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
Bacterial wilt （BW） caused by Ralstonia solanacearum is an important constraint to peanut （Arachis hypogaea L.） production in several Asian and African countries, and planting BW-resistant cultivars is the most fe...Bacterial wilt （BW） caused by Ralstonia solanacearum is an important constraint to peanut （Arachis hypogaea L.） production in several Asian and African countries, and planting BW-resistant cultivars is the most feasible method for controlling the disease. Although several BW-resistant peanut germplasm accessions have been identified, the genetic diversity among these has not been properly investigated, which has impeded efficient utilization. In this study, the genetic relationships of 31 peanut genotypes with various levels of resistance to BW were assessed based on SSR and AFLP analyses. Twenty-nine of 78 SSR primers and 32 of 126 AFLP primer combinations employed in this study were polymorphic amongst the peanut genotypes tested. The SSR primers amplified 91 polymorphic loci in total with an average of 3.14 alleles per primer, and the AFLP primers amplified 72 polymorphic loci in total with an average of 2.25 alleles per primer. Four SSR primers （14H06, 7G02, 3A8, 16C6） and one AFLP primer （P1M62） were found to be most efficient in detecting diversity. The genetic distance between pairs of genotypes ranged from 0.12 to 0.94 with an average of 0.53 in the SSR data and from 0.06 to 0.57 with an average of 0.25 in the AFLP data. The SSR-based estimates of the genetic distance were generally larger than that based on the AFLP data. The genotypes belonging to subsp, fastigiata possessed wider diversity than that of subsp, hypogaea. The clustering of genotypes based on the SSR and AFLP data were similar but the SSR clustering was more consistent with morphological classification ofA. hypogaea. Optimum diverse genotypes of both subsp, hypogaea and subsp.fastigiata can be recommended based on this analysis for developing mapping populations and breeding for high yielding and resistant cultivars.展开更多
Dear Editor Roots play a key role in plant growth regulation. It is well described that the below-ground plant architecture has a significant impact on plant performance under abiotic constraints and maintains stabili...Dear Editor Roots play a key role in plant growth regulation. It is well described that the below-ground plant architecture has a significant impact on plant performance under abiotic constraints and maintains stability under increased grain load （Lynch, 2013）.展开更多
Increased productivity in sorghum has been achieved in the developed world using hybrids.Despite their yield advantage,introduced hybrids have not been adopted in Ethiopia due to the lack of adaptive traits,their shor...Increased productivity in sorghum has been achieved in the developed world using hybrids.Despite their yield advantage,introduced hybrids have not been adopted in Ethiopia due to the lack of adaptive traits,their short plant stature and small grain size.This study was conducted to investigate hybrid performance and the magnitude of heterosis of locally adapted genotypes in addition to introduced hybrids in three contrasting environments in Ethiopia.In total,139 hybrids,derived from introduced seed parents crossed with locally adapted genotypes and introduced R lines,were evaluated.Overall,the hybrids matured earlier than the adapted parents,but had higher grain yield,plant height,grain number and grain weight in all environments.The lowland adapted hybrids displayed a mean better parent heterosis(BPH) of19%,equating to 1160 kg ha-1and a 29% mean increase in grain yield,in addition to increased plant height and grain weight,in comparison to the hybrids derived from the introduced R lines.The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52%in the intermediate environment equating to 698 kg ha-1and 2031 kg ha-1,respectively,in addition to increased grain weight.The magnitude of heterosis observed for each hybrid group was related to the genetic distance between the parental lines.The majority of hybrids also showed superiority over the standard check varieties.In general,hybrids from locally adapted genotypes were superior in grain yield,plant height and grain weight compared to the high parents and introduced hybrids indicating the potential for hybrids to increase productivity while addressing farmers' required traits.展开更多
The availability of reference genomes has been the foundation for genomics research in the last decade.However,as reports of presence/absenee variations of sequence and genes are growing in various species(Zhang et al...The availability of reference genomes has been the foundation for genomics research in the last decade.However,as reports of presence/absenee variations of sequence and genes are growing in various species(Zhang et al.,2016;Sun et al.,,2018)it is increasingly evident that a single reference genome provides an in adequate represe ntation of the whole landscape of sequence diversity within a species.Pan-genome analysis provides a platform to investigate the entire genome repertoire of a biological clade.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 work was supported by the National Natural Science Foundation of China(NSFC)(No.30070521 and 30270840).
文摘Bacterial wilt （BW） caused by Ralstonia solanacearum is an important constraint to peanut （Arachis hypogaea L.） production in several Asian and African countries, and planting BW-resistant cultivars is the most feasible method for controlling the disease. Although several BW-resistant peanut germplasm accessions have been identified, the genetic diversity among these has not been properly investigated, which has impeded efficient utilization. In this study, the genetic relationships of 31 peanut genotypes with various levels of resistance to BW were assessed based on SSR and AFLP analyses. Twenty-nine of 78 SSR primers and 32 of 126 AFLP primer combinations employed in this study were polymorphic amongst the peanut genotypes tested. The SSR primers amplified 91 polymorphic loci in total with an average of 3.14 alleles per primer, and the AFLP primers amplified 72 polymorphic loci in total with an average of 2.25 alleles per primer. Four SSR primers （14H06, 7G02, 3A8, 16C6） and one AFLP primer （P1M62） were found to be most efficient in detecting diversity. The genetic distance between pairs of genotypes ranged from 0.12 to 0.94 with an average of 0.53 in the SSR data and from 0.06 to 0.57 with an average of 0.25 in the AFLP data. The SSR-based estimates of the genetic distance were generally larger than that based on the AFLP data. The genotypes belonging to subsp, fastigiata possessed wider diversity than that of subsp, hypogaea. The clustering of genotypes based on the SSR and AFLP data were similar but the SSR clustering was more consistent with morphological classification ofA. hypogaea. Optimum diverse genotypes of both subsp, hypogaea and subsp.fastigiata can be recommended based on this analysis for developing mapping populations and breeding for high yielding and resistant cultivars.
文摘Dear Editor Roots play a key role in plant growth regulation. It is well described that the below-ground plant architecture has a significant impact on plant performance under abiotic constraints and maintains stability under increased grain load （Lynch, 2013）.
基金AusAID (Australian Agency for International Development) for a scholarship supporting TTM,Queensland Alliance for Agriculture and Food Innovation (QAAFI)the Ethiopian Institute of Agricultural Research (EIAR) for financially supporting the research activities
文摘Increased productivity in sorghum has been achieved in the developed world using hybrids.Despite their yield advantage,introduced hybrids have not been adopted in Ethiopia due to the lack of adaptive traits,their short plant stature and small grain size.This study was conducted to investigate hybrid performance and the magnitude of heterosis of locally adapted genotypes in addition to introduced hybrids in three contrasting environments in Ethiopia.In total,139 hybrids,derived from introduced seed parents crossed with locally adapted genotypes and introduced R lines,were evaluated.Overall,the hybrids matured earlier than the adapted parents,but had higher grain yield,plant height,grain number and grain weight in all environments.The lowland adapted hybrids displayed a mean better parent heterosis(BPH) of19%,equating to 1160 kg ha-1and a 29% mean increase in grain yield,in addition to increased plant height and grain weight,in comparison to the hybrids derived from the introduced R lines.The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52%in the intermediate environment equating to 698 kg ha-1and 2031 kg ha-1,respectively,in addition to increased grain weight.The magnitude of heterosis observed for each hybrid group was related to the genetic distance between the parental lines.The majority of hybrids also showed superiority over the standard check varieties.In general,hybrids from locally adapted genotypes were superior in grain yield,plant height and grain weight compared to the high parents and introduced hybrids indicating the potential for hybrids to increase productivity while addressing farmers' required traits.
文摘The availability of reference genomes has been the foundation for genomics research in the last decade.However,as reports of presence/absenee variations of sequence and genes are growing in various species(Zhang et al.,2016;Sun et al.,,2018)it is increasingly evident that a single reference genome provides an in adequate represe ntation of the whole landscape of sequence diversity within a species.Pan-genome analysis provides a platform to investigate the entire genome repertoire of a biological clade.
