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| 1 | Construction of a genetic linkage map for cotton based on SRAP显示文摘A genetic linkage map of cotton was constructed with a newly developed molecular marker-SRAP (sequence-related amplified polymorphism) using a population consisting of 129 F2 individuals derived from the interspecific cross of Handan208 Pima90. A total of 136 primer pairs were used to detect polymorphisms between the two parents and 76 primer pairs with better polymorphisms were picked out to analyze the F2 population. 285 polymorphic bands were generated in total with an average of 3.75 polymorphic bands per pair of primers. The primer pair showing most polymorphic bands was the combination of me3 and em2, which produced 13 polymorphic bands. The 285 loci were used to construct linkage map with MAPMAKER/EXP3.0 and 237 loci were mapped at a LOD≥3.0 on 39 linkage groups. The total length of the map is 3030.7 cM, covering 65.4% of the whole cotton genome, and the average distance between adjacent markers is 12.79 cM. All the markers are distributed evenly among the linkage groups without clustering of loci. This is the first linkage map of cotton comprised of SRAP markers. | LIN Zhongxu, ZHANG Xianlong, NIE Yichun, HE Daohua & WU Maoqing National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China | 2003 | Chinese Science Bulletin2003，48，19： | 111 |
| 2 | High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers显示文摘一张高密度的连锁图为从在 Gossypium hirsutum L 之间的 cultivatedallotetraploid 种类的一个种间的十字导出的一张 F_2 人口被构造。并且 G.barbadense L。从种间的十字的 186 个 F_2 个人的一个总数“ CRI36 x 哈尔 7124' 是在包括一个新奇标记系统的 1 252 多态的 loci 的 genotyped,目标区域扩大多型性(陷井) 。地图由 1 097 个标记组成,包括 697 简单顺序重复(SSR ) , 171 个陷井, 129 顺序相关的放大多型性, 98 放大 fragmentlengthpolymorphisms,和二个词法标记,并且跨越了 4 有 4.1cM 的平均遗传距离的 536.7 厘米每标记。用在染色体之中的 45 复制 SSR loci, 13 同源染色体中的 11 个在四倍体棉花被识别。这张地图将为量的特点 loci 并且在棉花的分子的繁殖印射的高分辨率提供一个必要资源。 | Jiwen Yu Shuxun Yu Cairui Lu Wu Wang Shuli Fan Meizhen Song Zhongxu Lin Xianlong Zhang Jinfa Zhang | 2007 | Journal of Integrative Plant Biology2007，49，5： | 29 |
| 3 | Studies of new EST-SSRs derived from Gossypium barbadense显示文摘Existing cotton EST-SSR markers are mostly derived from Gossypium arboreum and Gossypium hir-sutum, but EST-SSR markers from Gossypium barbadense are scarce. One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G. barbadense cv. Pima3-79. Among the SSRs, trinucleotide AAG appeared at a high frequency of 11.76%. 36 accessions (consisting of 13 diploids of the A genome, 11 diploids of the D genome and 12 allotetraploids of the AD genome) were employed to test new EST-SSRs. 76 EST-SSRs were successfully amplified, and 313 polymorphic fragments were yielded, with an average of 4.11 fragments per primer pair. The PIC ranged from 0.17 to 0.95 with an average of 0.53. Based on Jaccard’s genetic similarity coefficient, these 36 accessions were clustered into three groups. 21 EST-SSRs exhibited polymorphisms in BC1 population ((Emian22 × Pima3-79) × Emian22), 24 polymor- phic loci were generated, while 22 of the 24 polymorphic loci were integrated with our interspecific BC1 backbone genetic linkage map, and anchored in 12 chromosomes. This study effectively proved that EST-SSRs from G. barbadense are valuable for genetic diversity analysis and genetic mapping. | ZHANG YanXin LIN ZhongXu LI Wu TU LiLi NIE YiChun ZHANG XianLong | 2007 | Chinese Science Bulletin2007，52，18： | 7 |
| 4 | Effect of water and fertilizer coupling optimization test on water use efficiency of rice in black soil regions显示文摘How to improve the water use efficiency of rice in black soil regions was studied. The black soil region in paddy fields was chosen as the research object. The research showed the fertilizer coupling mathematical model with N,P,K,irrigation water( W) and water use efficiency( WUE),which was set up under the condition of controlled irrigation with quadratic D- 416 optimized saturation design. The results show that the decending order of single factor' s influence on the WUE was N,K,P and W. All the interactions between N&P,N&K,N&W,K&P,P&W and K&W on the WUE were raised initially,and when reached a certain value,they began to decline. The decending order of each interaction on the WUE was K&P,K&W,N&K,N&P,P&W and N&W. When the WUE was targeted within 1. 8- 2. 5 kg / km^3,an optimized proportion plan was obtained in the 95% confidence interval,i. e. N 87. 76- 103. 32 kg / hm^2,K_2 O 52. 37- 66. 53 kg / hm^2 and P_2O_536. 80- 46. 71 kg / hm^2. Furthermore,the late tillering of the soil moisture content was 70. 07%- 72. 57% of the saturated moisture content. | LIN Yanyu ZHANG Zhongxue XU Dan NIE Tangzhe | 2016 | 排灌机械工程学报2016，34，2： | 4 |
| 5 | Genetic variations in plant architecture traits in cotton(Gossypium hirsutum) revealed by a genomewide association study显示文摘Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brownfiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study(GWAS)identified 11 quantitative trait loci(QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02 G017510 and Ghir_D02 G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02 G017510. Ghir_A12 G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045(T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton. | Tianwang Wen Baosheng Dai Tao Wang Xinxin Liu Chunyuan You Zhongxu Lin | 2019 | The Crop Journal2019，7，2： | 4 |
| 6 | Genome-wide association mapping of stress-tolerance traits in cotton显示文摘Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate(RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt(the relative germination rates of seeds under salt stress),RGR-Cold(the relative germination rates of seeds under cold stress), and DIV(the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP(best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs(i02237 Gh, i02243 Gh)on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval(D01, 37771–1942912). Of these four genes,GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton. | Heng Sun Minghui Meng Zhenhua Yan Zhongxu Lin Xinhui Nie Xiyan Yang | 2019 | The Crop Journal2019，7，1： | 3 |
| 7 | Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors显示文摘An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium. | Hua Cheng Gaofei Sun Shoupu He Wenfang Gong Zhen Peng Ruiping Wang Zhongxu Lin Xiongming Du | 2019 | Journal of Integrative Plant Biology2019，61，1： | 2 |
| 8 | Transcriptome and QTL analyses reveal candidate genes for fiber quality in Upland cotton显示文摘With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum acc.DH962 and G.hirsutum cv.Jimian 5 using RNA-seq.Of 15 stable QTL for fiber quality identified in the same two parents in previous studies,4,3,6,1,and 1 QTL were associated with fiber length(FL),fiber strength(FS),micronaire(MIC),fiber elongation(FE)and fiber length uniformity ratio(FU),respectively.Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions,of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development.Gh_A01G0453(GhDTX19),Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers,with Gh_D04G0942 showing low expression in other tissues except pistil.Gh_D07G1799(GhGAUT9),Gh_D11G0326(GhVPS29),Gh_D11G0333(GhTCP14),and Gh_D11G0334(GhNRP2)were preferentially expressed in 5 or 10 DPA fibers;Gh_A01G0397(GhABCG10)and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers.These results suggest candidate genes for molecular improvement of cotton fiber quality. | Hantao Wang Ruiting Zhang Chao Shen Ximei Li De Zhu Zhongxu Lin | 2020 | The Crop Journal2020，8，1： | 2 |
| 9 | Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data显示文摘Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development. | XU Shudi PAN Zhenyuan YIN Feifan YANG Qingyong LIN Zhongxu WEN Tianwang ZHU Longfu ZHANG Dawei NIE Xinhui | 2020 | Journal of Cotton Research2020，3，4： | 1 |
| 10 | Evaluation of application of a new molecular marker SRAP analysis of F2 segregation population and genetic diversity in cotton显示文摘 | LIN Zhongxu ZHANG Xianlong NIE Yichun | 2004 | Acta Genet Sin2004，31，6： | 1 |
| 11 | QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum x Gossypium barbadense 显示文摘 | HE Daohua LIN Zhongxu ZHANG Xianlong | 2007 | Euphytica2007，153，： | 1 |
| 12 | Phenotypic plasticity and genetic variation of cotton yield and its related traits under water-limited conditions显示文摘Global warming is limiting availability of water resources in arid and semi-arid regions,and so understanding water use efficiency(WUE)is increasingly important for agricultural production in those areas.As China is the largest cotton producing area,the problem of balancing WUE and efficient cotton production is a major issue.In this study,we used a natural population of 517 Upland cotton accessions to conduct a water-controlled trial in south and north of Xinjiang over two years.A total of 18 traits including agronomic traits,fiber yield indices and fiber quality indices,were investigated for broad-sense heritability and coefficient of variation.Appropriate water limitation was found to promote the establishment of favorable agronomic traits in cotton,associated with an increased cotton yield of 8.46%in Xinjiang,at the expense of a certain degree of fiber quality,such as decreased fiber length and an over-higher micronaire value.We detected 33 QTL related to response to water limitation using a drought resistance coefficient(DRC),and 6 QTL were found using a comprehensive indicator of CIDT(comprehensive index of drought tolerance)at the genetic level by integrating resequencing data.Two novel QTL-hotspots including six differentially expressed genes(DEGs)were further identified related to the drought response of cotton.These findings not only suggested a new approach to irrigation of cotton fields in Xinjiang,but also provided abundant genetic evidence for genetic breeders to study drought improvement of crops. | Baoqi Li Qin Tian Xuwen Wang Bei Han Li Liu Xianhui Kong Aijun Si Juan Wang Zhongxu Lin Xianlong Zhang Yu Yu Xiyan Yang | 2020 | The Crop Journal2020，8，6： | 1 |
| 13 | A case study of a micro-inversion event in dark brown fibre cotton(Gossypium hirsutum)显示文摘Structural variation is a major type of genetic variation that can potentially induce powerful genetic effects.In this study,we examined the Inv(A07)p1.09 p2.23 genetic inversion in brown fibre cotton at the individual and population genetics levels.A dark-brown fibre mutant that resulted from a distant hybridization between Gossypium barbadense and G.hirsutum,and a natural population including 30 dark-brown,70 light-brown and 21 white fibre cotton accessions were collected to perform a functional study of this micro-inversion.The results showed that Inv(A07)p1.09 p2.23 can be detected by high-throughput resequencing method,and induce micro-deletion,gene disruption(Ghir_A07 G000980)and abnormal gene expression in the breakpoint regions.Inv(A07)p1.09 p2.23 existed in only dark-brown fibre cotton,had undergone negative selection in elite brown fibre cultivars,and was significantly associated with fibre colour and nine fibre traits.In the Inv(A07)p1.09 p2.23 region,nucleotide diversity was lower,recombination was absent,and linkage disequilibrium was higher.Overall,this inversion event in dark-brown fibre cotton produced significant genetic effects,and this study will guide us to better understand the genetic effects of inversion events in dark-brown fibre cotton. | Tianwang Wen Tian Yao Chunyuan You Zhongxu Lin | 2020 | The Crop Journal2020，8，4： | 0 |
| 14 | Boosting wheat functional genomics via an indexed EMS mutant library of KN9204显示文摘A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation.However,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding.In this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)mutagenesis.This library contains a vast developmental diversity of critical tissues and transition stages.Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type SNPs.We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and WFZP.We tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered sensitivity.Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic stress.Thus,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat. | Dongzhi Wang Yongpeng Li Haojie Wang Yongxin Xu Yiman Yang Yuxin Zhou Zhongxu Chen Yuqing Zhou Lixuan Gui Yi Guo Chunjiang Zhou Wenqiang Tang Shuzhi Zheng Lei Wang Xiulin Guo Yingjun Zhang Fa Cui Xuelei Lin Yuling Jiao Yuehui He Junming Li Fei He Xigang Liu Jun Xiao | 2023 | Plant Communications2023，4，4： | 0 |
| 15 | Investigation and Analysis of Crop Germplasm Resources in Coastal Areas of Shandong Province显示文摘This study focused on the investigation of crop germplasm resources in coastal areas of Shandong Province, including132 villages in 82 towns of 34 counties. The survey collected local varieties and wild resources of grain crops, economic crops,vegetables and fruit trees, and a total of 848 samples were collected, belonging to 54 species of 39 genera in 15 families. In this study, the current situation and growth and decline conditions of crop germplasm resources were investigated, and their botanical classification and utilization importance were analyzed. Furthermore, the conservation, development and utilization of crop germplasm resources in coastal areas of Shandong Province were also discussed in this paper. | Dong WANG Xiaodong ZHANG Runfang LI Zhan LI Yumin MA Yu ZHANG Nana LI Weijing CHEN Zhongxue FAN Shoujin FAN Libin ZHANG Hui ZHANG Yingjie LIN Hanfeng DING | 2017 | Agricultural Science & Technology2017，18，10： | 0 |
| 16 | Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses显示文摘The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding programs.In this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition.We constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and TaFUL2.By integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown functions.Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and TaWRKY37-A1.Of particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet number.Notably,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic traits.Finally,we constructed a free and open access Wheat Spike Multi-Omic Database(http://gffzz73a948f43eac4923h5pf05qn65nuw6cnf.ffgz.tsg.suse.edu.cn/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding. | Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu Chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao | 2024 | Molecular Plant2024，17，3： | 0 |
| 17 | Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China显示文摘Background: Cotton fiber yield is a complex trait,which can be influenced by multiple agronomic traits.Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton.Results: In this study,503 upland cotton varieties covering the four breeding stages(BS1–BS4,1911–2011)in China were used for association mapping and domestication analysis.One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified,among which,29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4,and 26 markers showed decreased trend effect.Four favorable alleles of 9 major loci(R^(2)≥3)were strongly selected during the breeding stages,and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data.Conclusions :The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China. | GUO Chunping PAN Zhenyuan YOU Chunyuan ZHOU Xiaofeng HUANG Cong SHEN Chao ZHAO Ruihai YANG Qingyong ZHU Longfu SHAHZAD Raheel MENG Fande LIN Zhongxu NIE Xinhui | 2021 | Journal of Cotton Research2021，4，2： | 0 |
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