Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that...Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan?genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.展开更多
Sorghum,a genetically diverse C_(4) cereal,is an ideal model to study natural variation in photosynthetic capacity.Specific leaf nitrogen(SLN)and leaf mass per leaf area(LMA),as well as,maximal rates of Rubisco carbox...Sorghum,a genetically diverse C_(4) cereal,is an ideal model to study natural variation in photosynthetic capacity.Specific leaf nitrogen(SLN)and leaf mass per leaf area(LMA),as well as,maximal rates of Rubisco carboxylation(V cmax),phosphoenolpyruvate(PEP)carboxylation(V pmax),and electron transport(J max),quantified using a C_(4) photosynthesis model,were evaluated in two field-grown training sets(n=169 plots including 124 genotypes)in 2019 and 2020.展开更多
Sorghum(Sorghum bicolor),the fifth most important cereal crop worldwide,serves as a staple food in arid and semi-arid regions and is a critical resource for livestock forage,bioenergy production,and industrial applica...Sorghum(Sorghum bicolor),the fifth most important cereal crop worldwide,serves as a staple food in arid and semi-arid regions and is a critical resource for livestock forage,bioenergy production,and industrial applications.Owing to its relatively small genome and strong tolerance to abiotic stresses such as drought,salinity-alkalinity,and heat,sorghum has emerged as an important model crop for abiotic stress research.This Perspective article synthesizes recent advances on sorghum genomics,including the development of gapless reference genome assemblies,pan-genome analyses of extensive structural variation,and population resequencing studies that have uncovered domestication signatures and loci associated with stress adaptation.We also summarize the progress in sorghum genetic resource collection,selection strategies,and breeding improvement.Functional genetic studies have identified key genes regulating yield-related traits,quality attributes,and tolerance to both abiotic and biotic stresses.In molecular breeding,notable achievements include the establishment of efficient transformation systems,CRiSPR/Cas9-mediated genome editing enhanced by morphogenic regulators,and the development of mutagenized populations for gene function validation.Nevertheless,major challenges remain,particularly in functional dissection of complex quantitative traits,the integration of multi-omics datasets,and genotypedependent transformation efficiency.Future research directions emphasize the exploitation of wild germplasm,in-depth analysis of structural variation,population-scale transcriptomics,investigation of plant—microbiome interactions,and the application of Al-driven intelligent breeding approaches.Together,these strategies are expected to accelerate the development of climate-resilient sorghum varieties,thereby enhancing global food security and supporting sustainable bioenergy production.展开更多
文摘Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan?genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.
基金This study was partially funded by the Centre of Excellence for Transla-tional Photosynthesis,Australian Research Council(grant CE140100015)the Bill&Melinda Gates Foundation(grant OPPGD1197 iMashilla“A targeted approach to sor-ghum improvement in moisture stress areas of Ethiopia”).
文摘Sorghum,a genetically diverse C_(4) cereal,is an ideal model to study natural variation in photosynthetic capacity.Specific leaf nitrogen(SLN)and leaf mass per leaf area(LMA),as well as,maximal rates of Rubisco carboxylation(V cmax),phosphoenolpyruvate(PEP)carboxylation(V pmax),and electron transport(J max),quantified using a C_(4) photosynthesis model,were evaluated in two field-grown training sets(n=169 plots including 124 genotypes)in 2019 and 2020.
基金supported in part by the National Key R&D Program of China(2023YFF1001400)the National Natural Science Foundation of China(32525045,32430077,32472124,and 32241042)+1 种基金the Ningxia Hui Autonomous Region Key R&D Program(2024BBF02001)the Pinduoduo-China Agricultural University Research Fund(PC2024B01004).
文摘Sorghum(Sorghum bicolor),the fifth most important cereal crop worldwide,serves as a staple food in arid and semi-arid regions and is a critical resource for livestock forage,bioenergy production,and industrial applications.Owing to its relatively small genome and strong tolerance to abiotic stresses such as drought,salinity-alkalinity,and heat,sorghum has emerged as an important model crop for abiotic stress research.This Perspective article synthesizes recent advances on sorghum genomics,including the development of gapless reference genome assemblies,pan-genome analyses of extensive structural variation,and population resequencing studies that have uncovered domestication signatures and loci associated with stress adaptation.We also summarize the progress in sorghum genetic resource collection,selection strategies,and breeding improvement.Functional genetic studies have identified key genes regulating yield-related traits,quality attributes,and tolerance to both abiotic and biotic stresses.In molecular breeding,notable achievements include the establishment of efficient transformation systems,CRiSPR/Cas9-mediated genome editing enhanced by morphogenic regulators,and the development of mutagenized populations for gene function validation.Nevertheless,major challenges remain,particularly in functional dissection of complex quantitative traits,the integration of multi-omics datasets,and genotypedependent transformation efficiency.Future research directions emphasize the exploitation of wild germplasm,in-depth analysis of structural variation,population-scale transcriptomics,investigation of plant—microbiome interactions,and the application of Al-driven intelligent breeding approaches.Together,these strategies are expected to accelerate the development of climate-resilient sorghum varieties,thereby enhancing global food security and supporting sustainable bioenergy production.
