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QTL Analysis in Tetraploid Cotton

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棉花学报 2008年第S1期20卷 19-页

作者： lin zhong-xu1,he dao-hua1,{2.,huazhong agricultural university,wuhan,hubei 430070,China 2.Cotton Research Institute,Chinese Academy of agricultural Sciences(CAAS) key laboratory of Cotton genetic improvement,Ministry of Agriculture,Anyang,henan 455000,China) national key {2. of {2. genetic improvement Huazhong Agricultural UniversityWuhanHubei 430070China Cotton Research Institute Chinese Academy of Agricultural Sciences (CAAS) key laboratory of Cotton {2. {2. Ministry of AgricultureAnyangHenan 455000China

QTL analyses were performed in tetraploid *** interspecific F2.population consisting of 69 plants,which was developed from the cross between Gossypium hirsutum L.,*** 2.8(characterized as high fiber yield) and *** L.,*** 90(characterized as excellent fiber quality),was genotyped with SSR,RAPD,SRAP,and REMAP markers.A 102.-locus linkage map

关键词： QTL Analysis in Tetraploid Cotton QTLs

CLAIR: An integrated lipid database across multiple crop species

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Plant Communications 2024年第7期5卷 5-7页

作者： Bing he Mengjia Bu Qiang lin Zhengwei Fu Junhua Xie Wei Fan Jianyang Li Ruonan Li Wei hua Wanfei Liu Peng Cui Guangdong laboratory for lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural AreaAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China key laboratory of Biology and {2. {2. of Oil crops Ministry of Agriculture and Rural AffairsOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan 430062China State key laboratory of {2. Stress Adaptation and {2. School of Life SciencesHenan UniversityKaifeng 475004China College of Agronomy Qingdao Agricultural UniversityQingdao 266109China These authors contributed equally to this article

Lipids are an important global commodity and industrial raw *** of the lipids consumed worldwide are derived from *** 2.17,the total production of vegetable oils and animal fats was estimated at 2.6.1 million tons per year,with vegetable oils accounting for∼87%of this total(Mielke,2.17).Oilseed crops,a major source of vegetable oils,store triglycerides primarily in seeds and fruits,with variation in the specific types of oils produced(Zanetti et al.,2.13).A comprehensive understanding of the genes and mechanisms associated with lipid biosynthesis in various oilseed crops is essential for improving oil content traits in these crops through molecular biology and breeding(xu and Shanklin,2.16).

关键词： crops commodity breeding

QTL for grain yield and yield parameters in winter wheat(Triticum aestivum L.)

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湖南农业大学学报（自然科学版） 2007年第S1期33卷 86-91页

作者： lin Hai,GUO Hui-jun,ZHANG Xiu-ying,wang Rui-xia,XIAO Shi-{2.(T{2. national key Facility for {2. Gene Resources and genetic improvement,Institute of {2. Science,12.zhongguancun South Street,Beijing,100081,P.R)

Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat ***9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,*** weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at *** on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two *** of these QTL located on chromosomes 1A and 2.,respectively,exhibited pleiotropic *** showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.

关键词： Doubled haploids Quantitative trait loci(QTL) Grain yield wheat(Triticum aestivum L.)

Genome-Wide Identification of Genes Responsive to ABA and Cold/Salt Stresses in Gossypium hirsutum by Data-Mining and Expression Pattern Analysis

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agricultural Sciences in China 2011年第4期10卷 499-508页

作者： ZHU Long-fu he Xin YUAN dao-jun {2. Lian {2. Li TU Li-li SheN Guo-xin ZHANG hong ZHANG Xian-long national key {2. of {2. genetic improvement Huazhong Agricultural University Wuhan 430070 P.R.China Department of Biological Science Texas Tech University Lubbock 79409 USA

For making better use of nucleic acid resources of Gossypium hirsutum, a data-mining method was used to identify putative genes responsive to various abiotic stresses in G. hirsutum. Based on the compiled database including genes involved in abiotic stress response in Arabidopsis thaliana and the comprehensive analysis tool of GENEVESTIGATOR v3, 82. genes up-regulated or down-regulated significantly in roots or leaves during salt or cold treatment in Arabidopsis were identified. As compared to these 82. Arabidopsis genes annotated, 38 homologous expressed sequence tags （ESTs） from G. hirsutum were selected randomly and their expression patterns were studied using a quantitative real-time reverse transcription-polymerase chain reaction method. Among these 38 ESTs, about 55% of the genes （2. of 38） were different in response to ABA between cotton and Arabidopsis, whereas 70% of genes had similar responses to cold and salt treatments, and some of them which had not been characterized in Arabidopsis are now being investigated in gene function studies. According to these results, this approach of analyzing ESTs appears effective in large-scale identification of cotton genes involved in abiotic stress and might be adopted to determine gene functions in various biologic processes in cotton.

关键词： cold stress salt stress data-mining gene Gossypium hirsutum

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

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Plant Communications 2024年第5期5卷 57-74页

作者： Guo Ai Chao he Siteng Bi Ziru Zhou Ankui Liu Xin Hu Yanyan Liu Liujie Jin JiaCheng Zhou heping Zhang Dengxiang Du Hao Chen Xin Gong Sulaiman Saeed Handong Su Caixia Lan Wei Chen Qiang Li Hailiang Mao lin Li Hao Liu Dijun Chen Kerstin Kaufmann Khaled FAlazab Wenhao Yan national key {2. of {2. genetic improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenomeAnalysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State key laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department for Plant Cell and Molecular Biology Institute for BiologyHumboldt-Universitat Zu Berlin10115 BerlinGermany Plant Research Department Nuclear Research CenterEgyptian Atomic Energy AuthorityCairo 13759Egypt

Spike architecture inﬂuences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the inﬂuence of various environmental factors pose challenges in mapping the causal genes that affect spike ***,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in *** identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL *** constructed gene regulatory networks for young inﬂorescences at the double ridge stage and theﬂoret primordium stage,in which the spikelet meristem and theﬂoret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome *** these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike *** functions of TaZF-B1,VRT-B2.and TaSPL15-A/D in establishment of wheat spike architecture were *** study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

关键词： bread wheat spike traits genetic variation protein–protein interaction gene regulatory network

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

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Rice science 2013年第3期20卷 200-206页

作者： JIANG Jian-hua CheN Lan LIU Qiang-ming he Ying-jun hong De-lin State key laboratory of {2. {2.s and Germplasm Enhancement Nanjing Agricultural University Institute of crops Anhui Academy of Agriculture Sciences

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration （GD） and productive panicle number per plant （PN） were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height （PH） in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat （SSR） marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102.176bp, RM72.170bp and RM72.178bp were associated with GD, and their carrier varieties were hongmangshajing, Nipponbare, hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72.182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

关键词： japonica rice growth duration productive panicle number per plant plant height association mapping with conditional phenotypic value elite allele

QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three genetic Statistical Models

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Rice science 2013年第1期20卷 31-38页

作者： LIU Qiang-ming JIANG Jian-hua NIU Fu-an he Ying-jun {2. De-lin State key laboratory of {2. {2.s and Germplasm Enhancement Nanjing Agricultural University Institute of crops Anhui Academy of Agricultural Sciences

QTL mapping for seven quality traits was conducted by using 2.4 recombinant inbred lines （RIL） derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length （GL）, grain length to width ratio （LWR）, chalk grain rate （CGR）, chalkiness degree （CD）, gelatinization temperature （GT）, amylose content （AC） and gel consistency （GC） of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model （MCIM）, inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model （ICIM） and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis （MIMR）. Results showed that five QTLs with additive effect （A-QTLs） were detected by all the three methods simultaneously, two by two methods simultaneously, and 2. by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 2. by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect （E-QTLs） detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142.pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 2..78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.

关键词： quantitative trait locus quality trait genetic statistical model japonica rice

Development and Application of SCAR Markers for Discriminating Cytoplasmic Male Sterile lines from Their Cognate Maintainer lines in Indica Rice

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Rice science 2013年第3期20卷 191-199页

作者： LU Chao LIU Jian JIANG Jian-hua Caleb Manamik BRERIA TAN he-{2. Masahiko ICHII hong De-{2. State key laboratory of {2. {2.s and Germplasm Enhancement Nanjing Agricultural University Faculty of Agriculture Kagawa University

The DNAfragments about 1 600 bp were amplified using random amplified polymorphism DNA （RAPD） primer OPAl2.with the templates of mitochondrial DNA of Zhenshan 97A and Zhenshan 97B, and were sequenced. The nucleotide sequences and lengths of the fragments from Zhenshan 97A and Zhenshan 97B showed no difference. The precise length of the fragment was 1 588 bp. Sequence characterized amplification region （SCAR） primers were then developed to discriminate the cytoplasmic male sterile （CMS） {12.es and their maintainer {12.es. A specific 1 588 bp fragment could be amplified with SCAR primers, CHI19F2.CHI19R2.and CHI2.F3/CHI2.R3, in the mitochondrial DNA of Zhenshan 97A, but not Zhenshan 97B. Furthermore, the specific fragment could be also amplified from the total DNA from green leaf tissues of Zhenshan 97A with SCAR primers, but not Zhenshan 97B. With the corresponding primers, the specific fragment could also be amplified from the total DNA of green leaves of other two CMS {12.es with wild abortive type cytoplasm （CMS-WA）, namely Zhenpin A and Tianfeng A, but not in their maintainer {12.es. Moreover, using total DNA as template, each of the four pairs of SCAR primers could also be used to amplify the 1 588 bp fragment in CMS-ID （Indonesia paddy type） {12.e 11-32. but not in 11-32., and the specific fragment was amplified from the DNA of both F1 and F2.seed{12.gs of Shanyou 63. The results of detecting the genetic purity of a man-made mixture of the seeds of Zhenshan 97A using CHI2.F3/CHI2.R3 were completely consistent with the phenotypes. Taken together, these results indicated that the specific 1 588 bp-fragment amplified by CHI2.F3/CHI2.R3 was the unique amplification products of CMS mitochondrial DNA, and could be used to distinguish CMS-WA and CMS-ID {12.es from their corresponding maintainer {12.es at the seed{12.g stage.

关键词： Oryza safiva cytoplasmic male sterile line maintainer line genetic purity sequence characterized amplification region marker

Constructing the barley model for genetic transformation in Triticeae

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Journal of Integrative Agriculture 2015年第3期14卷 453-468页

作者： Lü Bo WU Jia-jie FU dao-lin State key laboratory of {2. Biology/Shandong key laboratory of {2. Biology Shandong Agricultural University

Barley（Hordeum vulgare L.） is one of the oldest domesticated crops, showing dramatic adaptation to various climate and environmental conditions. As a major cereal crop, barley ranks the 4th after wheat, maize and rice in terms of planting area and production all over the world. Due to its diploid nature, the cultivated barley is considered as an ideal model to study the polyploid wheat and other Triticeae species. here, we reviewed the development, optimization, and application of transgenic approaches in barley. The most efficient and robust {2. transformation has been built on the Agrobacterium-mediated transfer in conjunction with the immature embryo-based regeneration. We then discussed future considerations of using more practical technologies in barley transformation, such as the T-DNA/transposon tagging and the genome editing. As a cereal crop amenable to {2. transformation, barley will serve as the most valuable carrier for global functional genomics in Triticeae and is becoming the most practical model for generating value-added products.

关键词： Agrobacterium-mediated transfer genetically modified organism Hordeum vulgare immature embryos