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作物学报（英文版）
作物学报（英文版）

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    Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution:An experimental demonstration in rice

    Yan ZhengEi Ei KhineKhin Mar ThiEi Ei Nyein...
    549-557页
    查看更多>>摘要：Bulked-segregant analysis by deep sequencing(BSA-seq)is a widely used method for mapping QTL(quantitative trait loci)due to its simplicity,speed,cost-effectiveness,and efficiency.However,the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs,as evidenced by numer-ous practical studies.Most BSA-seq studies have utilized small to medium-sized populations,with F2 populations being the most common choice.Nevertheless,theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq,with F3 populations offering notable advantages over F2 populations.To pro-vide an experimental demonstration,we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH)in a 7200-plant rice F3 population in two environments,with a pool size of approximately 500.Each experiment identified 34 QTL,an order of magnitude greater than reported in most BSA-seq experiments,of which 23 were detected in both experiments,with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice.These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power,resolution,and reliability.
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    Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

    Junqiao SongAngela PachecoAmos AlakonyaAndrea S.Cruz-Morales...
    558-568页
    查看更多>>摘要：Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We per-formed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpeño and non-Tuxpeño heterotic pools grown in three environ-ments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abi-otic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G × E)interaction increased genomic prediction accuracy.
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    A simple and efficient CRISPR/Cas9 system permits ultra-multiplex genome editing in plants

    Suting WuHtin KyawZhijun TongYirong Yang...
    569-582页
    查看更多>>摘要：The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement.Currently available genome-editing tools have a limited number of targets,restricting their application in genetic research.In this study,we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors,eight donor vectors,four destination vectors,and one primer-design software package.By combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombi-nation to assemble large fragments and by changing the structure of the amplicons used to assemble sgRNA expression cassettes,the plant ultra-multiplex genome editing system can assemble a single bin-ary vector targeting more than 40 genomic loci.A rice knockout vector containing 49 sgRNA expression cassettes was assembled and a high co-editing efficiency was observed.This plant ultra-multiplex gen-ome editing system advances synthetic biology and plant genetic engineering.
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    LociScan,a tool for screening genetic marker combinations for plant variety discrimination

    Yang YangHongli TianHongmei YiZi Shi...
    583-593页
    查看更多>>摘要：To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrim-ination,it is desirable to identify the optimal marker combinations.We describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,LociScan.Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions.Among GA parameters,an increase in population size and generation number enlarged opti-mization depth but also calculation workload.Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time.In comparison with two other software tools,LociScan accommodated missing data,reduced calculation time,and offered more fitness functions.In large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.
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    Effects of dense planting patterns on photosynthetic traits of different vertical layers and yield of wheat under different nitrogen rates

    Cuicun WangKe ZhangQing LiuXiufeng Zhang...
    594-604页
    查看更多>>摘要：A two-year field experiment was conducted to measure the effects of densification methods on photosyn-thesis and yield of densely planted wheat.Inter-plant and inter-row distances were used to define rate-fixed pattern(RR)and row-fixed pattern(RS)density treatments.Meanwhile,four nitrogen(N)rates(0,144,192,and 240 kg N ha-1,termed N0,N144,N192,and N240)were applied with three densities(225,292.5,and 360 × 104 plants ha-1,termed D225,D292.5,and D360).The wheat canopy was clipped into three equal vertical layers(top,middle,and bottom layers),and their chlorophyll density(ChD)and pho-tosynthetically active radiation interception(FIPAR)were measured.Results showed that the response of ChD and FIPAR to N rate,density,and pattern varied with different layers.N rate,density,and pattern had significant interaction effects on ChD.The maximum values of whole-canopy ChD in the two seasons appeared in N240 combined with D292.5 and D360 under RR,respectively.Across two growing seasons,FIPAR values of RR were higher than those of RS by 29.37％for the top layer and 5.68％for the middle layer,while lower than those of RS by 20.62％for the bottom layer on average.With a low N supply(N0),grain yield was not significantly affected by density for both patterns.At N240,increasing density significantly increased yield under RR,but D360 of RS significantly decreased yield by 3.72％and 9.00％versus D225 in two seasons,respectively.With an appropriate and sufficient N application,RR increased the yield of densely planted wheat more than RS.Additionally,the maximum yield in two seasons appeared in the combination of D360 with N144 or N192 rather than of D225 with N240 under both pat-terns,suggesting that dense planting combined with an appropriate N-reduction application is feasible to increase photosynthesis capacity and yield.
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    Synergistic effects of planting density and nitrogen fertilization on chlorophyll degradation and leaf senescence after silking in maize

    Tianqiong LanLunjing DuXinglong WangXiaoxu Zhan...
    605-613页
    查看更多>>摘要：Regulating planting density and nitrogen(N)fertilization could delay chlorophyll(Chl)degradation and leaf senescence in maize cultivars.This study measured changes in ear leaf green area(GLAear),Chl con-tent,the activities of Chl a-degrading enzymes after silking,and the post-silking dry matter accumulation and grain yield under multiple planting densities and N fertilization rates.The dynamic change of GLAear after silking fitted to the logistic model,and the GLAear duration and the GLAear at 42 d after silking were affected mainly by the duration of the initial senescence period(T1)which was a key factor of the leaf senescence.The average chlorophyllase(CLH)activity was 8.3 times higher than pheophytinase activity and contributed most to the Chl content,indicating that CLH is a key enzyme for degrading Chl a in maize.Increasing density increased the CLH activity and decreased the Chl content,T1,GLAear,and GLAear duration.Under high density,appropriate N application reduced CLH activity,increased Chl content,prolonged T),alleviated high-density-induced leaf senescence,and increased post-silking dry matter accumulation and grain yield.
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    Mapping upland crop-rice cropping systems for targeted sustainable intensification in South China

    Bingwen QiuLinhai YuPeng YangWenbin Wu...
    614-629页
    查看更多>>摘要：Upland crop-rice cropping systems(UCR)facilitate sustainable agricultural intensification.Accurate UCR cultivation mapping is needed to ensure food security,sustainable water management,and rural revital-ization.However,datasets describing cropping systems are limited in spatial coverage and crop types.Mapping UCR is more challenging than crop identification and most existing approaches rely heavily on accurate phenology calendars and representative training samples,which limits its applications over large regions.We describe a novel algorithm(RRSS)for automatic mapping of upland crop-rice cropping systems using Sentinel-1 Synthetic Aperture Radar(SAR)and Sentinel-2 Multispectral Instrument(MSI)data.One indicator,the VV backscatter range,was proposed to discriminate UCR and another two indi-cators were designed by coupling greenness and pigment indices to further discriminate tobacco or oil-seed UCR.The RRSS algorithm was applied to South China characterized by complex smallholder rice cropping systems and diverse topographic conditions.This study developed 10-m UCR maps of a major rice bowl in South China,the Xiang-Gan-Min(XGM)region.The performance of the RRSS algorithm was validated based on 5197 ground-truth reference sites,with an overall accuracy of 91.92％.There were 7348 km2 areas of UCR,roughly one-half of them located in plains.The UCR was represented mainly by oilseed-UCR and tobacco-UCR,which contributed respectively 69％and 15％of UCR area.UCR patterns accounted for only one-tenth of rice production,which can be tripled by intensification from single rice cropping.Application to complex and fragmented subtropical regions suggested the spatiotemporal robustness of the RRSS algorithm,which could be further applied to generate 10-m UCR datasets for application at national or global scales.
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    Rice AGL1 determines grain size and sterile lemma identity

    Haiping YuAn WangGuangheng ZhangGuojun Dong...
    630-634页
    查看更多>>摘要：The grass spikelet is a unique inflorescence structure that determines grain size.Although many genetic factors have been well characterized for grain size and glume development,the underlying molecular mechanisms in rice are far from established.Here,we isolated rice gene,AGL1 that controlled grain size and determines the fate of the sterile lemma.Loss of function of AGL1 produced larger grains and reduced the size of the sterile lemma.Larger grains in the agl1 mutant were caused by a larger number of cells that were longer and wider than in the wild type.The sterile lemma in the mutant spikelet was converted to a rudimentary glume-like organ.Our findings showed that the AGL1(also named LAX1)protein positively regulated G1 expression,and negatively regulated NSG1 expression,thereby affecting the fate of the ster-ile lemma.Taken together,our results revealed that AGL1 played a key role in negative regulation of grain size by controlling cell proliferation and expansion,and supported the opinion that rudimentary glume and sterile lemma in rice are homologous organs.
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    A telomere-to-telomere genome assembly of Hongyingzi,a sorghum cultivar used for Chinese Baijiu production

    Yanqing DingYilin WangJianxia XuFeng Jiang...
    635-640页
    查看更多>>摘要：Sorghum(Sorghum bicolor(L.)Moench)is a world cereal crop used in China for producing Baijiu,a dis-tilled spirit.We report a telomere-to-telomere genome assembly of the Baijiu cultivar Hongyingzi,HYZ-T2T,using ultralong reads.The 10 chromosome pairs contained 33,462 genes,of which 93％were functionally annotated.The 20 telomeres and 10 centromeric regions on the HYZ-T2T chromosomes were predicted and two consecutive large inversions on chromosome 2 were characterized.A 65-gene recon-struction of the metabolic pathway of tannins,the flavor substances in Baijiu,was performed and may advance the breeding of sorghum cultivars for Baijiu production.
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    Brief Guide for Authors

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