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
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.
