上的抗病机制,利用iBAQ(intensity-basedabsolute-protein-quantification)非标记定量蛋白质组学技术分析鉴定具有高抗麻口病特性的甘芪纯系群体(HQ_(1)、HQ_(6)、HQ_(19))与高感麻口病黄芪(CK)在蛋白质水平上的表达差异,收集HQ_(1)、HQ_(6)、HQ_(19)及CK中的总蛋白,通过SDS-聚丙烯酰氨凝胶电泳对总蛋白进行分离,胶内酶解,提出肽段,运用LC-MS/MS获得质谱图,于Uniport蛋白数据库中检索以及iBAQ非标定量分析,筛选出差异蛋白与特异性表达蛋白,对其进行基因本体(gene ontology,GO)功能和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路富集分析。结果表明,通过LC-MS/MS分析共鉴定到蛋白质169个,其中8个蛋白质在甘芪品系与CK之间的差异具有统计学意义(P<0.05),有6个蛋白质特异性表达,NADH脱氢酶亚基7与蔗糖合酶在差异蛋白与特异性蛋白中均存在。生物学分析发现差异蛋白大多富集在分子功能方面的ATP合成上,特异性蛋白多富集在生物过程方面,包括参与肉桂酸、麦角甾醇等生物合成以及蔗糖、乙酰辅酶A、L-苯丙氨酸分解等代谢过程,对以上蛋白进行KEGG通路富集,发现50%的蛋白参与了新陈代谢通路,包括能量代谢、氨基酸代谢、脂质代谢等。该方法筛选出了与甘芪品系高抗麻口病特性相关的多种蛋白质,包括NADH脱氢酶亚基7、蔗糖合酶、查尔酮合酶及非特异性丝氨酸/苏氨酸蛋白激酶等。展开更多
基金supported by the National Key Research and Development Program of China (2016YFD0101804)the National Natural Science Foundation of China (31671280)HarvestPlus (part of the CGIAR Research Program on Agriculture for Nutrition and Health, http://www.harvestplus.org/)
文摘Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations.
基金Supported by Implementation Plan of Subsidy Project for the Reform and Construction of Grassroots Agricultural Technology Extension System
文摘Mature wild-type yellow catfish( Pelteobagrus fulvidraco Richardson) individuals with excellent traits have been screened from the Yangtze River as broodstock to establish the germplasm bank of pure-line yellow catfish by artificial gynogenesis technique and hormonal sex reversal method. Based on pure lines of yellow catfish,super-males and physiological females of yellow catfish were selected by GMT technique,hormonal sex reversal method and test-crossing to establish the germplasm bank of YY physiological females( YY♀). The propagation system of male yellow catfish( XY♂) was established based on the combination of super-males( YY♂) and pure-line female( XX♀) for large-scale production of pure-line yellow catfish males,which effectively overcome the disadvantages in the production of common fingerlings and male fingerlings using low-grade fish with slow growth and small size at the bottom of the fish grader as broodfish,such as progeny germplasm degeneration,loss of growth vigor and reduction of breeding benefits. The technical route of breeding pure-line YY physiological females( YY♀) and YY super-males( YY♂) laid the foundation for large-scale production of environmentally friendly yellow catfish males with pure germplasm and strong stress resistance,and provided an efficient,stable,healthy,environmentally friendly,energy-saving and income-increasing approach for sustainable development of yellow catfish breeding industry.
文摘为探讨甘芪品系高抗麻口病特性在蛋白质水平上的抗病机制,利用iBAQ(intensity-basedabsolute-protein-quantification)非标记定量蛋白质组学技术分析鉴定具有高抗麻口病特性的甘芪纯系群体(HQ_(1)、HQ_(6)、HQ_(19))与高感麻口病黄芪(CK)在蛋白质水平上的表达差异,收集HQ_(1)、HQ_(6)、HQ_(19)及CK中的总蛋白,通过SDS-聚丙烯酰氨凝胶电泳对总蛋白进行分离,胶内酶解,提出肽段,运用LC-MS/MS获得质谱图,于Uniport蛋白数据库中检索以及iBAQ非标定量分析,筛选出差异蛋白与特异性表达蛋白,对其进行基因本体(gene ontology,GO)功能和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路富集分析。结果表明,通过LC-MS/MS分析共鉴定到蛋白质169个,其中8个蛋白质在甘芪品系与CK之间的差异具有统计学意义(P<0.05),有6个蛋白质特异性表达,NADH脱氢酶亚基7与蔗糖合酶在差异蛋白与特异性蛋白中均存在。生物学分析发现差异蛋白大多富集在分子功能方面的ATP合成上,特异性蛋白多富集在生物过程方面,包括参与肉桂酸、麦角甾醇等生物合成以及蔗糖、乙酰辅酶A、L-苯丙氨酸分解等代谢过程,对以上蛋白进行KEGG通路富集,发现50%的蛋白参与了新陈代谢通路,包括能量代谢、氨基酸代谢、脂质代谢等。该方法筛选出了与甘芪品系高抗麻口病特性相关的多种蛋白质,包括NADH脱氢酶亚基7、蔗糖合酶、查尔酮合酶及非特异性丝氨酸/苏氨酸蛋白激酶等。
