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Genome assembly of KA105,a new resource for maize molecular breeding and genomic research

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The Crop Journal 2023年第6期11卷 1793-1804页

作者： Ting Li Shutu Xu Jiawen Zhao Yapeng Wang Jun Zhang Xin Wei Jianzhou Qu Ruisu Yu Xinghua Zhang Chuang Ma jiquan xue The Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region Northwest A&F UniversityYangling 712100ShaanxiChina Maize Engineering&Technology Research Centre College of AgronomyNorthwest A&F UniversityYangling 712100ShaanxiChina State Key Laboratory of Crop Stress Biology for Arid Areas Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling 712100ShaanxiChina

Superior inbred lines are central to maize breeding as sources of natural *** many elite lines have been sequenced,less sequencing attention has been paid to newly developed *** constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for *** pedigree showed genetic divergence from B73 and other lines in its *** with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight *** than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel *** KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

关键词： Genome assembly Pedigree analysis Structural variation Transcriptome atlas Differential network

Genome-wide prediction in a hybrid maize population adapted to Northwest China

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The Crop Journal 2020年第5期8卷 830-842页

作者： Guoliang Li Yuan Dong Yusheng Zhao Xiaokang Tian Tobias Würschum jiquan xue Shaojiang Chen Jochen C.Reif Shutu Xu Wenxin Liu National Maize Improvement Center of China Key Laboratory of Crop Heterosis and Utilization(MOE)China Agricultural UniversityBeijing 100193China Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region(Ministry of Agriculture) College of AgronomyNorthwest A&F UniversityYangling 712100ShaanxiChina Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)06466 Stadt SeelandGermany Institute of Plant Breeding Seed Science and Population GeneticsUniversity of Hohenheim70599 StuttgartGermany

Genome-wide prediction is a promising approach to boost selection gain in hybrid *** main objective was to evaluate the potential and limits of genome-wide prediction to identify superior hybrid combinations adapted to Northwest China.A total of 490 hybrids derived from crosses among 119 inbred lines from the Shaan A and Shaan B heterotic pattern were used for genome-wide prediction of ten agronomic *** tested eight different statistical prediction models considering additive(A)effects and in addition evaluated the impact of dominance(D)and epistasis(E)on the prediction *** five-fold cross validation,we show that the average prediction ability ranged from 0.386 to 0.794 across traits and *** parametric methods,*** regression,LASSO,Elastic Net,Bayes B,Bayes C and reproducing kernel Hilbert space(RKHS)approach,displayed a very similar prediction ability for each trait and two non-parametric methods(random forest and support vector machine)had a higher prediction performance for the trait rind penetrometer resistance of the third internode above ground(RPR_TIAG).The models of A+D RKHS and A+D+E RKHS were slightly better for predicting traits with a relatively high non-additive *** trait-specific markers into the A+D RKHS model improved the prediction ability of grain yield by 3%,from 0.528 to *** all 6328 potential hybrids,selection of the top 44 hybrids would lead to a 6%increase in grain yield compared with Zhengdan 958,a commercially successful hybrid *** conclusion,our results substantiate the value of genome-wide prediction for hybrid breeding and suggest dozens of promising single crosses for developing high-yielding hybrids for Northwest China.

关键词： breeding prediction forest

The effect of amylose on kernel phenotypic characteristics,starch-related gene expression and amylose inheritance in naturally mutated high-amylose maize

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Journal of Integrative Agriculture 2020年第6期19卷 1554-1564页

作者： ZHANG Xu-dong GAO xue-chun LI Zhi-wei XU Lu-chun LI Yi-bo ZHANG Ren-he xue jiquan GUO Dong-wei Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region Ministry of Agriculture and Rural Affairs/College of AgronomyNorthwest A&F UniversityYa ng ling 712100P.R.China Institute of Crop Science Quality of Plant ProductsUniversity of HohenheimStuttgart 70599Germany

High-amylose maize starch has great pote ntial for widespread in dustrial use due to its ability to form strong gels and film and in the food processi ng field,thus servi ng as a resista nt starch ***,there is still a substa ntial shortage of high-amylose maize due to the limitation of natural germplasm resources,although the well-known amylose extender(ae)gene mutants have bee n found to produce high-amylose maize lines since *** this con text,high-amylose maize lines(13 inbreds and 18 hybrids)originating from a natural amylose mutant in our testing field were utilized to study the correlation between amylose content(AC)and phenotypic traits(kernel morphology and endosperm glossiness),grain filling characteristics,gene expression,and amylose *** results showed that AC was negatively correlated with total starch con tent but was not correlated with grain phe no types,such as kernel full ness,kernel morphology and endosperm *** lines with higher amylose had a greater grain filling rate than that of the controI(B73)during the first 20 days after pollination(DAP).Both starch debranching enzyme(DBE)groups and starch branching enzyme lib(SBEIIb)groups showed a greater abundance in the control(B73)than in the high-amylose maize *** parents directly predicted AC of Fv which was moderately positively correlated with the F2 generation.

关键词： starch biosynthesis amylose inheritance high-amylose maize grain filling rate

A cost-effective ts CUT&Tag method for profiling transcription factor binding landscape

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Journal of Integrative Plant Biology 2022年第11期64卷 2033-2038页

作者： Leiming Wu Zi Luo Yanni Shi Yizhe Jiang Ruonan Li Xinxin Miao Fang Yang Qing Li Han Zhao jiquan xue Shutu Xu Tifu Zhang Lin Li National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China The National Engineering Laboratory of Crop Resistance Breeding School of Life SciencesAnhui Agricultural UniversityHefei 230036China Jiangsu Provincial Key Laboratory of Agrobiology Institute of Germplasm Resources and BiotechnologyJiangsu Academy of Agricultural SciencesNanjing 210014China The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region Ministry of AgricultureNorthwest A&F UniversityYangling 712100China Hubei Hongshan Laboratory Wuhan 430070China

Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic ***,a low-cost and high-throughput in vivo chromatin profiling method is still lacking in ***,we developed a transient and simplified cleavage under targets and tagmentation(tsCUT&Tag)that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus *** tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ***,we developed a strategy combining tsCUT&Tag with machine learning,which has great potential for profiling the TFBL across plant development.

关键词： binding sites ChIP-seq CUT&Tag machine learning transcription factor transient expression

玉米宽窄行深旋免耕精量播种机田间试验及效果

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农业工程学报 2014年第14期30卷 34-41页

作者：楚杰路海东薛吉全赵明西北农林科技大学农学院杨凌712100 中国农业科学院作物科学研究所北京100081

为了解决目前玉米播种机械播种质量不高,良好农艺措施与农机不配套等问题,研发了一种基于宽窄行条带深旋免耕技术的玉米精量播种机。该文对该机作业后的土壤质量、土壤含水率、玉米出苗、群体光照、根系生长和产量等性状进行了分析。结... 详细信息

为了解决目前玉米播种机械播种质量不高,良好农艺措施与农机不配套等问题,研发了一种基于宽窄行条带深旋免耕技术的玉米精量播种机。该文对该机作业后的土壤质量、土壤含水率、玉米出苗、群体光照、根系生长和产量等性状进行了分析。结果表明:采用该机播种后,土壤耕层容重显著降低(P<0.05),土壤蓄水保水能力提高,玉米的播种质量明显提高,群体整齐度增加,群体透光性明显改善,具有显著的增产作用。与普通播种机械相比,该机播种后的玉米出苗率平均提高6.2个百分点,玉米株高变异系数降低8.33%,玉米根系生长量增加15.79%,玉米生育后期的群体光能截获量明显增加,产量增加11.15%。实现了优良农艺措施与农机的有效结合。

关键词：农业机械试验耕作玉米播种机条带深松宽窄行免耕

Dark Response of Seedlings Evaluated by Chlorophyll Concentration in Maize Natural Population

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American Journal of Plant Sciences 2015年第13期6卷 2209-2219页

作者： Aye Nyein Chan Shutu Xu Dongwei Guo Yaqin Shi Yanan Li Yajun Li jiquan xue College of Agronomy Northwest A&F University Yangling China Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region Ministry of Agriculture Yangling China

Chlorophyll, one of the major chloroplast components for photosynthesis, has a positive relationship with the photosynthetic rate. The chlorophyll content is an important assessment parameter in agronomy and plant biology research. This study was conducted to evaluate the natural variation in the chlorophyll content and to determine the differential response of the chlorophyll concentration to dark treatment in a natural population containing 139 maize inbreds. A five-fold higher chlorophyll concentration was measured in the light compared with the dark. Meanwhile, the wide variation in the chlorophyll concentration showed the differential response of the natural maize population to dark. Finally, we identified some inbreds that were highly sensitive to the dark with more than 70% difference between the light and dark treatment, such as Dan598, Zheng29, Zheng35, DH29, and R08, as well as some inbreds that had lower sensitivity to the dark, with less than 35% difference in the chlorophyll content between the light and dark treatment, such as Chuan48-2, 4F1, 303WX, 9642, and LY042.

关键词： Maize Inbred Lines Seedlings Chlorophyll Dark Treatment

Genetic analysis of chlorophyll contents before and after dark treatment at V2 stage in maize

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Genetic analysis of chlorophyll contents before and after da...

黑色地膜覆盖对旱地玉米土壤环境和植株生长的影响

第一届全国玉米生物学学术研讨会

作者：徐淑兔 Aye Nyein Chan Yaqin Shi Ya'nan Li jiquan xue College of Agronomy Northwest A&F University Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region Ministry of Agriculture

As the most important pigment in the world,chlorophylls are responsive for photosynthesis in plants and some *** is a great meaning to explain genetic basis of chlorophyll *** model plant Arabidopsis,chlorophylls metabolics had been clearly elucidated and most of the key gene involving in pathway were clone and *** provide a good base to characterize chlorophyll-related gene

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生态学报 2016年第7期36卷 1997-2004页

作者：路海东薛吉全郝引川高杰西北农林科技大学农学院杨凌712100

针对渭北旱塬地区使用普通白色地膜导致玉米生长出现的早衰、减产等问题,2012—2013年开展了黑色地膜覆盖、白色地膜覆盖和裸地玉米栽培试验,系统分析了黑色地膜对土壤温度、水分和玉米生长的影响。结果表明,黑色地膜与白色地膜的土壤... 详细信息

针对渭北旱塬地区使用普通白色地膜导致玉米生长出现的早衰、减产等问题,2012—2013年开展了黑色地膜覆盖、白色地膜覆盖和裸地玉米栽培试验,系统分析了黑色地膜对土壤温度、水分和玉米生长的影响。结果表明,黑色地膜与白色地膜的土壤保水效果相同,均使0—120cm土壤水分含量显著(P<0.05)高于裸地对照。与白色地膜覆盖相比,黑色地膜覆盖能够有效降低0—15 cm土壤白天温度,可以使白天0—15cm土壤日地温平均降低0.8℃。黑色地膜覆盖后,玉米的籽粒灌浆期延长,吐丝后单株干物质积累量快速增加。玉米生殖生长期较裸地栽培延长2—3 d,成熟期单株干物质积累量增加18.11%;较普通白色地膜覆盖玉米生殖生长期延长2 d,成熟期单株干物质积累量提高7.31%。黑色地膜覆盖玉米产量和水分利用效率显著提高(P<0.05),较白色地膜分别提高10.36%和10.40%,较裸地对照分别提高22.11%和25.28%。在旱地春玉米区,用黑色地膜代替普通白色地膜,对促进玉米增产具有一定的可行性。

关键词：玉米黑色地膜土壤温度土壤水分生长

Performance and stability of yield in response to plant density,year and location in maize hybrids of Northwest China

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Technology in Agronomy 2022年第1期2卷 18-24页

作者： Yuan Dong Zhiqian Feng Ting Li Ali Farhan Xiaokang Tian Yonghui Lao Yinxin Duan Leiyong Si Xinghua Zhang jiquan xue Shutu Xu Key Laboratory of Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region Ministry of Agriculture and Rural AffairsCollege of AgronomyNorthwest A&F UniversityYanglingShaanxi 712100China Maize Engineering Technology Research Centre of Shaanxi Province Northwest A&F UniversityYangling Shaanxi 712100China Cereal Crop Research Institute(CCRI) NowsheraKyber Pakhtunkhwa 25000Pakistan

Identifying desirable genotypes with the best performance in diverse environments is a perpetual aim of plant breeding,and the interaction between genotype and environment(G×E)always plays a key *** study was conducted to elucidate the genetic behaviour of different hybrid combinations at various densities in diverse *** to a line×tester design,32 hybrid combinations were obtained from 16 inbred individuals crossed with two testers and planted at three locations at three density levels(45,000,67,500 and 90,000 plants ha-1)during ***(G),environment(E)and the interaction of genotype and environment(G×E)significantly affected grain yield at different *** planting density enhanced grain yield and improved the efficiency of germplasm screening,where the effect of location on grain yield at different densities was larger than that of year and the GCA was larger than the ***,four inbred lines(KB102,KB081,KA105,and KB106)with a high GCA,environmental adaptability,and several combinations using them as parents have been approved in ShannXi Province and National of *** conclusion,the evaluation of combining ability at multiple densities and locations can effectively screen inbred lines and improve breeding efficiency.

关键词： breeding Northwest planted