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Boosting proso millet yield by altering canopy light distribution in proso millet/mung bean intercropping systems

The crop Journal 2020年第2期8卷 365-377页

作者： Xiangwei Gong Uzizerimana Ferdinand Ke Dang Jing Li Guanghua Chen Yan Luo Pu Yang Baili Feng State Key Laboratory of crop Stress Biology in Arid Areas Shaanxi Research Station of Crop Gene Resources&Germplasm EnhancementMinistry of AgricultureCollege of AgronomyNorthwest A&F UniversityYangling 712100ShaanxiChina

To elucidate the mechanism by which intercropping proso millet(Panicum miliaceum L.)with mung bean(Vigna radiata L.)increases proso millet yield and to determine how this higher yield results from maximization of resources use efficiency,we designed and conducted four strip intercropping row arrangements,including two rows of proso millet alternating with two rows of mung bean(2P2M),four rows of proso millet alternating with two rows of mung bean(4P2M),four rows of proso millet alternating with four rows of mung bean(4P4M),two rows of proso millet alternating with four rows of mung bean(2P4M),sole proso millet(SP,control)and sole mung bean(SM,control)in Yulin,shaanxi,*** active radiation(PAR)in the canopy,radiation use efficiency(RUE),leaf photosynthetic characteristics,dry matter accumulation and allocation,and yield of proso millet were *** results showed that the intercropping systems had higher PAR than the *** PAR intensities were increased by respectively 2.2%–23.4%,19.8%–59.7%,and 61.2%–133.3%in the proso millet upper,middle and lower canopies compared with *** increase in PAR directly increased RUE,a result attributed mainly to the increase in photosynthetic capacity,including net photosynthetic rate and chlorophyll *** responses resulted in increased dry matter allocation to plant *** of intercropped proso millet was 6.8%–37.3%higher than that under monoculture and the land equivalent ratios for the different intercropping patterns were all greater than unity(>1).In general,yield followed a positive linear function of PAR in the intercropping *** results indicated that intercropping can boost proso millet yield,evidently by altering light distribution within its canopy and consequently increasing RUE,thereby increasing leaf photosynthetic capacity,dry matter accumulation,and allocation to the *** optimum combination for improving the growth and yield of proso millet on the Loe

关键词： intercropping distribution thereby

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Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq

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Journal of Integrative Agriculture 2024年第12期23卷 3953-3965页

作者： Yongfu Wang Jianzhong Fan Hong Zhang Pingchuan Deng Tingdong Li ChunhuanChen Wanquan Ji Yajuan Wang college of agronomy Northwest A&F UniversityYangling 712100China State Key Laboratory of crop Stress Biology for Arid Areas Yangling 712100China shaanxi research station of crop gene resources and germplasm enhancement Ministry of Agriculture and Rural AffairsYangling 712100China

The constant evolution of pathogens poses a threat to wheat resistance against diseases,endangering food *** resistant wheat varieties is the most practical approach for circumventing this *** a close relative of wheat,Aegilops geniculata,particularly accession SY159,has evolved numerous beneficial traits that could be applied to improve *** this study,we established the karyotype of SY159 by fluorescence in situ hybridization(FISH)using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–*** accession TA2899 addition lines as a *** specific-locus amplified fragment sequencing(SLAF-seq)technology,400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.The SY159-specific markers were used to classify the different homologous groups of SY159 against the *** addition *** used these specific markers on the 7Mg chromosome after classification,and successfully confirmed their suitability for studying the different chromosomes of *** study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat.

关键词： Aegilops geniculata Roth chromosome karyotype analysis FISH SLAF-seq specific molecular marker

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Identification of genetic locus with resistance to take-all in the wheat-Psathyrostachys huashanica Keng introgression line H148

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Journal of Integrative Agriculture 2021年第12期20卷 3101-3113页

作者： BAI Sheng-sheng ZHANG Han-bing HAN Jing WU Jian-hui LI Jia-chuang GENG Xing-xia LU Bo-ya XIE Song-feng HAN De-jun ZHAO Ji-xin YANG Qun-hui WU Jun CHEN Xin-hong shaanxi Key Laboratory of Plant genetic Engineering Breeding/college of agronomy Northwest A&F UniversityYangling 712100P.R.China State Key Laboratory of crop Stress Biology for Arid Areas/college of agronomy Northwest A&F UniversityYangling 712100P.R.China shaanxi research station of crop gene resources and germplasm enhancement/college of agronomy Northwest A&F UniversityYangling 712100P.R.China

Take-all is a devastating soil-borne disease of wheat(Triticum aestivum L.).Cultivating resistant line is an important measure to control this *** huashanica Keng is a valuable germplasm resource with high resistance to *** study reported on a wheat-/R huashanica introgression line H148 with improved take-all resistance compared with its susceptible parent *** elucidate the genetic mechanism of resistance in H148,the F_(2)genetic segregating population of H148×XN585 was *** mixed genetic model analysis showed that the take-all resistance was controlled by two major genes with additive,dominant and epistasis *** segregant analysis combined with wheat axiom 660K genotyping array analysis showed the polymorphic SNPs with take-all resistance from *** alien introgression were mainly distributed on the chromosome *** of the F_(2)population using the KASP marker mapped a major QTL in an interval of 68.8-70.1 Mb on ***-two genes were found in the target interval of the Chinese Spring reference genome *** to the functional annotation of genes,two protein genes that can improve the systematic resistance of plant roots were predicted as candidate *** development of *** introgression line H148 and the resistant QTL mapping information are expected to provide some valuable references for the fine mapping of disease-resistance gene and development of take-all resistant varieties through molecular marker-assisted selection.

关键词： wheat Psathyrostachys huashanica Keng take-all genetic analysis quantitative trait loci

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RNA-Seq analysis and development of SSR and KASP markers in lentil(Lens culinaris Medikus subsp. culinaris)

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The crop Journal 2020年第6期8卷 953-965页

作者： Dong Wang Tao Yang Rong Liu Nana Li Xiaomu Wang Ashutosh Sarker Xiaodong Zhang Runfang Li Yanyan Pu Guan Li Yuning Huang Yishan Ji Zhaojun Li Qian Tian Xuxiao Zong Hanfeng Ding Shandong Center of crop germplasm resources Shandong Research Station of Crop Gene Resource&Germplasm EnhancementMinistry of AgricultureShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinan 250100ShandongChina National Key Facility for crop gene resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China college of Life Science Shandong Normal UniversityJinan 250014ShandongChina International Center for Agricultural research in the Dry Areas(ICARDA) New Delhi 110012India

Lentil(Lens culinaris Medikus ***,2 n=14)is a cool-season legume with high production potential for multiple ***,limited molecular research has been conducted in this species owing to its large genome,which impedes the generation of genome sequences and the development of molecular *** this study,more than 1.37 billion filtered clean reads were collected by RNA-Seq of six diverse lentil accessions and217,836 transcripts and 161,095 unigenes were de novo assembled,yielding respectively 257.1 and 240.6 million *** mean transcript length was 1180 bp and the N50 and N90 lengths were respectively 2075 and 479 *** mean length of the unigenes was 1494 bp and their N50 and N90 values were respectively 2203 and 714 *** unigenes were annotated against seven *** FLOWERING LOCUS T(FT)gene homolog in lentil showed high protein sequence similarity to the FT gene homologs of pea and *** the basis of the RNA-Seq analysis,26,449 EST-SSR markers were designed in silico,and 276 preliminarily screened markers were selected to evaluate polymorphism in 94 diverse lentil *** total,125(45.29%)of 276 EST-SSR markers were found to be polymorphic.A total of 130,073 SNP loci were detected and 78(61.41%)of 127 SNPs were successfully converted to KASP *** genetic analyses of the lentil accessions with EST-SSR and KASP markers revealed similar genetic structures,suggesting that the RNA-Seq-generated resources and the developed markers are reliable for use in molecular marker-assisted breeding of lentil.

关键词： Lentil RNA-Seq EST-SSR KASP genetic diversity

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genetic analysis and fine mapping of a grain size QTL in the smallgrain sterile rice line Zhuo201S

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Journal of Integrative Agriculture 2024年第7期23卷 2155-2163页

作者： Bin Lei Jiale Shao Feng Zhang Jian Wang Yunhua Xiao Zhijun Cheng Wenbang Tang Jianmin Wan college of agronomy Hunan Agricultural UniversityChangsha 410128China National Key Facility for crop gene resources and genetic Improvement/Institute of crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory for crop genetics and germplasm enhancement/Jiangsu Plant gene Engineering research Center Nanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China

The development and application of the small-grain rice sterile line Zhuo201S(Z201S)has demonstrated its potential for mechanized hybrid rice seed production,leading to significant cost ***,the molecular mechanism responsible for the small-grain size characteristic of Z201S remains *** this study,we conducted a genetic analysis using near-isogenic lines constructed from Z210S,a small-grain rice sterile line,and R2115,a normal-grain *** results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain *** mapping,we localized the causal gene to the short arm of chromosome 2,within a 113 kb physical region delimited by the molecular markers S2-4-1 and *** analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene,suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

关键词： rice grain size map-based cloning

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Pm67, a new powdery mildew resistance gene transferred from Dasypyrum villosum chromosome 1V to common wheat(Triticum aestivum L.)

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The crop Journal 2021年第4期9卷 882-888页

作者： Ruiqi Zhang Chuanxi Xiong Huanqing Mu Ruonan Yao Xiangru Meng Lingna Kong Liping Xing Jizhong Wu Yigao Feng Aizhong Cao college of agronomy/JCIC-MCP/National Key Lab of crop genetics and germplasm enhancement Nanjing Agricultural UniversityNanjing 210095JiangsuChina Institute of germplasm resources and Biotechnology/Provincial Key Lab of Agrobiology Jiangsu Academy of Agricultural SciencesNanjing 210014JiangsuChina

Powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici(Bgt), is a global disease that poses a serious threat to wheat production. To explore additional resistance gene, a wheatDasypyrum villosum 1 V#5(1 D) disomic substitution line NAU1813(2 n = 42) with high level of seedling resistance to powdery mildew was used to generate the recombination between chromosomes 1 V#5 and1 D. Four introgression lines, including t1 VS#5 ditelosomic addition line NAU1815, t1 VL#5 ditelosomic addition line NAU1816, homozygous T1 DL·1 VS#5 translocation line NAU1817, and homozygous T1 DS·1 VL#5 translocation line NAU1818 were developed from the selfing progenies of 1 V#5 and 1 D double monosomic line that derived from F1 hybrids of NAU1813/NAU0686. All of them were characterized by fluorescence in situ hybridization, genomic in situ hybridization, 1 V-specific markers analysis, and powdery mildew tests at different developmental stages. A new powdery mildew resistance gene named Pm67 was physically located in the terminal bin(FL 0.70–1.00) of 1 VS#5. Lines with Pm67 exhibited seedling stage immunity and tissue-differentiated reactions at adult plant stage. The sheaths, stems, and spikes of the Pm67 line were still immune, but the leaves showed a low degree of *** observation showed that most penetration attempts were stopped in association with papillae on the sheath, and colonies cannot form conidia on the susceptible leaf of Pm67 line at adult plant stage, suggesting that the defence layers of the Pm67 line is tissue-differentiated. Thus, the T1 DL·1 VS#5 translocation line NAU1817 provides a new germplasm in wheat breeding for improvement of powdery mildew resistance.

关键词： Wheat Dasypyrum villosum Powdery mildew Pm67

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TWAS facilitates gene-scale trait genetic dissection through gene expression,structural variations,and alternative splicing in soybean

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Plant Communications 2024年第10期5卷 16-32页

作者： Delin Li Qi Wang Yu Tian Xiangguang Lyv Hao Zhang Huilong Hong Huawei Gao Yan-Fei Li Chaosen Zhao Jiajun Wang Ruizhen Wang Jinliang Yang Bin Liu Patrick S.Schnable James C.Schnable Ying-Hui Li Li-Juan Qiu The National Key Facility for crop gene resources and genetic Improvement(NFCRI)/Key Laboratory of crop gene Resource and germplasm enhancement(MOA)/State Key Laboratory of crop gene resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China college of Agriculture Northeast Agricultural UniversityHarbin 150030China National Nanfan research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China crops research Institute of Jiangxi Academy of Agricultural Sciences Nanchang 330200China Soybean research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086China Department of agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68583USA Department of agronomy Iowa State UniversityAmesIA 50011USA

A genome-wide association study(GWAS)identifies trait-associated loci,but identifying the causal genes can be a bottleneck,due in part to slow decay of linkage disequilibrium(LD).A transcriptome-wide association study(TWAS)addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS ***,we used self-pollinated soybean(Glycine max[L.]Merr.)as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD *** generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29286 soybean *** TWAS solutions were less affected by LD and were robust to the source of expression,identifing known genes related to traits from different tissues and developmental *** novel pod-color gene L2 was identified via TWAS and functionally validated by genome *** introducing a new exon proportion feature,we significantly improved the detection of expression variations that resulted from structural variations and alternative *** a result,the genes identified through our TWAS approach exhibited a diverse range of causal variations,including SNPs,insertions or deletions,gene fusion,copy number variations,and alternative *** this approach,we identified genes associated with flowering time,including both previously known genes and novel genes that had not previously been linked to this trait,providing insights complementary to those from *** summary,this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.

关键词： eQTLs TWAS structural variation alternative splicing soybean

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Identification of a novel seed size associated locus SW9-1 in soybean

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The crop Journal 2019年第4期7卷 548-559页

作者： Jiajia Li Jinghui Zhao Yinghui Li Yali Gao Sunan Hua Muhammad Nadeem Genlou Sun Wenming Zhang Jinfeng Hou Xiaobo Wang Lijuan Qiu School of agronomy Anhui Agricultural University Hefei 230036 Anhui China The National Key Facility for crop gene resources and genetic Improvement (NFCRI)/Key Laboratory of crop gene Resource and germplasm enhancement (MOA) Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China Biology Department Saint Mary's University Halifax NS B3H 3C3 Canada college of Horticulture Anhui Agricultural University Hefei 230036 Anhui China

Seed size is one of the vital traits determining seed appearance, quality, and yield. Untangling the genetic mechanisms regulating soybean 100-seed weight (100-SW), seed length and seed width across environments may provide a theoretical basis for improving seed yield. However, there are few reports related to QTL mapping of 100-SW across multiple ecological regions. In this study, 21 loci associated with seed size traits were identified using a genome-wide association of 5361 single nucleotide polymorphisms (SNPs) across three ecoregions in China, which could explain 8.12%–14.25% of the phenotypic variance respectively. A new locus, named as SW9-1 on chromosome 9 that explained 10.05%–10.93% of the seed weight variance was found significantly related to seed size traits, and was not previously reported. The selection effect analysis showed that SW9-1 locus has a relatively high phenotypic effect (13.67) on 100-SW, with a greater contribution by the accessions with bigger seeds (3.69) than the accessions with small seeds (1.66). Increases in seed weight were accompanied by increases in the frequency of SW9-1T allele, with >90% of the bred varieties with a 100-SW >30 g carrying SW9-1T. Analysis of SW9-1 allelic variation in additional soybean accessions showed that SW9-1T allele accounting for 13.83% of the wild accessions, while in 46.55% and 51.57% of the landraces and bred accessions, respectively, this results indicating that the SW9-1 locus has been subjected to artificial selection during the early stages of soybean breeding, especially the utilization of SW9-1T in edamame for big seed. These results suggest that SW9-1 is a novel and reliable locus associated with seed size traits, and might have an important implication for increasing soybean seed weight in molecular design breeding. Cloning this locus in future may provide new insights into the genetic mechanisms underlying soybean seed size traits.

关键词： Soybean [Glycine max (L.) Merr.] Seed size/weight SW9-1 Molecular breeding

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Engineer and split an efficient hypercompact CRISPR–CasΦ genome editor in plants

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Plant Communications 2024年第7期5卷 8-11页

作者： Yan Sun Jianjian Hu Zhichao Hu Hejie Zhou Yuhong Gao Yini Liu Yuan Ji Gencheng Xu Yifan Guo Yuanyan Zhang Yunlu Tian Xi Liu Shirong Zhou Yuqiang Liu Tingdong Li Chao Li Jianmin Wan State Key Laboratory of crop genetics&germplasm enhancement and Utilization Jiangsu Engineering Research Center for Plant Genome EditingNational Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjing 210095China Zhongshan Biological Breeding Laboratory Nanjing 210095China Sanya Institute of Nanjing Agricultural University Hainan Seed Industry LaboratorySanya 572025China State Key Laboratory of crop Stress Biology for Arid Areas College of AgronomyNorthwest A&F UniversityYangling 712100China State Key Laboratory of crop gene resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China These authors contributed equally to this article

The programmable CRISPR-Cas genome editing technology,adopted from prokaryotic adaptive immune systems,has revolutionized genome engineering in plants(Liu et al.,2022a).Many efforts have been made to improve the activity,specificity,and protospacer adjacent motif(PAM)variants of Class 2 Cas nucleases,such as Cas9,Cas12a,and Cas12b(Liu et al.,2022a).However,their large size(∼1000–1400 amino acids)poses a challenge in scenarios requiring a compact Cas nuclease,particularly in urgent situations like plant virus-induced genome editing(Cheuk and Houde,2018;Li et al.,2021;Varanda et al.,2021).

关键词： CRISPR genome editor

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Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean

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Journal of Integrative Plant Biology 2023年第1期65卷 117-132页

作者： Delin Li Dong Bai Yu Tian Ying-Hui Li Chaosen Zhao Qi Wang Shiyu Guo Yongzhe Gu Xiaoyan Luan Ruizhen Wang Jinliang Yang Malcolm J.Hawkesford James C.Schnable Xiuliang Jin Li-Juan Qiu The National Key Facility for crop gene resources and genetic Improvement(NFCRI)/Key Laboratory of crop gene Resource and germplasm enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081 China crops research Institute of Jiangxi Academy of Agricultural Sciences Nanchang 330200 China college of Agriculture Northeast Agricultural University Harbin 150030 China Soybean research Institute Heilongjiang Academy of Agricultural Sciences Harbin 150086 China Department of agronomy and Horticulture University of Nebraska-Lincoln Lincoln Nebraska 68583 USA Plant Sciences Department Rothamsted ResearchWest CommonHarpendenHertfordshire AL52JQ UK

Advances in plant phenotyping technologies are dramatically reducing the marginal costs of collecting multiple phenotypic measurements across several time ***,most current approaches and best statistical practices implemented to link genetic and phenotypic variation in plants have been developed in an era of single-time-point ***,we used time-series phenotypic data collected with an unmanned aircraft system for a large panel of soybean(Glycine max(L.)Merr.)varieties to identify previously uncharacterized ***,we focused on the dissection of canopy coverage(CC)variation from this rich data *** also inferred the speed of canopy closure,an additional dimension of CC,from the time-series data,as it may represent an important trait for weed ***-wide association studies(GWASs)identified 35 loci exhibiting dynamic associations with CC across developmental *** time-series data enabled the identification of 10 known flowering time and plant height quantitative trait loci(QTLs)detected in previous studies of adult plants and the identification of novel QTLs influencing *** novel QTLs were disproportionately likely to act earlier in development,which may explain why they were missed in previous single-time-point ***,this time-series data set contributed to the high accuracy of the GWASs,which we evaluated by permutation tests,as evidenced by the repeated identification of loci across multiple time *** novel loci showed evidence of adaptive selection during domestication,with different genotypes/haplotypes favored in different geographic *** summary,the time-series data,with soybean CC as an example,improved the accuracy and statistical power to dissect the genetic basis of traits and offered a promising opportunity for crop breeding with quantitative growth curves.

关键词： canopy coverage dynamic regulation GWAS soybean time series unmanned aircraft system

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