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Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform

Journal of Integrative Plant Biology 2015年第11期57卷 980-991页

作者： Yang L Xiao Cui Rui Li Piaopiao Huang Jie Zong Danqing Yao Gang Li Dabing Zhang Zheng Yuan State Key Laboratory of Hybrid Rice School of Life Sciences and BiotechnologyShanghai Jiao Tong University Novel Bioinformatics Company shanghai agricultural Technology extension and service center

DNA markers play important roles in plant breed- ing and genetics. The Insertion/Deletion （InDel） marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor- intensive. We developed an end-to-end computational solution （InDel Markers Development Platform, IMDP） to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequen- ces alignment pipeline （AGA-pipe） and next-generation re- sequencing data mapping pipeline （NGS-pipe）. With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA- pipe and NGS-pipe, we developed 2o5,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction （PCR） analysis of subgroup-specific markers indicated that the precision reached 90% （86 of 95）. Finally, to make them available to the public, we have integrated the InDels/markers information into a website （Rice InDel Marker Database, RIMD, http：I/2o2.12o.45.71/）. The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

关键词： Genetic polymorphism genome alignment InDel marker molecular breeding next-generation sequencing

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Drip fertigation and plant hedgerows significantly reduce nitrogen and phosphorus losses and maintain high fruit yields in intensive orchards

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Journal of Integrative Agriculture 2023年第2期22卷 598-610页

作者： SONG Ke QIN Qin YANG Ye-feng SUN Li-juan SUN Ya-fei ZHENG Xian-qing Lü Wei-guang XUE Yong Eco-Environmental Protection Research Institute Shanghai Academy of Agricultural SciencesShanghai 201403P.R.China Pudong New District Agro-Technology extension service center Shanghai 201300P.R.China

A field experiment was carried out to evaluate the effects of drip fertigation combined with plant hedgerows on nitrogen and phosphorus runoff losses in intensive pear orchards in the Tai Lake *** and phosphorus runoff over a whole year were measured by using successional runoff water collection *** four experimental treatments were conventional fertilization(CK),drip fertigation(DF),conventional fertilization combined with plant hedgerows(C+H),and drip fertigation combined with plant hedgerows(D+H).The results from one year of continuous monitoring showed a significant positive correlation between precipitation and surface runoff *** runoff discharge under the treatments without plant hedgerows totaled 15.86%of precipitation,while surface runoff discharge under the treatments with plant hedgerows totaled 12.82%of *** hedgerows reduced the number of runoff events and the amount of surface *** is the main driving force for the loss of nitrogen and phosphorus in surface runoff,and fertilization is an important factor affecting the losses of nitrogen and *** CK,approximately 7.36%of nitrogen and 2.63%of phosphorus from fertilization entered the surface water through *** fertigation reduced the accumulation of nitrogen and phosphorus in the surface soil and lowered the runoff loss concentrations of total nitrogen(TN)and total phosphorus(TP).Drip fertigation combined with plant hedgerows significantly reduced the overall TN and TP losses by 45.38 and 36.81%,respectively,in comparison to the CK *** fertigation increased the vertical migration depth of nitrogen and phosphorus nutrients and reduced the accumulation of nitrogen and phosphorus in the surface soil,which increased the pear *** promotion of drip fertigation combined with plant hedgerows will greatly reduce the losses of nitrogen and phosphorus to runoff and maintain the high fruit yields in the intensive orchards of

关键词： drip fertigation plant hedgerows surface runoff nitrogen and phosphorus losses fruit yields

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Nmnoparticle-mediated double-stranded RNA delivery system: A promising approach for sustainable pest management

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Insect Science 2021年第1期28卷 21-34页

作者： Shuo Yan Bin-Yuan Ren Jie Shen Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant ProtectionChina Agricultural UniversityBeijingChina National agricultural Technology extension and service center BeijingChina

RNA interference(RNAi)targeting lethal genes in insects has great potential for sustainable crop *** with traditional double-stranded(ds)RNA delivery systems,nanoparticles such as chitosan,liposomes,and cationic dendrimers offer advantages in delivering dsRNA/small interfering(si)RNA to improve RNAi efficiency,thus promoting the development and practice of RNAi-based pest management ***,we illustrate the limitations of traditional dsRNA delivery systems,reveal the mechanism of nanoparticle-mediated RNAi,summarize the recent progress and successful applications of nanoparticle-mediated RNAi in pest management,and finally address the prospects of nanoparticle-based RNA pesticides.

关键词： dsRNA delivery nanocarrier pest control RNAi efficiency RNA pesticide

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Overview on current criteria for heavy metals and its hint for the revision of soil environmental quality standards in China

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Journal of Integrative Agriculture 2018年第4期17卷 765-774页

作者： CHEN Shi-bao WANG Meng LI Shan-shan ZHAO Zhong-qiu E Wen-di Key Laboratory of Plant Nutrition and Fertilizer Ministry of Agriculture/Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural Sciences School of Land Science and Technology China University of Geosciences National agricultural Technology extension and service center Ministry of Agriculture

Following rapid social and economic development over the past several decades, soil pollution by heavy metals(HMs) has been both serious and widespread in China. The Soil Environmental Quality Standards(SEQSs) in China(GB 15618-1995) have been introduced to encourage and enforce sustainable soil HM management. However, in recent years, HM contents in soils have frequently been found to exceed their associated standard values, while the crops growing on them might still meet regulatory standards, and vice versa. There is thus growing awareness that GB 15618-1995 does not effectively regulate current soil HM pollution, as it has encountered bottlenecks, and disappointing outcomes caused by poor execution along with deficiencies and gaps in the policies. However, due to the deficiency of scientific research about relationships between soil HM concentrations and their ecological or human health effects, the development of SEQSs in China is still greatly restricted. This paper discusses international SEQSs of HMs as well their development in China over time, then examines current Chinese SEQSs to demonstrate their potential regulatory deficiencies by referring to international SEQSs. The corresponding legislative policies are described, and scientific information or responses are outlined for maintaining soil environmental quality. China’s experience has shown that policy and science can be linked to work in tandem to better understand and manage soil quality issues.

关键词： soil heavy metals regulatory standards soil science policy

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Evaluation of yield,stability and adaptability of national winter rapeseed regional trials in the upper Yangtze River region in 2017-2018

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Oil Crop Science 2020年第3期5卷 121-128页

作者： Ze’en Yu Lixia Luo Fang Zhang Meiyan Hong Xiangxiang Zhang Ruixing Guo Oil Crops Research Institute Chinese Academy of Agricultural SciencesWuhanChina National agricultural Technology extension and service center BeijingChina

Rapeseed variety needs to be tested by regional trial in multiple sites for many years before being applied in market in *** of rapeseed were affected by the interaction of sites and *** of regional trials is very important for guiding rapeseed ***(genotype main effects and genotypeenvironment interaction)biplot was used to evaluate yield,stability,adaptability,representativeness and discrimination of national winter rapeseed trials in the upper reaches of Yangtze River in *** showed that the main effects of genotype(G),environment(E)and genotypeenvironment interaction(GE)were significant(P<0.01)for *** them,E accounted for 46.95%total variation on average,G and GE accounted for 19.34%and 33.71%*** varieties were found with high-yield,excellent stability and adaptability,including‘Yiyou 29’,‘Xiwang 920’,‘Liyouza 108’,‘Nanyou 546’,‘Dadi 195’,‘Jiayou 1’,‘Huayouza 28’and‘Yuhua 2’.Test sites included Nanchong,Mianyang,Wanzhou,Shuangliu and Chengdu in Sichuan Province and Zunyi together with Guiyang in Guizhou Province were selected for their excellent representativeness and *** results would provide theoretical basis for rapeseed breeding.

关键词： National regional trial GGE biplot High yield Yield stability Adaptability Representativeness Discrimination

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Cool-season annual pastures with clovers to supplement wintering beef cows nursing calves

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Journal of Animal Science and Biotechnology 2012年第4期3卷 221-226页

作者： Stacey A Gunter Whitney A Whitworth T Gregory Montgomery Paul A Beck United States Department of Agriculture Agricultural Research Service Southern Plains Range Research Station University of Arkansas at Monticello Division of Agriculture Southeast Research & Extension Center University of Arkansas Division of Agriculture Southwest Research & Extension Center University of Arkansas

In December of 3 years, 87 beef cows with nursing calves （.594 ± 9.8 kg; calving season, September to November） at side were stratified by body condition score, body weight, cow age, and calf gender and divided randomly into 6 groups assigned to 1 of 6 cool-season annual pastures （0.45 ha/cow） that had been interseeded into a dormant common bermudagrass （Cynodon dactylon [L.] Pers.）/bahiagrass （Paspalum notatum Flugge） sod. Pastures contained 1 of the following 3 seeding mixtures （2 pastures/mixture）： 1） wheat （Triticum aestivurn L.） and ryegrass （Lofium multiflorum Lain., WRG）, 2） wheat and ryegrass plus red clover （Trifolium pretense L, WRR）, or 3） wheat and ryegrass plus white （Trifofium repens L.） and crimson clovers （Trifolium incarnatum L., WRW）. All groups had ad libitum access to grass hay （12% crude protein; 58% total digestible nutrients）. The second week in December, cow estrous cycles were synchronized and artificially inseminated. In late December, a bull was placed with each group for 60-d. Data were analyzed with an analysis of variance using a mixed model containing treatment as the fixed effect and year as the random effect. Body weight and condition scores did not differ （P ≥ 0.27） among cows between February and June. Calf birth weights or average daily gain did not differ （P≥ 0.17） among treatments; however, calves grazing pastures with clovers did tend （P= 0.06） to weigh more than calves grazing grass only. Weaning weight per cow exposed to a bull was greater （P= 0.02） for WRR and WRW than WRG. Cows grazing winter-annual pastures containing clovers tended to wean more calf body weight per cow exposed to a bull than cows grazing the grass only pastures.

关键词： Annual ryegrass Beef cows Clovers Nitrogen Pasture 1

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Construction of an anchoring SSR marker genetic linkage map and detection of a sex-linked region in two dioecious populations of red bayberry

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Horticulture Research 2020年第1期7卷 2262-2270页

作者： Yan Wang Hui-Min Jia Yu-Tong Shen Hai-Bo Zhao Qin-Song Yang Chang-Qing Zhu De-Li Sun Guo-Yun Wang Chao-Chao Zhou Yun Jiao Chun-Yan Chai Li-Ju Yan Xiong-Wei Li Hui-Juan Jia Zhong-Shan Gao Fruit Science Institute College of Agriculture and BiotechnologyZhejiang University310058 HangzhouChina shanghai center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of Sciences201602 ShanghaiChina Yuyao Forestry Technology extension center 315400 NingboChina Institute of Forestry Ningbo Academy of Agricultural ScienceNingboChina Cixi Forestry Technology extension center 315300 CixiChina Linhai Forestry Technology extension center 317000 TaizhouChina Forest&Fruit Tree Institute Shanghai Academy of Agricultural Sciences201403 ShanghaiChina

Red bayberry(Morella rubra)is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been *** updated the linkage map of the species by adding 118 SSR markers and the femalespecific marker MrFT2_*** integrated map included eight linkage groups and spanned 491 *** sexassociated markers were identified,six of which were located in linkage group 8,in agreement with the previously reported location of the sex-determining *** MrFT2_BD-SEX marker was genotyped in 203 cultivated *** the females of the accessions,we found two female-specific alleles,designated W-b(151 bp)and W-d(129 bp).We previously found that‘Dongkui’,a female cultivar,could produce viable pollen(we refer to such plants‘Dongkui-male’)and serve as the paternal parent in *** genotypes of the MrFT2_BD-SEX marker were W-b/Z in‘Biqi’and W-d/Z in‘Dongkui-male’.The progeny of a cross between these parents produced a 3:1 female(W-)to male(ZZ)ratio and the expected 1:1:1:1 ratio of W-b/W-d:W-b/Z:W-d/Z:Z/*** addition,the flowering and fruiting phenotypes of all the F1 progeny fit their *** results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus(W)in a small genomic region(59 kb and less than 3.3 cM).Furthermore,we have produced a homozygous“super female”(WW)that should produce all-female offspring in the F2 generation,providing a foundation for commercial use and presenting great potential for use in modern breeding programs.

关键词： breeding cultivar linkage

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Combined application of organic fertilizer and chemical fertilizer alleviates the kernel position effect in summer maize by promoting post-silking nitrogen uptake and dry matter accumulation

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Journal of Integrative Agriculture 2024年第4期23卷 1179-1194页

作者： Lichao Zhai Lihua Zhang Yongzeng Cui Lifang Zhai Mengjing Zheng Yanrong Yao Jingting Zhang Wanbin Hou Liyong Wu Xiuling Jia Institute of Cereal and Oil Crops Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Crop Cultivation Physiology and Green Production of Hebei ProvinceShijiazhuang 050035China Hebei Science and Technology Innovation service center Shijiazhuang 050051China Yongnian agricultural Technology extension center Handan 057150China Ningjin agricultural Technology extension center Xingtai 055550China

Adjusting agronomic measures to alleviate the kernel position effect in maize is important for ensuring high *** order to clarify whether the combined application of organic fertilizer and chemical fertilizer(CAOFCF)can alleviate the kernel position effect of summer maize,field experiments were conducted during the 2019 and 2020 growing seasons,and five treatments were assessed:CF,100%chemical fertilizer;OFCF1,15%organic fertilizer+85%chemical fertilizer;OFCF2,30%organic fertilizer+70%chemical fertilizer;OFCF3,45%organic fertilizer+55%chemical fertilizer;and OFCF4,60%organic fertilizer+40%chemical *** with the CF treatment,the OFCF1 and OFCF2 treatments significantly alleviated the kernel position effect by increasing the weight ratio of inferior kernels to superior kernels and reducing the weight gap between the superior and inferior *** effects were largely due to the improved filling and starch accumulation of inferior ***,there were no obvious differences in the kernel position effect among plants treated with CF,OFCF3,or OFCF4 in most *** area indexes,post-silking photosynthetic rates,and net assimilation rates were higher in plants treated with OFCF1 or OFCF2 than in those treated with CF,reflecting an enhanced photosynthetic capacity and improved postsilking dry matter accumulation(DMA)in the plants treated with OFCF1 or *** with the CF treatment,the OFCF1 and OFCF2 treatments increased post-silking N uptake by 66.3 and 75.5%,respectively,which was the major factor driving post-silking photosynthetic capacity and ***,the increases in root DMA and zeatin riboside content observed following the OFCF1 and OFCF2 treatments resulted in reduced root senescence,which is associated with an increased post-silking N *** showed that post-silking N uptake,DMA,and grain yield in summer maize were negatively correlated with the kernel position *** conclusion,the combined application of

关键词： chemical fertilizer dry mater accumulation kernel position effect N uptake organic fertilizer

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Assessment of wheat variety distinctness using SSR markers

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Journal of Integrative Agriculture 2015年第10期14卷 1923-1935页

作者： WANG Li-xin QIU Jun CHANG Li-fang LIU Li-hua LI Hong-bo PANG Bin-shuang ZHAO Chang-ping Beijing Engineering and Technique Research center for Hybrid Wheat Beijing Academy of Agricultural and Forestry Sciences National Agriculture Technology extension and service center Ministry of Agriculture National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science Chinese Academy of Agricultural Sciences

Assessment of variety distinctness is important for both the registration and the protection of particular variety. However, the current testing system, which assesses a range of morphological characters of each pair of varieties grown side-by-side, is time-consuming and is not suitable for the assessment of hundreds of samples. The objective of this study was to develop a procedure for the assessment of wheat variety distinctness using simple sequence repeat（SSR） markers. A comparison between the molecular and morphological profile of 797 varieties was made. On the basis of the comparison, pairs of varieties with a genetic similarity value（GSV） ≤90% were deemed to be distinct, accounting for ~85% of varieties assessed in wheat regional trials. For the remaining ~15% of varieties, GSVs between different varieties were 〉90%, among which ~35% were not distinct and the other ~65% were distinct. Therefore, if given a GSV〉90%, the pairs of varieties should be morphologically assessed in the field. To avoid any errors in the assessments, we proposed the elimination of contaminant plants from the sample before comparing the varietal genotypes, scoring of the genotype at each locus with a pair of allele numbers when constructing a molecular profile, and faithfully recording two alleles at a non-homozygous locus. To reduce the workload and cost, a three-grade markers comparison among varieties is suggested. In addition, 80 SSR markers and a technical procedure for assessment of wheat variety distinctness have been proposed. Based on the procedure, the distinctness assessment of ~85% of all wheat varieties is completed in our laboratory annually. Consequently, total field assessment has been reduced considerably.

关键词： wheat variety distinctness assessment SSR markers

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Improved root zone temperature buffer capacity enhancing sweet pepper yield via soil-ridged substrate-embedded cultivation in solar greenhouse

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International Journal of agricultural and Biological Engineering 2018年第2期11卷 41-47页

作者： Guohai Fu Zonggeng Li Wenke Liu Qichang Yang Institute of Environment and Sustainable Development in Agriculture Chinese Academy of Agricultural Sciences/Key Laboratory of Energy Conservation and Waste Management of Agricultural StructuresMinistry of AgricultureBeijing 100081China National agricultural Technology extension and service center Beijing 100125China

A novel soilless cultivation method,called as soil-ridged substrate-embedded cultivation(SSC)was invented,and an experiment was designed to investigate root zone temperature and production efficiency of sweet pepper cultivated by two SSC patterns,i.e.,SSC-P(polyethylene groove inserted)and SSC-W(wire-mesh groove inserted),and also other two cultivation methods,i.e.,soil ridge(SR)and naked polyethylene groove(PG).Results showed that PG,SSC-P and SSC-W increased the average minimal root zone temperature by 1.01℃,0.75℃,and 1.16℃ compared to SR(16.33℃)during March 16-20,*** June 1-5,SSC-P and SSC-W decreased the average maximal root zone temperature by 1.28℃ and 1.29℃ compared to SR(34.99℃),while PG increased it by 1.44℃.PG,SSC-P,and SSC-W decreased the differences of average daytime and night time temperatures by 1.34℃,2.13℃,and 2.88℃ compared to SR(4.56℃)during early ***,SSC-P and SSC-W decreased temperature differences of average daytime and night time by 0.9℃ and 1.07℃ compared to SR(0.95℃)during later stage,but PG improved by 2.85℃.Temperature difference of daytime and night time of SSC-W was minimal,and the temperature difference between the diurnal highest and the lowest temperature of SSC-W was also *** buffer capacity of SSC-W was slightly better than that of ***-W significantly improved the growth of sweet pepper compared to ***,fruit yield per square meter of sweet pepper cultivated on SSC-P and SSC-W improved by 21.24%and 50.33%,respectively compared to SR(3.06 kg/m^(2)),while PG lowered the yield by 13.72%.SSC-W was a better SSC pattern compared with SSC-P in terms of production efficiency.

关键词： soil cultivation SSC substrate cultivation solar greenhouse diurnal temperature difference root zone temperature

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