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A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an F_(2)population

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Plant Communications 2022年第3期3卷 127-141页

作者： Pei Li Guo Li Ya-Wen Zhang Jian-Fang Zuo Jin-Yang Liu Yuan-Ming Zhang crop Information Center College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Jiangsu Key Laboratory for Horticultural crop Genetic Improvement Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjing 210014China

Theoretical and applied studies demonstrate the difficulty of detecting extremely over-dominant and smalleffect genes for quantitative traits via bulked segregant analysis(BSA)in an F_(2)*** address this issue,we proposed an integrated strategy for mapping various types of quantitative trait loci(QTLs)for quantitative traits via a combination of BSA and whole-genome *** this strategy,the numbers of read counts of marker alleles in two extreme pools were used to predict the numbers of read counts of marker *** observed and predicted numbers were used to construct a new statistic,G_(w),for detecting quantitative trait genes(QTGs),and the method was named *** method was significantly better than existing BSA *** the goal was to identify extremely over-dominant and smalleffect genes,another reserved DNA/RNA sample from each extreme phenotype F_(2)plant was sequenced,and the observed numbers of marker alleles and genotypes were used to calculate G_(w)to detect QTGs;this method was named *** simulated and real rice dataset analyses,dQTG-seq2 could identify many more extremely over-dominant and small-effect genes than BSA and QTL mapping ***2 may be extended to other heterogeneous mapping *** significance threshold of G_(w)in this study was determined by permutation *** addition,a handbook for the R software ***,which is available at https://***/web/packages/***/***,has been provided in the supplemental materials for the users’*** study provides a new strategy for identifying all types of QTLs for quantitative traits in an F_(2)population.

关键词： F_(2) bulked segregant analysis dQTG-seq extremely over-dominant gene small-effect gene rice

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Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis

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The crop Journal 2021年第2期9卷 476-486页

作者： Xiaojiao Hu Hongwu Wang Kun Li Xiaogang Liu Zhifang Liu Yujin Wu Shuqiang Li Changling Huang National Engineer Laboratory of crop Molecular Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis is a well-known phenomenon widely applied in *** studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in *** splicing(AS)is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in ***,genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively *** report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and *** results revealed a large number of significant differential AS(DAS)events in ZD808 relative to its parents,which can be further classified into parental-dominant and novel DAS ***-dominant,especially NG5-dominant,events were prevalent in the hybrid,accounting for 42%of all analyzed DAS *** enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear *** ZD808,CL11,and NG5,32.5%of DAS contained or lacked binding sites of at least one annotated maize microRNA(miRNA)and may be involved in miRNA-mediated posttranscriptional *** regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear *** study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.

关键词： Maize Heterosis Dominant alternative splicing Cis-regulation

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Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice(Oryza sativa L.)

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Journal of Integrative Agriculture 2014年第8期13卷 1609-1620页

作者： CHAI Lu ZHANG Jian PAN Xiao-biao ZHANG Fan ZHENG Tian-qing ZHAO Xiu-qing WANG Wen-sheng Ali Jauhar XU Jian-long LI Zhi-kang National Key Facility for crop Gene Resources and Genetic Improvement/institute of crop Sciences Chinese Academy of Agricultural Sciences crop Research institute Taizhou Academy of Agricultural Sciences of Zhejiang Province International Rice Research institute DAPO 777 Metro Malina The Philippines

Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the wholeplant growth duration salt tolerance（ST） was genetically dissected by phenotyping two sets of BC2F5 introgression lines（ILs） for four yield traits under severe natural salt stress and non-stress filed conditions using SSR markers and the methods of advanced backcross QTL（AB-QTL） analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and nonstress conditions were identified, most（〉90%） of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan（HHZ） ILs with favorable donor alleles at multiple QTLs and significantly improved yield traits under salt stress and non-stress conditions were identified, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection（MAS） or genome selection.

关键词： rice whole plant growth duration salt tolerance quantitative trait loci(QTLs) epistasis

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Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future crop Breeding

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Molecular Plant 2021年第1期14卷 77-94页

作者： Leiming Wu Linqian Han Qing Li Guoying Wang Hongwei Zhang Lin Li National Key Laboratory of crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China lnstitute of crop Science Chinese Academy of Agricultural SciencesBeijing 100081China

The functional genes underlying phenotypic variation and their interactions represent“genetic mysteries”.Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food *** to advances in highthroughput multi-omics technologies,we are stepping into an Interactome Big Data era that is certain to revolutionize genetic *** this article,we provide a brief overview of current strategies to explore genetic *** then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome ***,we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic *** propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning,which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits,and also provide a detailed procedure for systematic dissection of genetic mysteries,Finally,we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.

关键词： genetic mystery interactome big data machine learning crop breeding

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Response of the enzymes to nitrogen applications in cotton fiber (Gossypium hirsutum L.) and their relationships with fiber strength

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Science China(Life Sciences) 2009年第11期52卷 1065-1072页

作者： WANG YouHua1, FENG Ying1, XU NaiYin1,2, CHEN BingLin1, MA RongHui1 & ZHOU ZhiGuo1 1 Key Laboratory of crop Growth Regulation of the Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China 2 institute of industrial crops, Jiangsu Academy of Agricultural Science, Nanjing 210014, China Key Laboratory of crop Growth Regulation of the Ministry of Agriculture Nanjing Agricultural University Nanjing China institute of industrial crops Jiangsu Academy of Agricultural Science Nanjing China

To investigate the response of key enzymes to nitrogen (N) rates in cotton fiber and its relationship with fiber strength, experiments were conducted in 2005 and 2006 with cotton cultivars in Nanjing. Three N rates 0, 240 and 480 kgN/hm2, signifying optimum and excessive nitrogen application levels were *** activities and the gene expressions of the key enzymes were affected by N, and the characteristics of cellulose accumulation and fiber strength changed as the N rate varied. Beta-1,3-glucanase activity in cotton fiber declined from 9 DPA till boll opening, and the beta-1, 3-glucanase coding gene expression also followed a unimodal curve in 12—24 DPA. In 240 kgN/hm2 condition, the characteristics of enzyme activity and gene expression manner for sucrose synthase and beta-1,3-glucanase in developing cotton fiber were more favorable for forming a longer and more steady cellulose accumulation process, and for high strength fiber development.

关键词： cotton (Gossypium hirsutum L.) nitrogen fiber development enzyme activity gene expression fiber strength

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Effects of tridimensional uniform sowing on water consumption, nitrogen use, and yield in winter wheat

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The crop Journal 2019年第4期7卷 480-493页

作者： Zhiqiang Tao Shaokang Ma Xuhong Chang Demei Wang Yanjie Wang Yushuang Yang Guangcai Zhao Jiancang Yang institute of crop Sciences Chinese Academy of Agricultural Sciences Key Laboratory of Crop Physiology and Ecology Ministry of Agriculture and Rural Affairs

Wheat is a staple crop worldwide, but yields may diminish as climate change causes increasingly unpredictable patterns of precipitation and soil nutrient availability. Farmers are thus challenged to maximize planting efficiency to increase yield, while also improving their resource use efficiency. In this study the effectiveness of tridimensional uniform sowing was tested across a range of planting densities for winter wheat crops on the North China Plain. Tridimensional uniform sowing was tested against conventional drilling at three planting densities (180 × 104, 270 × 104, and 360 × 104 plants ha 1) and assessed for water consumption, biomass, nitrogen uptake and allocation, and aspects of yield. The tridimensional uniform sowing treatment outperformed the conventional drilling treatment in most metrics and at most planting densities, while performing markedly better at higher planting densities. Water consumption decreased and nitrogen efficiency increased. Tiller number and percentage of productive tillers, leaf area index, dry weight, and yield increased without a significant decline in grain protein. Nitrogen allocation was more efficient under tridimensional uniform sowing than with conventional drilling, and also varied according to annual precipitation and planting density. Both yield and grain protein contents were significantly correlated with the amount of pre-anthesis accumu- lated nitrogen translocated from vegetative organs to kernels after anthesis. Overall, a density of 270 × 104 plants ha 1 provided the highest water use efficiency and grain yield. Tridimensional uniform sowing will benefit farmers by forming stronger overall crops, promoting the coordinated improvement of yield, nitrogen uptake and efficiency, and increasing grain protein content at higher planting densities.

关键词： Winter wheat Sowing pattern Nitrogen absorption and utilization Yield Grain protein content

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Progress of the Research on the Conservation of crop Germplasm Resources in China

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Agricultural Sciences in China 2003年第8期2卷 825-835页

作者： LU Xin-xiong and CHEN Xiao-ling(Key Laboratory of crop Germplasm and Biotechnology > Ministry of Agriculture/institute of crop Germplasm Resources , Chinese Academy of Agricultural Sciences , Beijing 100081, P.R.China) Key Laboratory of crop Germplasm and Biotechnology Ministry of Agriculture/Institute of Crop Germplasm Resources Chinese Academy of Agricultural Sciences Beijing 100081 P.R.China

In the last 20 years, China has made considerable achievements in the conservation of crop germplasm resources. A network for crop germplasm conservation has been established by the end of 2002, which includes a national long-term seed genebank and its duplicated genebank, 8 national medium-term seed genebanks, 30 national field genebanks. 2 national in vitro genebanks, and 3 in situ conservation sites including 1 for wild soybean and 2 for wild rice. More than 334 000 crop germplasm accessions are currently stored in the national long-term genebank, covering 35 families, 192 genera and 712 species, which rank in the first place in the world. More than 43 000 accessions of vegetatively propagated crops and perennial crops covering more than 900 species are conserved in the national field genebanks. In addition, 2 300 accessions are stored in the national in vitro genebanks. This paper reviewed the latest advances of techniques for safety preservation of stored germplasm in seed genebank, ultra-dried seed storage and in vitro preservation in China and discussed current highlights in germplasm conservation.

关键词： crop germplasm resources Seed preservation Ultra-dry storage In vitro preservation Preservation techniques

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Development of a wheat material with improved bread-making quality by overexpressing HMW-GS 1S^(l)x2.3^(*)from Aegilops longissima

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The crop Journal 2022年第6期10卷 1717-1726页

作者： Yuliang Qiu Haiqiang Chen Shuangxi Zhang Jing Wang Lipu Du Ke Wang Xingguo Ye institute of crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China crop Research institute Ningxia Academy of Agri-Forestry SciencesYinchuan 750105NingxiaChina

Wheat bread-making quality can be improved by use of high-molecular-weight glutenin subunits(HMW-GSs)from wild *** longissima is a close relative of wheat that contains a number of HMW-GS-encoding genes including 1S^(l)x2.3^(*).In this study,transgenic wheat lines overexpressing 1S^(l)x2.3^(*)were obtained by Agrobacterium-mediated transformation and used to investigate the genetic contribution of 1S^(l)x2.3^(*)to wheat flour-processing *** 1S^(l)x2.3^(*)transgene was stably inherited and expressed over *** of 1S^(l)x2.3^(*)increased the relative expression of 1Dx2 and 1Dy12 and reduced that of 1By18 during grain *** general,integration of 1S^(l)x2.3^(*)stimulated the accumulation of endogenous HMW-GSs and low-molecular-weight glutenin subunits in wheat kernels,greatly increasing the glutenin:gliadin ratio and resulting in faster formation of protein bodies in the endosperm during grain development.A wheat material with improved flour-making quality was developed in which 1S^(l)x2.3^(*)improved wheat bread-making quality.

关键词： Wheat Aegilops longissima High-molecular-weight glutenin subunits 1S^(l)x2.3^(*) Bread-making quality

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Mapping of the heading date gene HdAey2280 in Aegilops tauschii

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Journal of Integrative Agriculture 2016年第12期15卷 2719-2725页

作者： LIU Guo-xiang ZHANG Li-chao XIA Chuan JIA Ji-zeng ZHANG Jun-cheng ZHANG Qiang DONG Chun-hao KONG Xiu-ying LIU Xu Key Laboratory of crop Germplasm Resources and Utilization Ministry of Agriculture/National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural Sciences

An optimum heading date is essential for sustainable crop productivity and ensuring high yields. In the present study, F2：3 populations were generated by crossing an early-heading accession, Y2280, with a late-heading accession, Y2282. The heading dates of the F2 and F3 populations were investigated in a field study. Using publicly available simple sequence repeat （SSR） markers, the early heading date gene HdAey2280 was mapped onto Aegilops tauschfi chromosome 7DS between the flanking markers wmc438 and barc126 at distances of 15 and 9.1 cM, respectively. Further analysis indicated that HdAey2280 is a novel heading date gene. New SSR markers were developed based on the Ae. tauschfi draft genome sequence, resulting in four new markers that were linked to the heading date gene HdAey2280. The closest distance of these markers was 1.9 cM away from the gene. The results collected in this study will serve as a framework for map-based cloning and marker-assisted selection in wheat breeding programs in the future.

关键词： Aegilops tauschii heading date molecular markers HdAey2280

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Organic amendments increase corn yield by enhancing soil resilience to climate change

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The crop Journal 2015年第2期3卷 110-117页

作者： Zhenwei Song Hongjun Gao Ping Zhu Chang Peng Aixing Deng Chengyan Zheng Md Abdul Mannaf Md Nurul Islam Weijian Zhang institute of crop Sciences Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology Ministry of Agriculture Jilin Academy of Agricultural Sciences Bangladesh Agricultural Research institute

A 22-year field experiment was conducted in Gongzhuling, Jilin province, China to investigate corn yield response to fertilization practice. Compared to an unfertilized control(CK), all fertilization treatments, including inorganic nitrogen fertilizer only(N), balanced inorganic fertilizers(NPK), NPK plus corn straw(SNPK), and NPK plus farmyard manure(MNPK), resulted in significant increases in corn yield. However, only organic matter amendments sustained increasing yield trends, with annual rates of 0.137 and 0.194 t ha-1for the SPNK and MNPK treatments, respectively(P crop production by enhancing soil quality.

关键词： Long-term fertilization Maize cropping Soil quality Global warming Northeast China

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