A rice low temperature-induced albino variant was determined by the recessive ltia1 and ltia2 genes.LTIA1 and LTIA2 encode highly conserved mini-ribonucleasesⅢlocated in chloroplasts and expressed in aerial parts of ...A rice low temperature-induced albino variant was determined by the recessive ltia1 and ltia2 genes.LTIA1 and LTIA2 encode highly conserved mini-ribonucleasesⅢlocated in chloroplasts and expressed in aerial parts of the plant.At low temperature,LTIA1 and LTIA2 redundantly affect chlorophyll levels,non-photochemical quenching,photosynthetic quantum yield of PSⅡand seedling growth.LTIA1 and LTIA2 proteins are involved in splicing of atp F and the biogenesis of 16S and 23S rRNA in chloroplasts.Presence/absence variation of LTIA1,the ancestral copy,was found only in japonica but that of LTIA2 in all rice subgroups.Accessions with LTIA2 presence tended to be distributed more remote from the equator compared to those with LTIA2 absence.LTIA2 duplicated from LTIA1 at the early stage of divergence of the AA genome Oryza species but deleted againin O.nivara.In cultivated rice,absence of LTIA2 is derived from O.nivara.LTIA1 absence occurred more recently in japonica.展开更多
This study was designed to reveal the genome‐wide distribution of presence/absence variation（PAV） and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole‐genome sequences were compa...This study was designed to reveal the genome‐wide distribution of presence/absence variation（PAV） and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole‐genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518（1.8%） overlapped with simple sequence repeats（SSRs） in BARCSOYSSR_1.0database. In a random sample of 800 PAVs, 713（89.13%） showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max（L.） Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR（polymerase chain reaction） products showed better in PAVs than in SSRs, potential in accurate marker‐assisted allele selection. The association mapping results showed SSR t PAV was more powerful than any single marker systems.The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers.展开更多
Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between mul...Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.展开更多
It is important to predict how many individuals of a predator species can survive in a given area on the basis of prey sufficiency and to compare predictive estimates with actual numbers to understand whether or not k...It is important to predict how many individuals of a predator species can survive in a given area on the basis of prey sufficiency and to compare predictive estimates with actual numbers to understand whether or not key threats are related to prey availability.Rugged terrain and low detection probabilities do not allow for the use of traditional prey count techniques in mountain areas.We used presence–absence occupancy modeling and camera-trapping to estimate the abundance and densities of prey species and regression analysis to predict leopard(Panthera pardus)densities from estimated prey biomass in the mountains of the Nuvadi area,Meghri Ridge,southern Armenia.The prey densities were 12.94±2.18 individuals km–2 for the bezoar goat(Capra aegagrus),6.88±1.56 for the wild boar(Sus scrofa)and 0.44±0.20 for the roe deer(Capreolus capreolus).The detection probability of the prey was a strong function of the activity patterns,and was highest in diurnal bezoar goats(0.59±0.09).Based on robust regression,the estimated total ungulate prey biomass(720.37±142.72 kg km–2)can support a leopard density of 7.18±3.06 individuals 100 km–2.The actual leopard density is only 0.34 individuals 100 km–2(i.e.one subadult male recorded over the 296.9 km2),estimated from tracking and camera-trapping.The most plausible explanation for this discrepancy between predicted and actual leopard density is that poaching and disturbance caused by livestock breeding,plant gathering,deforestation and human-induced wild fires are affecting the leopard population in Armenia.展开更多
基金supported by Zhejiang Provincial Natural Science Foundation of China (LD24C130002)Scientific Research Foundation of China Jiliang University。
文摘A rice low temperature-induced albino variant was determined by the recessive ltia1 and ltia2 genes.LTIA1 and LTIA2 encode highly conserved mini-ribonucleasesⅢlocated in chloroplasts and expressed in aerial parts of the plant.At low temperature,LTIA1 and LTIA2 redundantly affect chlorophyll levels,non-photochemical quenching,photosynthetic quantum yield of PSⅡand seedling growth.LTIA1 and LTIA2 proteins are involved in splicing of atp F and the biogenesis of 16S and 23S rRNA in chloroplasts.Presence/absence variation of LTIA1,the ancestral copy,was found only in japonica but that of LTIA2 in all rice subgroups.Accessions with LTIA2 presence tended to be distributed more remote from the equator compared to those with LTIA2 absence.LTIA2 duplicated from LTIA1 at the early stage of divergence of the AA genome Oryza species but deleted againin O.nivara.In cultivated rice,absence of LTIA2 is derived from O.nivara.LTIA1 absence occurred more recently in japonica.
基金supported by the National Basic Research Program of China (973 Program) (2011CB1093, 2010CB1259)the National High‐tech R&D Program (863 Program) (2011AA10A105, 2012AA101106)+5 种基金the National Natural Science Foundation of China (31071442, 31271750)the MOE 111 Project (B08025)the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT13073)NCET‐12‐0891the Special Fund for Agro‐Scientific Research in Public Interest (200803060)the PAPD Project of Jiangsu Higher Education
文摘This study was designed to reveal the genome‐wide distribution of presence/absence variation（PAV） and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole‐genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518（1.8%） overlapped with simple sequence repeats（SSRs） in BARCSOYSSR_1.0database. In a random sample of 800 PAVs, 713（89.13%） showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max（L.） Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR（polymerase chain reaction） products showed better in PAVs than in SSRs, potential in accurate marker‐assisted allele selection. The association mapping results showed SSR t PAV was more powerful than any single marker systems.The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers.
基金supported by the Deutsche Forschungsgemeinschaft(MA6473/1-1,MA6473/2-1)
文摘Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.
文摘It is important to predict how many individuals of a predator species can survive in a given area on the basis of prey sufficiency and to compare predictive estimates with actual numbers to understand whether or not key threats are related to prey availability.Rugged terrain and low detection probabilities do not allow for the use of traditional prey count techniques in mountain areas.We used presence–absence occupancy modeling and camera-trapping to estimate the abundance and densities of prey species and regression analysis to predict leopard(Panthera pardus)densities from estimated prey biomass in the mountains of the Nuvadi area,Meghri Ridge,southern Armenia.The prey densities were 12.94±2.18 individuals km–2 for the bezoar goat(Capra aegagrus),6.88±1.56 for the wild boar(Sus scrofa)and 0.44±0.20 for the roe deer(Capreolus capreolus).The detection probability of the prey was a strong function of the activity patterns,and was highest in diurnal bezoar goats(0.59±0.09).Based on robust regression,the estimated total ungulate prey biomass(720.37±142.72 kg km–2)can support a leopard density of 7.18±3.06 individuals 100 km–2.The actual leopard density is only 0.34 individuals 100 km–2(i.e.one subadult male recorded over the 296.9 km2),estimated from tracking and camera-trapping.The most plausible explanation for this discrepancy between predicted and actual leopard density is that poaching and disturbance caused by livestock breeding,plant gathering,deforestation and human-induced wild fires are affecting the leopard population in Armenia.
