DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the A_T- and D_T-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.     

Comparative Analysis between Homoeologous Genome Segments of Brassica napus and Its Progenitor Species Reveals Extensive Sequence-Level Divergence

Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.     

陆地棉叶形及棉酚腺体变异的遗传研究

阔叶、有棉酚腺体陆地棉干种子经250Gy^60 Coγ射线辐照,在M1代筛选到鸡脚叶γ-1、γ-2和γ-5突变体。3株突变体自交后代（M2）中,阔叶：鸡脚叶：超鸡脚叶的分离比例符合1：2：1;γ—1和γ-2自交后代中的所有棉株均有棉酚腺体;γ-5自交后代中,有棉酚腺体株：无棉酚腺体株的分离比例符合3：1,阔叶、有棉酚腺体株：阔叶、无棉酚腺体株：鸡脚叶、有棉酚腺体株：鸡脚叶、无棉酚腺体株：超鸡脚叶、有棉酚腺体株：超鸡脚叶、无棉酚腺体株的分离比例符合3／16：1／16：6／16：2／16：3／16：1／16。该结果表明,3株突变体的叶形变异由1对不完全显性基因控制,γ-5的无棉酚腺体基因由1对隐性基因控制,且γ-5的叶形基因与棉酚腺体基因为独立遗传。通过对γ-5自交后代各种变异株的SSR标记研究表明,BNL3649、BNL2440度BNL1414为候选标记。为进一步对突变基因进行定位奠定了基础。     

利用RFLP分子标记确定导入小麦的鹅观草(R. kamoji)染色体的部分同源群归属

选用来自小麦族7个部分同源群的26个DNA探针对45个小麦-鹅观草衍生后代株系及鹅观草、中国春和扬麦5号亲本进行RFLP分析,结果表明16个小麦-鹅观草异附加系、异代换系或可能的易位系中所涉及鹅观草染色体分别属于第1、3、5、6、7部分同源群。小麦-鹅观草异染色体系中导入的成对鹅观草染色体能够较稳定地遗传给后代。K139、K141、K214、K218、K219、K224二体附加系所添加的鹅观草染色体属第1部分同源群,但K214和K218所添加的鹅观草染色体与K219、K224的添加的鹅观草染色体分别来自鹅观草不同的染色体组。K147端体添加系涉及鹅观草第1部分同源群染色体长臂,而K139、K141和K147所涉及的鹅观草染色体长臂分别来自鹅观草3个不同的染色体组。鹅观草U染色体与小麦第1部分同源群有同源关系,属第1部分同源群的鹅观草染色体尤其是其长臂与赤霉病抗性有关。鹅观草第1部分同源群与第6部分同源群染色体之间可能涉及重排。K203添加的2条鹅观草染色体分别与第1和6部分同源群同源。K166导入鹅观草染色体涉及第5部分同源群短臂。K177（2n=41,20Ⅱ I）中,所渗入的鹅观草染色质涉及第5（5L）、6（6S）、7（SL）部分同源群。鹅观草S、H和Y3个染色体组间具部分同源性。     

Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, low-copy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.     

棉花WRKY基因GhWRKY25的克隆和表达分析

棉花是一种重要的经济作物,在国民生产中起着重要的作用。然而干旱盐碱等不良环境严重地制约着棉花的种植区域及其产量和品质。近年来,利用分子育种改良棉花对这些逆境的耐性的研究成为热点。本文从棉花中克隆了一个对干旱和盐碱具有应答的WRKY基因,定名为GhWRKY25。该基因编码的蛋白包含两个典型的WRKY结构域,每个WRKY结构域的C端含有一个C2H2类型的锌指蛋白结构,进化树分析表明其属于Ⅰ类WRKY蛋白,与可可的WRKY3同源性最高。利用qPCR分析发现该基因在棉花里为组成型表达,但在花中表达量较高。GhWRKY25在施用SA、JA、ABA、GA 中表达表现为上调。干旱和NaCl处理时发现GhWRKY25基因表达均显著上调。通过上述结果可以推测GhWRKY25在棉花对于逆境的适应中具有重要的作用,为该基因功能的进一步研究提供基础。     

Genome- Wide Analysis and Characterization of the TRX Gene Family in Upland Cotton

Thioredoxins (TRX) are small molecules of proteins that are present in all organisms. TRXs play an important role in diverse functions of plant growth and development. In this study, we performed genome-wide, characterization and expression levels of TRX gene family in cotton. A total of 150 GhTRX proteins were identified in upland cotton and classified into five subfamilies based on their domain compositions. Phylogenetic tree analysis divided TRX genes into seven subgroups. GhTRX genes covered all upland cotton chromosomes, with duplicated gene events. Ka/Ks ratio of three gene pairs was less than 1, suggesting purifying selection. The functions of GhTRX genes were studied using gene ontology, protein localization, and promoter analysis. Furthermore, six GhTRX genes were randomly selected to examine their expression level in cotton development and under various exogenous treatments. The genes showed high expressions in various tissues and at different stages of leaf senescence, also showed high expression under abscisic acid, ethylene, drought, and salinity. This study reveals the first report of TRX family genes in upland cotton. However further studies are needed to elucidate their specific functions in cotton plant.     

陆地棉体细胞胚胎发生与植株再生

利用陆地棉品种下胚轴为外植体进行体外培养研究。激素和品种是影响愈伤诱导和胚胎发生的主要因素。去除激素后胚性愈伤在固体培养基上只能形成少量的成熟胚。悬浮培养是获得大量成熟胚的中间步骤。悬培两周后,悬培物转到固体培养基上促进胚状体成熟,30—60目之间的悬培物比大于30目的悬培物易形成成熟胚。KT 0.1ppm、Zea 0.1ppm分别有效地促进了胚状体成熟。活性碳250mg/L、NAA 0.1ppm、IBA 0.1ppm和IAA 0.1ppm能使胚状体萌发并健壮生长。目前已得到100多株幼苗,大苗已达八片真叶。     

陆地棉产量性状的遗传效应及其与环境互作的分析

本研究根据加性-显性与环境互作的遗传模型, 分析了陆地棉10个杂交亲本和20个F1皮棉产量、单株铃数、单铃重、衣分和前期收花率的两年资料,估算了各项遗传方差分量和成对性状间各项遗传效应的相关。方差分析结果表明,衣分受基因型×环境互作效应影响较小,其它4个性状受基因型×环境互作影响较大,其中皮棉产量、单株铃数和前期收花率受显性×环境互作效应影响较大。遗传相关分析表明,皮棉产量与单株铃数、衣分和前期收花率加性相关系数值较大,皮棉产量与单株铃数、单铃重和前期收花率间存在较强的加性与环境互作负相关。皮棉产量与单株铃数、单铃重和前期收花率间存在显著的显性正相关,但与单株铃数、单铃重间存在显性与环境互作相关。 Abstract:Ten parents and their 20 F1s of upland cotton were analyzed for five yield traits in two years by a genetic model of additive-dominance with interaction effects.Genetic variance components and correlations were estimated.It was indicated that the gene by year effects interaction were small for lint percentage,but large for the other four traits,the dominance by year effects interaction were very large for lintvield,boll number and first picking percentage,especially.The additive correlation between lint yield with boll number,lint percentage and first picking percentage were significantly and high.The dominance correlations between lint yield and boll number,and between boll weight and first picking percentage were significantly too.The correlation of additive by year interaction between lint yield and boll number,boll weight and first picking percentage and those of dominance interaction by year between lint yield and boll number,boll weight were significant and large.The dominance correlation between boll number and boll weight were large too.     

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes in Brassica napus Allohaploids

Allopolyploid species contain more than two sets of related chromosomes (homoeologs) that must be sorted during meiosis to ensure fertility. As polyploid species usually have multiple origins, one intriguing, yet largely underexplored, question is whether different mechanisms suppressing crossovers between homoeologs may coexist within the same polyphyletic species. We addressed this question using Brassica napus, a young polyphyletic allopolyploid species. We first analyzed the meiotic behavior of 363 allohaploids produced from 29 accessions, which represent a large part of B. napus genetic diversity. Two main clear-cut meiotic phenotypes were observed, encompassing a twofold difference in the number of univalents at metaphase I. We then sequenced two chloroplast intergenic regions to gain insight into the maternal origins of the same 29 accessions; only two plastid haplotypes were found, and these correlated with the dichotomy of meiotic phenotypes. Finally, we analyzed genetic diversity at the PrBn locus, which was shown to determine meiotic behavior in a segregating population of B. napus allohaploids. We observed that segregation of two alleles at PrBn could adequately explain a large part of the variation in meiotic behavior found among B. napus allohaploids. Overall, our results suggest that repeated polyploidy resulted in different levels of crossover suppression between homoeologs in B. napus allohaploids.     

六种新疆陆地棉棉籽脂肪酸成分分析

目的:通过分析六种新疆陆地棉棉籽脂肪酸成分与含量的变化,为更好的开发,利用丰富的棉籽资源提供实验数据.方法:采用索氏提取法提取了6种新疆陆地棉棉籽油,其棉籽脂肪酸经甲酯化后用气相色谱-质谱联用仪进行分析.结果:不同品种棉籽油所含脂肪酸成分基本相同,但各脂肪酸成分的相对含量差异较大,其中亚油酸含量变化范围为50.30%～57.25%,棕榈酸、油酸含量的变化范围分别为22.24%～30.98%和12.93%～16.84%.不同棉花品种棉籽的多不饱和脂肪酸(PUFA)与饱和脂肪酸(SFA)相对含量比值也不同,变化范围为1.66～2.59.结论:不同品种棉籽,其营养价值及经济价值存在较大差异,其中,新陆早27号棉籽具有相对更好的开发利用价值.     

棉花2个多标记基因系及其杂交后代AFLP分析

应用AFLP分子标记技术,对陆地棉两个多标记基因系T582和T586及其杂交后代F1等进行了DNA多态性分析。结果表明:在58对EcoRI/MseI引物组合中,筛选出41对引物组合具有多态性,多态性的引物组合占筛选总组合的70.69%。AFLP分子标记具有高度的多态性,非常适于基因组差异较小的(棉花)材料之间的多态性筛选。采用聚丙烯酰胺银染法显带技术,AFLP进行PCR扩增能看到30~80条DNA亮带,且检测灵敏度高,可区别只相差十几个bp甚至几个bp大小的DNA片段。但AFLP标记以显性标记占绝对优势,共显性标记比率极少,故而难以区分种质的杂合和纯合,这是它的惟一不足之处。     

陆地棉SUPERMAN类似锌指蛋白基因的克隆与表达分析

锌指蛋白是生物体内数量最多的转录调控因子,它在动植物的生长发育中都起到十分重要的作用。SUPERMAN类锌指蛋白只含有1个锌指结构。我们根据这类蛋白的保守结构域设计简并引物,通过RT-PCR从棉花中获得了3个这个家族成员的EST,得到1个锌指蛋白基因的全长序列,该基因的编码区长744 bp,编码长248个氨基酸的多肽,其氨基酸序列与GenBank中登录的一个拟南芥RBE蛋白有40%的同源性。此基因被命名为GZFP。它含有保守的锌指结构并在多肽链的C-端具有富含亮氨酸的保守结构域,GZFP含有核定位信号并且没有内含子。GZFP基因在棉花花蕾、子房、花瓣和根中的表达量要高于木质部、韧皮部、叶片、纤维和种子。GZFP基因的表达量很低,在GenBank中没有任何和它同源的EST序列存在。对GZFP 5′侧翼区进行分析发现有数个花粉和根特异表达相关元件,4个与Dof蛋白作用的核心序列,4个与光诱导相关的元件。      

短季棉早熟不早衰生化性状的遗传分析

用5个早熟不早衰的短季棉品种和5个早衰的短季棉品种进行双列杂交,并对亲本、F1和F2代于2001年和2002年田间试验研究与短季棉早熟不早衰有关的抗氧化系统保护酶(SOD、POD和CAT)、叶绿素及激素(生长素和脱落酸)的遗传特性。结果表明：抗氧化系统保护酶CAT、POD和SOD存在着不同的遗传特性,CAT酶以加性上位性效应为主,其次为显性效应;POD酶以加性效应为主,其次为加性上位性效应;SOD酶活以显性效应为主,其次为加性上位性效应;IAA以显性效应为主,其次为加性效应;ABA以加性效应为主,其次为显性效应。且这些生化性状的遗传率较高,在后代能稳定遗传;同时棉株在不同发育时期体内生化性状表达不同,在花铃期CAT、POD和SOD酶以显性效应为主,其次为加性上位性效应,加性效应表达量很小;棉株体内生化性状的表达也是相互联系、相互制约,CAT酶与POD酶存在着遗传和表型负相关,与SOD酶存在着遗传和表型正相关;POD酶与SOD酶存在着遗传和表型负相关;抗氧化系统保护酶与激素之间存在着复杂的遗传关系。因此,研究生化性状的遗传特性和表达特征,为选育短季棉早熟不早衰新品种和生化性状的QTLs定位提供理论依据。     

基于SSR标记的陆地棉早熟相关种质遗传多样性分析

丰富的遗传变异对于提高作物的环境适应性和遗传改良进度至关重要。为了解我国早熟陆地棉种质资源遗传多样性,本研究利用136对SSR引物对186份陆地棉材料(96份早熟陆地棉材料和90份中、晚熟陆地棉材料)进行了遗传多样性分析,共检测到等位基因变异355个,平均2.61个。在早熟棉材料中,有134对多态性SSR引物扩增出341个条带,平均2.54个;中、晚熟材料中有133对多态性SSR引物,扩增出345个条带,平均2.59个。早熟棉材料的位点多态性信息含量(PIC)、有效等位基因数(Ne)、基因型多样性(H')分别为0.684、3.994和1.361;中、晚熟棉材料的PIC、Ne、H'分别为0.668、3.852和1.343。早熟棉材料和中、晚熟棉材料的Jaccard相似性系数分别在0.349~0.935和0.270~0.907之间,平均为0.635、0.666。遗传相似性系数总体平均值接近,但早熟棉变化范围较中、晚熟棉小。用类平均法(UPGMA)进行聚类可将186份材料分成2个类群。总体上来看,供试材料遗传相似性系数较高,说明我国陆地棉早熟相关种质遗传基础狭窄。本研究结果为早熟棉育种亲本选配,早熟棉种质创新提供依据。