In the face of climate change and the growing global population,there is an urgent need to accelerate the development of high-yielding crop varieties.To this end,vast amounts of genotype-to-phenotype data have been co...In the face of climate change and the growing global population,there is an urgent need to accelerate the development of high-yielding crop varieties.To this end,vast amounts of genotype-to-phenotype data have been collected,and many machine learning(ML)models have been developed to predict phenotype from a given genotype.However,the requirement for high densities of single-nucleotide polymorphisms(SNPs)and the labor-intensive collection of phenotypic data are hampering the use of these models to advance breeding.Furthermore,recently developed genomic selection(GS)models,such as deep learning(DL),are complicated and inconvenient for breeders to navigate and optimize within their breeding programs.Here,we present the development of an intelligent breeding platform named AutoGP(http://autogp.hzau.edu.cn),which integrates genotype extraction,phenotypic extraction,and GS models of genotype-to-phenotype data within a user-friendly web interface.AutoGP has three main advantages over previously developed platforms:1)an efficient sequencing chip to identify high-quality,high-confidence SNPs throughout gene-regulatory networks;2)a complete workflow for extraction of plant phenotypes(such as plant height and leaf count)from smartphone-captured video;and 3)a broad model pool,enabling users to select from five ML models(support vector machine,extreme gradient boosting,gradient-boosted de-cision tree,multilayer perceptron,and random forest)and four commonly used DL models(deep learning genomic selection,deep learning genomic-wide association study,deep neural network for genomic pre-diction,and SoyDNGP).For the convenience of breeders,we use datasets from the maize(Zea mays)com-plete-diallel design plus unbalanced breeding-like inter-cross population as a case study to demonstrate the usefulness of AutoGP.We show that our genotype chips can effectively extract high-quality SNPs asso-ciated with days to tasseling and plant height.The models show reliable predictive accuracy on different populations and can provide effective guidance for breeders.Overall,AutoGP offers a practical solution to streamline the breeding process,enabling breeders to achieve more efficient and accurate genomic selection.展开更多
[Purpose] The paper is to discuss the high-efficient breeding technology platform of dwarf male-sterile wheat.[Method] Conclusion was made upon the development of the creation and application of dwarf male-sterile whe...[Purpose] The paper is to discuss the high-efficient breeding technology platform of dwarf male-sterile wheat.[Method] Conclusion was made upon the development of the creation and application of dwarf male-sterile wheat,and the conception of introducing haploid breeding technology into the technological system of high-efficient breeding of dwarf male-sterile wheat was proposed.[Result] Dwarf male-sterile wheat not only retains the properties of total male abortion of Taigu Genetic Sterile Wheat,steady sterility,and high hybrid rate after open pollination,but also has the characteristic of high dwarfing ability of Aibian No.1,becoming a comparatively ideal population modification means.At present,the application of dwarf male-sterile wheat mainly includes germplasm resources platform of population modification by using dwarf male-sterile wheat,technology platform of constructing new high-efficient breeding system by using dwarf male-sterile wheat,and production platform of using dwarf male-sterile wheat to breed new varieties.Through the introduction of haploid breeding into the already established wheat high-efficient breeding system,a new system of high-efficient biological breeding technology of dwarf male-sterile wheat was constructed theoretically.[Conclusion] The study provides references to the further study and application of dwarf male-sterile wheat.展开更多
Progress in plant breeding depends on the development of genetic resources,genetic knowledge,and breeding techniques.The core of plant breeding is the use of naturally occurring variation.At the beginning of the post-...Progress in plant breeding depends on the development of genetic resources,genetic knowledge,and breeding techniques.The core of plant breeding is the use of naturally occurring variation.At the beginning of the post-genomic era,a new concept of"breeding by design"was proposed,which aims to control all allelic variation for all genes of agronomic importance.In the past two decades,we have applied a three-step strategy for research on rice breeding by design.In the first step,we constructed a singlesegment substitution line(SSSL)library using Huajingxian 74(HJX74),an elite xian(indica)rice cultivar,as the recipient in which to assemble genes from the rice AA genome.In the second step,we identified a series of desirable genes in the SSSL library.In the third step,we designed new rice lines,and achieved the breeding goals by pyramiding target genes in the HJX74-SSSL library.This review introduces the background,concept,and strategy of breeding by design,as well as our achievements in rice breeding by design using the HJX74-SSSL platform.Our practice shows that target chromosome-segment substitution is a way to breeding by design.展开更多
基金supported by Biological Breeding-National Science and Technology Major Project(2023ZD04076)the National Key Research and Development Program of China(2023YFF1000100)+2 种基金the National Natural Science Foundation of China(32321005 and 32261143463)the Fundamental Research Funds for the Central Universities of China(2662024XXPY001)the Outstanding Youth Team Cultivation Project of Center Universities(2662023PY007).
文摘In the face of climate change and the growing global population,there is an urgent need to accelerate the development of high-yielding crop varieties.To this end,vast amounts of genotype-to-phenotype data have been collected,and many machine learning(ML)models have been developed to predict phenotype from a given genotype.However,the requirement for high densities of single-nucleotide polymorphisms(SNPs)and the labor-intensive collection of phenotypic data are hampering the use of these models to advance breeding.Furthermore,recently developed genomic selection(GS)models,such as deep learning(DL),are complicated and inconvenient for breeders to navigate and optimize within their breeding programs.Here,we present the development of an intelligent breeding platform named AutoGP(http://autogp.hzau.edu.cn),which integrates genotype extraction,phenotypic extraction,and GS models of genotype-to-phenotype data within a user-friendly web interface.AutoGP has three main advantages over previously developed platforms:1)an efficient sequencing chip to identify high-quality,high-confidence SNPs throughout gene-regulatory networks;2)a complete workflow for extraction of plant phenotypes(such as plant height and leaf count)from smartphone-captured video;and 3)a broad model pool,enabling users to select from five ML models(support vector machine,extreme gradient boosting,gradient-boosted de-cision tree,multilayer perceptron,and random forest)and four commonly used DL models(deep learning genomic selection,deep learning genomic-wide association study,deep neural network for genomic pre-diction,and SoyDNGP).For the convenience of breeders,we use datasets from the maize(Zea mays)com-plete-diallel design plus unbalanced breeding-like inter-cross population as a case study to demonstrate the usefulness of AutoGP.We show that our genotype chips can effectively extract high-quality SNPs asso-ciated with days to tasseling and plant height.The models show reliable predictive accuracy on different populations and can provide effective guidance for breeders.Overall,AutoGP offers a practical solution to streamline the breeding process,enabling breeders to achieve more efficient and accurate genomic selection.
基金Supported by Innovation Center of Agricultural Sciences,HubeiProvince~~
文摘[Purpose] The paper is to discuss the high-efficient breeding technology platform of dwarf male-sterile wheat.[Method] Conclusion was made upon the development of the creation and application of dwarf male-sterile wheat,and the conception of introducing haploid breeding technology into the technological system of high-efficient breeding of dwarf male-sterile wheat was proposed.[Result] Dwarf male-sterile wheat not only retains the properties of total male abortion of Taigu Genetic Sterile Wheat,steady sterility,and high hybrid rate after open pollination,but also has the characteristic of high dwarfing ability of Aibian No.1,becoming a comparatively ideal population modification means.At present,the application of dwarf male-sterile wheat mainly includes germplasm resources platform of population modification by using dwarf male-sterile wheat,technology platform of constructing new high-efficient breeding system by using dwarf male-sterile wheat,and production platform of using dwarf male-sterile wheat to breed new varieties.Through the introduction of haploid breeding into the already established wheat high-efficient breeding system,a new system of high-efficient biological breeding technology of dwarf male-sterile wheat was constructed theoretically.[Conclusion] The study provides references to the further study and application of dwarf male-sterile wheat.
基金supported by the Major Program of Transgenic New Variety Breeding of China(2009ZX08009005)the National Natural Science Foundation of China(91435207 and 91735304)。
文摘Progress in plant breeding depends on the development of genetic resources,genetic knowledge,and breeding techniques.The core of plant breeding is the use of naturally occurring variation.At the beginning of the post-genomic era,a new concept of"breeding by design"was proposed,which aims to control all allelic variation for all genes of agronomic importance.In the past two decades,we have applied a three-step strategy for research on rice breeding by design.In the first step,we constructed a singlesegment substitution line(SSSL)library using Huajingxian 74(HJX74),an elite xian(indica)rice cultivar,as the recipient in which to assemble genes from the rice AA genome.In the second step,we identified a series of desirable genes in the SSSL library.In the third step,we designed new rice lines,and achieved the breeding goals by pyramiding target genes in the HJX74-SSSL library.This review introduces the background,concept,and strategy of breeding by design,as well as our achievements in rice breeding by design using the HJX74-SSSL platform.Our practice shows that target chromosome-segment substitution is a way to breeding by design.
