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QTL mapping of agronomic and economic traits for four F_(2)populations of upland cotton

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Journal of Cotton Research 2021年第1期4卷 12-23页

作者： LI Hongge PAN Zhaoe HE Shoupu JIA Yinhua GENG Xiaoli CHEN Baojun WANG Liru pang baoyin DU Xiongming State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural SciencesAnyangHenan 455000China

Background:Upland cotton(Gossypium hirsutum)accounts for more than 90%of the annual world cotton output because of its high yield ***,yield and fiber quality traits often show negative *** constructed four F_(2)populations of upland cotton,using two normal lines(4133B and SGK9708)with high yield potential but moderate fiber quality and two introgression lines(Suyuan04–3 and J02–247)with superior fiber quality,and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland *** also phenotyped eight agronomic and economic traits and mapped quantitative trait loci(QTLs).Results:Extensive phenotype variations and transgressive segregation were found across the segregation *** constructed four genetic maps of 585.97 centiMorgan(cM),752.45 cM,752.45 cM,and 1163.66 cM,one for each of the four F_(2)*** QTLs were identified across the four populations(7 for plant height,27 for fiber quality and 16 for yield).The same QTLs were identified in different populations,including qBW4 and qBW2,which were linked to a common simple sequence repeat(SSR)marker,NAU1255.A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B×Suyuan04–3 ***:These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

关键词： Upland cotton Yield traits Fiber quality traits QTL mapping Simultaneous improvement

A genome-wide association study of lateral root number for Asian cotton(Gossypium arboreum L.)

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Journal of Cotton Research 2022年第2期5卷 207-216页

作者： HU Daowu HE Shoupu SUN Gaofei JIA Yinhua GENG Xiaoli WANG Liru PAN Zhaoe CHEN Baojun LI Hongge ZUBAIR Iqbal WANG Xiaoyang ZHAO Zibo GE Yuting pang baoyin DU Xiongming Institute of Cotton Research of Chinese Academy of Agricultural Science/State Key Laboratory of Cotton Biology Anyang 455000HenanChina Anyang Institute of Technology Anyang 455000China School of Agricul-ture Sciences Zhengzhou UniversityZhengzhou 450000HenanChina.

Background:The lateral root is one of the most important organs that constitute the root architecture system in *** can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient *** root architecture systems can greatly increase crop *** study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease ***:The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions.A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits,but negatively correlates with lint percentage.A Genome-wide association study(GWAS)identified 18 significant SNPs with 19 candidate genes associated with the lateral root *** analysis identified three genes(FLA 12,WRKY29,and RBOHA)associated with lateral root ***:GWAS an alysis identified key SNPs and candidate gen esfor lateral root number,a nd gen es of FLA 12,WRKY29,and RBOHA may play a pivotal role in lateral root development in Asian cotton.

关键词： GWAS Lateral root Asian cotton SNPs Candidate genes

Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum

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Journal of Cotton Research 2021年第1期4卷 66-75页

作者： RAZA Irum HU Daowu AHMAD Adeel LI Hongge HE Shoupu NAZIR Mian Faisal WANG Xiaoyang JIA Yinhua PAN Zhaoe ZHANG Peng YASIR Muhammad IQBAL Muhammad Shahid GENG Xiaoli WANG Liru pang baoyin DU Xiongming State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000HenanChina School of Agricultural Sciences Zhengzhou UniversityZhengzhou 450001China

Background:Stem hardness is one of the major influencing factors for plant architecture in upland cotton(Gossypium hirsutum L.).Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum *** breeders are interested in using diverse genotypes to enhance fiber quality and *** pieces of research for hardness and its relationship with fiber quality and yield were *** study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland ***:Experiments were carried out to measure the bending,acupuncture,and compression properties of the stem from a collection of upland cotton genotypes,comprising 237 *** results showed that the genotypic difference in stem hardness was highly significant among the genotypes,and the stem hardness traits(BL,BU,AL,AU,CL,and CU)have a positive association with fiber quality traits and yield-related *** analyses of the results showed that in descriptive statistics result bending(BL,BU)has a maximum coefficient of variance,but fiber length and fiber strength have less coefficient of variance among the *** component analysis(PCA)trimmed quantitative characters into nine principal *** first nine principal components(PC)with Eigenvalues>1 explained 86%of the variation among 237 accessions of *** 2017 and 2018,PCA results indicated that BL,BU,FL,FE,and LI contributed to their variability in PC1,and BU,AU,CU,FD,LP,and FWPB have shown their variability in ***:We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength,acupuncture,and compression properties of ***.

关键词： Bending Compression Acupuncture Principle component analysis Stem hardness

Strigolactone-gibberellin crosstalk mediated by a distant silencer fine-tunes plant height in upland cotton

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Molecular Plant 2024年第10期17卷 1539-1557页

作者： Zailong Tian Baojun Chen Hongge Li Xinxin Pei Yaru Sun Gaofei Sun Zhaoe Pan Panhong Dai Xu Gao Xiaoli Geng Zhen Peng Yinhua Jia Daowu Hu Liru Wang baoyin pang Ai Zhang Xiongming Du Shoupu He State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina Zhengzhou Research Base State Key Laboratory of Cotton Bio-breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhouChina National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainanChina School of Computer Science&Information Engineering Anyang Institute of TechnologyAnyangChina National Supercomputing Center in Zhengzhou Zhengzhou UniversityZhengzhouChina

Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally;however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1) in upland cotton. This locus encodes gibberellin 2-oxidase 1A (GhPH1) and features a 1133-bp structural variation (PAVPH1) located approximately 16 kb upstream. The presence or absence of PAVPH1 influences the expression of GhPH1, thereby affecting plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes and binds to a specific CATTTG motif in both the GhPH1 promoter and PAVPH1. This interaction downregulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that DWARF53 (D53), a key repressor of the strigolactone (SL) signaling pathway, directly interacts with GhGARF to inhibit its binding to targets. Moreover, we identified a previously unrecognized gibberellin-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, which is crucial for regulating plant height in upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height, providing valuable insights for the development of semi-dwarf cotton varieties through precise modulation of GhPH1 expression.

关键词： plant height gibberellin 2-oxidase 1A silencer phytohormone crosstalk

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棉花盐胁迫下叶片miRNAs的鉴定与分析

棉花学报 2014年第5期26卷 377-386页

作者：许菲菲彭振龚文芳何守朴庞保印杜雄明中国农业科学院棉花研究所/棉花生物学国家重点实验室河南安阳455000

microRNAs（miRNAs）是一类21~24个核酸长度的非编码小分子RNA（sRNA,small RNA）,通过介导目标mRNA的切割或者抑制翻译来调节植物基因的表达。本文利用200 mmol·L^-1NaCl分别处理3叶期耐盐品系早熟长绒7号和盐敏感品系南丹巴地大花4 h... 详细信息

microRNAs（miRNAs）是一类21~24个核酸长度的非编码小分子RNA（sRNA,small RNA）,通过介导目标mRNA的切割或者抑制翻译来调节植物基因的表达。本文利用200 mmol·L^-1NaCl分别处理3叶期耐盐品系早熟长绒7号和盐敏感品系南丹巴地大花4 h,构建了4个小RNA文库并测序。以雷蒙德氏棉（Gossypium raimondii L.）D5基因组和本实验室陆地棉（Gossypium hirsutum L.）盐胁迫转录组测序拼接得到的序列作为参考,共发现360个miRNA,包括308个保守的miRNA和52个可信度高的新miRNA。2个品系共出现94个差异表达的miRNA,表达模式可分为2大类,筛选出20个候选miRNA。KEGG（Kyoto encyclopedia of genes and genomes）分析表明,耐盐品系显著富集的信号通路是抗原加工过程,而盐敏感品系显著富集的是生物碱合成途径。

关键词：盐胁迫 miRNA 小RNA测序靶基因预测

三个栽培种中天然彩色棉的遗传多样性及关联分析

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棉花学报 2015年第4期27卷 291-299页

作者：许鸿越孙君灵潘兆娥贾银华庞保印杜雄明中国农业科学院棉花研究所/棉花生物学国家重点实验室河南安阳455000

本研究利用主要农艺性状和SSR标记分析了137份陆地棉、13份海岛棉以及27份亚洲棉等不同纤维色泽的种质资源。170对SSR引物共检测到1036个等位基因变异。其中有多态性的等位基因923个,平均每个SSR位点有5.43个等位变异,变化范围为1~10。... 详细信息

本研究利用主要农艺性状和SSR标记分析了137份陆地棉、13份海岛棉以及27份亚洲棉等不同纤维色泽的种质资源。170对SSR引物共检测到1036个等位基因变异。其中有多态性的等位基因923个,平均每个SSR位点有5.43个等位变异,变化范围为1~10。位点多态性信息量（PIC）的变化范围为0.56~0.93,PIC在0.85以上的多态性SSR位点为122个。结果表明,实验材料存在着丰富的遗传多样性。在群体结构分析基础上,使用TASSEL软件中的混合线性模型（MLM）,在陆地棉中得到与11个性状相关联的SSR标记23个;在海岛棉群体得到与5个性状关联的17个标记;在亚洲棉中检测到与8个性状关联的15个标记位点。在三个栽培种中与纤维色泽度相关的标记位点一共有6个,分别是CIR51-4、BNL1421-2、BNL2656-2、DPL570-2、GH268-6和TMB131-1,表型变异解释率从3.12%到18.97%。三个栽培种中天然彩色棉种质具有丰富的遗传多样性,为棉花的种间、种内杂交育种以及拓宽棉花新品种的遗传背景提供了物质基础和理论依据。

关键词：彩色棉遗传多样性关联分析 SSR标记

基于棉花参比种质的SSR多态性核心引物筛选

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生物多样性 2008年第6期16卷 555-561页

作者：潘兆娥孙君灵王西文贾银华周忠丽庞保印杜雄明中国农业科学院棉花研究所/农业部棉花遗传改良重点开放实验室河南安阳455000

棉花品种间遗传多样性的评价和遗传图谱构建都需要大量多态性的SSR标记。本研究通过构建棉花参比种质(panel),高效快速地筛选出棉花多态性核心引物。本实验选用12份表型性状和遗传差异较大的棉花种质作为参比种质,对来自Cotton Microsat... 详细信息

棉花品种间遗传多样性的评价和遗传图谱构建都需要大量多态性的SSR标记。本研究通过构建棉花参比种质(panel),高效快速地筛选出棉花多态性核心引物。本实验选用12份表型性状和遗传差异较大的棉花种质作为参比种质,对来自Cotton Microsatellite Database(CMD)网站上(http://***)的5,914对棉花SSR引物进行了PCR扩增。结果表明:在不同棉种间多态性的引物有4,800对,约占有效扩增引物(5,300对)的90.6%;能区分不同品种间差异的引物大约有500对,占有效扩增引物的9.4%。我们推荐其中319对扩增效果好、条带清晰的引物作为棉花种质资源鉴定和分子指纹分析的核心引物,其中277对能把陆地棉品种间的差异鉴别出来。此外,我们还找到了在陆地棉、海岛棉及亚洲棉三大栽培棉中都有差异的13对共同SSR引物,建议作为分子指纹分析和种质鉴定的首选引物。本研究公开了319对核心SSR引物及其多态性信息,有利于规范引物筛选程序、提高引物筛选效率,对棉花种质资源的遗传多样性分析、指纹图谱构建,以及种子真伪性和纯度的鉴定等都具有现实意义。

关键词：棉花 SSR 引物多态性

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376份陆地棉棉铃早期性状的多样性分析

分子植物育种 2022年第17期20卷 5846-5854页

作者：葛浩胡道武何守朴李洪戈王晓阳庞保印陈全家杜雄明新疆农业大学农学院棉花教育工程研究中心乌鲁木齐830052 中国农业科学院棉花研究所棉花生物学国家重点实验室安阳455000

为解析不同品种陆地棉的棉铃性状之间关系,本研究调查和分析了采自不同地区的376份陆地棉品种的11个棉铃性状多样性。结果表明:(1)11个棉铃相关性状间的变异系数均大于10%,不同性状的变异系数为籽棉重>体积>壳重>铃重>壳厚>铃容重>横径(... 详细信息

为解析不同品种陆地棉的棉铃性状之间关系,本研究调查和分析了采自不同地区的376份陆地棉品种的11个棉铃性状多样性。结果表明:(1)11个棉铃相关性状间的变异系数均大于10%,不同性状的变异系数为籽棉重>体积>壳重>铃重>壳厚>铃容重>横径(上)>横径(下)>纵径>横径(中)>壳重率,说明棉花的产量易受环境影响;(2)相关性分析表明纵径与横径(上,中,下)、体积、壳厚、壳重、籽棉重、铃重呈极显著正相关,与壳重率和铃容重呈极显著负相关;壳厚与纵径、横径(中)呈极显著正相关,与体积呈显著正相关;(3)主成分分析表明:第1个主成分中,棉铃的重量和长度对第1个主成分影响较大,尤其是铃重对第1个主成分影响最大;第2个主成分主要反映单位体积的铃重;第3主成分中,壳重率的特征向量正值最大,因此第3主成分可以表示为铃壳占铃重的比例;第4个主成分中,壳厚的特征向量最大;(4)聚类分析结果表明376份陆地棉可分为大铃、中铃和小铃3个类群,说明所选材料具有一定的差异性,能够代表陆地棉品种材料。本研究结果为深入评价棉铃性状间的遗传多样性及品种选育提供理论依据。

关键词：陆地棉(Gossypium hirsutum L.) 棉铃性状相关性分析

陆地棉亲本间遗传距离与杂种优势的相关性研究

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中国农业科学 2019年第9期52卷 1488-1500页

作者：曲玉杰孙君灵耿晓丽王骁 Zareen Sarfraz 贾银华潘兆娥何守朴龚文芳王立如庞保印杜雄明中国农业科学院棉花研究所/棉花生物学国家重点实验室

【目的】通过1 500个陆地棉杂交组合分析杂种优势与其亲本间数量性状遗传距离的相关性,探讨能否利用大规模杂交组合亲本间遗传距离提高陆地棉杂种优势预测效果,以期为棉花杂交育种和杂种优势利用提供理论指导。【方法】选择来自15个国... 详细信息

【目的】通过1 500个陆地棉杂交组合分析杂种优势与其亲本间数量性状遗传距离的相关性,探讨能否利用大规模杂交组合亲本间遗传距离提高陆地棉杂种优势预测效果,以期为棉花杂交育种和杂种优势利用提供理论指导。【方法】选择来自15个国家和中国23个省(市)的305份陆地棉核心种质为亲本,采用L×T(Line×Tester)杂交设计配制1 500个杂交组合。2012—2013年,在中国南北方13个生态环境下考察其株高、单铃重、衣分、纤维长度等10个产量和纤维品质相关性状,分析F1杂种优势、亲本间遗传距离和群体结构,并采用4种方式(Cor1—Cor4)计算遗传距离与杂种优势的相关性。【结果】10个性状中亲优势(MPH)均值的变幅为1.70%—7.40%,平均为4.36%,按父本不同将F1分成5组(A—E),其MPH均值A>E>B>C>D;超亲优势(HB)均值的变幅为-4.17%—1.87%,平均为-0.17%,A、B和E组的HB均值皆为正。10个性状在5组中除D、E组的马克隆值之外,其他性状普遍具有明显的中亲优势,其中,单铃重和纤维长度的中亲优势在5组中均以正优势为主(达80%以上),最大值分别为34.01%和9.83%,对应的超亲优势分别为24.25%和5.80%。F1和亲本差异显著性分析表明单铃重、株高、纤维长度、伸长率和整齐度指数整体表现出一定的超亲优势。父本(测试种)与300个母本之间的遗传距离介于2.280—61.430,平均为21.550,5个测试种与母本间的平均遗传距离D>C>E>A>B,其中,最近值为11.721,最远值为33.271。按最小方差聚类,将305个陆地棉亲本划分为2个主群,包括5个亚群。4种遗传距离与杂种优势的相关性分析结果显示,因样本量、遗传距离变幅和父本不同其结果有所差异,相关性随样本量的增大而有所增强。其中,Cor1是Cor2结果的整体体现;Cor3与Cor1和Cor2相比,部分性状的中亲优势与遗传距离的相关性有所不同;Cor4的相关性最弱。综合来看,遗传距离与衣分、断裂比强度、整齐度指数和纺纱均匀性指数的中亲优势呈显著正相关,遗传距离与其他性状的中亲优势的相关性因采用的分析方案不同,结果有所不同;在4种方案中,除整齐度指数外,遗传距离与超亲优势的相关性整体表现负相关。其中,遗传距离与马克隆值、纤维长度和衣分的超亲优势相关性较强。【结论】陆地棉亲本间数量性状遗传距离与杂种优势有一定的线性关系,不同性状的杂种优势与遗传距离的相关性存在正负和强弱差异,且样本量越大相关性越强。说明基于大规模杂交组合研究陆地棉亲本间遗传距离与杂种优势的关系效果显著。

关键词：陆地棉核心种质数量性状 L×T 遗传距离聚类分析杂种优势预测