利用SSR标记技术研究棉属A、D染色体组的进化

利用SSR分子标记技术,对棉属A、D染色体二倍体及四倍体代表棉种进行了遗传多样性分析。供试的10个二倍体代表棉种间遗传多态性丰富,分子聚类结果与Fryxell棉属分类结果相同。分子水平上进一步揭示出属于D染色体组的拟似棉与其他D染色体组棉种的相似系数最低,A,D染色体组间相似系数很高,该结果支持拟全民族似棉是D染色体组最原始棉种,棉属不同染色体组是共同起源,单元进化的理论,利用栽培的异源四倍体棉种不太适于研究棉属A、D染色体组的进化。     

关于棉属四倍体种起源问题的过氧化物酶同工酶研究

本文采用聚丙烯酰胺凝胶垂直板电泳和等电聚焦技术,对棉属(Gossypium)A基因组2个二倍体种、D基因组10个二倍体野生种和四倍体2(AD)基因组的3个种进行过氧化物酶同工酶酶谱分析。种间酶谱关系符合形态学,细胞学和遗传学的研究结果,但G.gossypioides,G.thurberi和G.trilobum的酶谱与D基因组其他种有较大差异却与A基因组相似。由二倍体种酶液组成的体外人工混合体与自然四倍体的比较分析表明,四倍体棉种G.darwinii,G.barbadense和G.hirsutum是A基因组和D基因组的异质组合,G.raimondii而不是G.thurberi或G.trilobum为四倍体种祖先基因组的最可能的D亚基因组供体。对过氧化物酶同工酶分析为棉属种间亲缘关系和四倍体起源的研究提供生化遗传依据的可行性进行了阐述。     

不同倍性水稻胚乳蛋白的差异表达研究

以4份同源四倍体水稻和4份相应的二倍体水稻为研究材料, 对其种子内清、球蛋白(清蛋白和球蛋白)、醇溶蛋白和谷蛋白的含量进行了测定, 利用聚丙烯酰胺凝胶电泳(SDS-PAGE)技术分析了其特异性。结果表明: 同源四倍体水稻胚乳蛋白各组分含量与相应的二倍体相比, 大部分呈增加趋势; 同源四倍体水稻胚乳蛋白的亚基类型与相应的二倍体水稻基本一致, 仅在全蛋白电泳和清、球蛋白电泳中各发现1条差异条带。研究结果认为: 二倍体水稻经过染色体组加倍之后, 同源四倍体水稻重复基因组在蛋白质水平上的表达结果趋于“二倍化”, 即与二倍体水稻表现出相似的特点, 但在蛋白质表达量上前者往往高于后者。基因组多倍化对同源四倍体水稻重复基因组进化最主要的影响并不是体现在蛋白质结构上的差异, 而是体现在蛋白质表达量上的差异。     

小麦进化过程中叶片气孔和光合特征演变趋势

根据小麦属内种间的进化关系选取21种小麦品种为实验材料,研究了小麦进化过程中气孔特征和光合特征的演变趋势。结果表明,无论是A,B,D染色体组还是A,G染色体组,气孔长度、宽度、周长、面积均随倍性水平的升高而呈增大趋势,而气孔指数无显著变化;A,B,D染色体组气孔密度随倍性升高呈减少趋势。二倍体小麦的Pn值最高,六倍体小麦的Fv/Fm值较高,二倍体小麦叶片叶绿素含量显著高于四倍体和六倍体小麦。不同倍性小麦的净光合速率与气孔导度间均存在极显著相关关系,表明气孔传导力是小麦光合能力的主要限制因素之一。气孔导度与单一气孔特征之间无显著相关关系。A,B,D染色体组不同倍性小麦叶片气孔密度差异显著,其大小顺序为二倍体〉四倍体〉六倍体;A,B,D染色体组不同倍体小麦叶片的气孔长度、宽度、周长、面积差异显著,顺序均为六倍体〉四倍体〉二倍体,气孔密度降低可能是A,B,D染色体组六倍体小麦光合能力降低的原因。随着倍性的升高,小麦的抵抗光抑制能力越强,因此光化学能转换效率可能不是小麦进化过程中光合能力变化的原因。A,B,D染色体组中二倍体的叶绿素含量显著大于四倍体和六倍体,而A,G染色体组中倍体间叶绿素含量差异不显著,说明叶绿素的降低可能是A,B,D染色体组六倍体光合能力降低的原因之一。     

人腺病毒B、D亚种基因组中简单重复序列分析

本文以人腺病毒B亚种31条基因组序列及D亚种39条基因组序列为研究材料,利用ImperfectMicrosatelliteExtractor和DNAMAN软件对这些基因组序列中简单重复序列(SSR)的分布情况进行了系统性分析和比较。分析结果显示:人腺病毒B、D亚种基因组中简单重复序列的平均相对密度是十分接近的,但在不同类型SSR中分布情况又有所不同。D亚种中二型SSR明显高于B亚种,在两亚种一型SSR中(A)n、(T)n都是比较多的,而在两亚种二型SSR中的(CG/GC)n表现出了较高的偏好性。在同亚种多序列比对分析中,D亚种表现出了更高的稳定性。B、D亚种中SSR的这种特异性分布可能与它们的进化机制和致病性有关。     

芸薹属蔬菜Chs基因序列多态性

为探讨我国芸薹属蔬菜的起源及遗传多样性,克隆、测序芸薹属不同种的Chs基因序列。A基因组二倍体、A基因组多倍体、B基因组多倍体和C基因组二倍体的Chs基因突变位点数分别为120、172、194和25个,Chs基因多态性表现为:B基因组多倍体A基因组二倍体A基因组多倍体C基因组多倍体。Tajima'D、Fu and Li'D和Fu and Li'F检验表明A基因组二倍体、C基因组二倍体Chs基因是中性进化基因。HKA平衡检验及误配分析表明A基因组多倍体和B基因组多倍体Chs基因进化中存在选择作用。A基因组和B基因组间存在较低的共有差异和较高的共有多态性,C基因组与A、B基因组存在较高的共有差异和较低的共有多态性。系统发育树将芸薹属Chs基因序列分成4个亚支、10个支系。网状分析表明,白菜可能是四倍体A基因组的供体,黑芥可能是四倍体B基因组的供体,甘蓝可能是四倍体C基因组的供体。中国芸薹属蔬菜在Chs基因位点有较高的遗传多态性,不同基因组间分化程度不一样,B基因组分化较大,A和C基因组分化较小。A和B基因组的亲缘关系较A和C基因组以及B和C基因组更为接近。建议根据基因组的不同将中国芸薹蔬菜分成白菜组、芥菜组和甘蓝组,研究结果支持芸薹属进化的禹式三角模型。     

天南星科植物叶绿体基因组结构特征及系统发育分析：以天南星等20个物种为例

目的：天南星科植物资源丰富、分布广泛。研究天南星科植物叶绿体基因组特征,为天南星科的系统发育及进化研究提供依据。方法：本研究以GenBank数据库中获得的20条该科植物叶绿体全基因组序列为基础数据,利用REPuter、MISA、mVISTA和MAFFT等软件分析其重复序列、基因组差异、IR边界和系统发育等特征。结果：天南星科植物叶绿体基因组长度介于158 521～175 906 bp之间,共编码129～139个基因。在20个该科物种中,均检测出50条重复序列,正向重复和反向重复为主要类型,并鉴定出253～482个SSR位点,单核苷酸和二核苷酸重复居多。序列全局比对表明其非编码区的差异较大,并发现accD、ycf2和ycf1三个高度可变区。共线性分析可知,基因组序列同源性较高,只有一个物种发现重排或倒位现象。IR边界分析表明天南星科植物有一定保守性。所筛选的SSR位点和高度可变区可用于遗传多样性分析、物种鉴定和DNA条形码等。结论：本研究明确了天南星科物种的系统发育关系,为天南星科物种进化和遗传多样性研究提供了一定的科学依据。     

St基因组中的CRW同源序列在偃麦草中的FISH分析

为了确定十倍体长穗偃麦草(Thinopyrum ponticum, Liu & Wang)和六倍体中间偃麦草(Th. intermedium, [Host] Barkworth & Dewey )的基因组组成, 根据野生一粒小麦(Triticum boeoticum)着丝粒自主型反转录转座子(CRW)序列设计特异引物, 以二倍体拟鹅观草(Pseudoroegneria spicata, Á Löve )基因组 DNA为模板进行PCR扩增, 筛选到一条St基因组着丝粒区相对特异反转录转座子的部分序列pStC1, 长度为1.755 kb (GenBank登录号: FJ952565), 其中有800 bp与小麦着丝粒反转录转座子(CRW)的LTR区高度同源, 另有小部分片段与其外壳蛋白编码基因(gag)部分同源, 并且包含一段富含AGCAAC碱基的重复序列。以pStC1为探针, 对十倍体长穗偃麦草的FISH检测结果显示其基因组组成为两个St组3个E组(St₁St₂E^eE^bE^x); pStC1与中间偃麦草杂交时, 不仅St基因组上有强烈的荧光信号, 而且E基因组一些染色体的近着丝粒区域也有杂交信号, 说明偃麦草属异源多倍体物种在其形成及进化过程中St与E基因组之间在着丝粒及近着丝粒相关区域可能存在协同进化。     

长穗偃麦草中E和E1基因组高分子量麦谷蛋白基因启动子部分序列的进化分析

通过PCR克隆的方法,获得了分别来自二倍体长穗偃麦草的E基因组和四倍体长穗偃麦草的E_1基因组的4个高分子量麦谷蛋白亚基(HMW-GS)基因启动子的部分序列。序列分析表明,它们之间的同源性较高,两个x型亚基启动子序列之间只有1个碱基的差异,而两个y型亚基启动子序列完全相同,x和y型亚基启动子序列之间的长度和部分碱基位点都有差异。推测四倍体长穗偃麦草中的E_1基因组可能起源于二倍体的E基因组。与来自小麦族的A、B、D和G基因组部分亚基基因的启动子序列比较表明,小麦族的这一区域在进化上是相当保守的,不同基因组来源的序列同源性都在90％以上。经过对这些序列的聚类分析,表明长穗偃麦草的y型HMW-GS基因与其他亚基基因的进化关系较远,而x型亚基基因与一个来自小麦1B染色体的亚基基因关系最近。     

四倍体长穗偃麦草(Agropyron elongatum 4x)染色体组构成的生化和SSR标记分析

应用等电聚焦(IEF)和SDS PAGE方法分析了二倍体长穗偃麦草(Agropyronelongatum2x)和四倍体长穗偃麦草(Ag.elongatum4x)的16种同工酶和3种贮藏蛋白的电泳图谱。结果表明,只有两种同工酶在四倍体和二倍体长穗偃麦草之间表现相同的酶谱,该类型仅占分析标记总数的10.5%;而10种同工酶和3种贮藏蛋白的电泳图谱在四倍体中除了具有全部二倍体的谱带以外,还有自己独特的条带,该类型最多,占分析标记总数的63.2%;另外5种同工酶在二倍体和四倍体之间只有部分条带相同,同时具有各自特异的条带,该类型占分析标记总数的26.3%。由此推测,四倍体长穗偃麦草可能是一个异源四倍体,即只含有一个起源于二倍体类型的染色体组Ee,而另一个染色体组在所分析的生化标记上明显不同于近缘种中的St、J和N染色体组,其起源尚待进一步研究。进一步用小麦的SSR引物对二倍体和四倍体长穗偃麦草进行扩增,结果表明大多数SSR引物在四倍体中既能扩出与二倍体相同的条带,同时还有其特异的条带,这一结果验证了由生化标记得出的四倍体长穗偃麦草是异源四倍体的初步结论。     

Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich)

Background

Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.

Results

A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available.

Conclusion

Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1265-2) contains supplementary material, which is available to authorized users.     

Uniqueness of the Gossypium mustelinum Genome Revealed by GISH and 45S rDNA FISH

Gossypium mustelinum ((AD)₄) is one of five disomic species in Gossypium. Three 45S ribosomal DNA (rDNA) loci were detected in (AD)₄ with 45S rDNA as probe, and three pairs of brighter signals were detected with genomic DNA (gDNA) of Gossypium D genome species as probes. The size and the location of these brighter signals were the same as those detected with 45S rDNA as probe, and were named GISH-NOR. One of them was super-major, which accounted for the fact that about one-half of its chromosome at metaphase was located at chromosome 3, and other two were minor and located at chromosomes 5 and 9, respectively. All GISH-NORs were located in A sub-genome chromosomes, separate from the other four allopolyploid cotton species. GISH-NOR were detected with D genome species as probe, but not A. The greatly abnormal sizes and sites of (AD)₄ NORs or GISH-NORs indicate a possible mechanism for 45S rDNA diversification following (AD)₄ speciation. Comparisons of GISH intensities and GISH-NOR production with gDNA probes between A and D genomes show that the better relationship of (AD)₄ is with A genome. The shortest two chromosomes of A sub-genome of G. mustelinum were shorter than the longest chromosome of D sub-genome chromosomes. Therefore, the longest 13 chromosomes of tetraploid cotton being classified as A sub-genome, while the shorter 13 chromosomes being classified as D sub-genome in traditional cytogenetic and karyotype analyses may not be entirely correct.     

Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton （Gossypium spp.） species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species, including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat （SSR） motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides （Ulbr.） Standl. and three other D-genome species （G. raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.） was 98.5%, 98.6%, and 98.5%, respectively. Phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.     

Genetic mapping and QTL analysis of fiber-related traits in cotton (<Emphasis Type="Italic">Gossypium</Emphasis>)

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton (Gossypium hirsutum L.) and Pima or Egyptian cotton (G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F₂ population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.Communicated by J. Dvorak     

Chromosome structural changes in diploid and tetraploid A genomes of Gossypium.

The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2 interspecific Gossypium arboreum x Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and At genomes. The recombination rates are similar between the 2 diploid genomes; however, the At genome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.     

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.     

The cotton centromere contains a Ty3-gypsy-like LTR retroelement

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.     

Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)

Genome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of the CesA region in two cotton genomes that diverged 5–10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A ( AdhA ) from four cotton genomes: the two co-resident genomes (A_T and D_T) of the allotetraploid, Gossypium hirsutum , as well as the model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). In contrast to earlier work, evolution in the AdhA region reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of 'genomic downsizing' in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post-polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.     

Phylogenetic diversity and relationship among Gossypium germplasm using SSRs markers

Gossypium species represent a vast resource of genetic multiplicity for the improvement of cultivated cotton. To determine genetic diversity and relationships within a diverse collection of Gossypium, we employed 120 SSR primers on 20 diploid species representing seven basic genome groups of the genus Gossypium, five AD allotetraploid cotton accessions while T. populnea served as an outgroup species. Out of 120 SSR primers, 49 pairs are polymorphic, which produced a total of 99 distinct alleles with an average of 2.0 alleles per primer pair. A total of 1139 major SSR bands were observed. Genetic similarities among all the diploid species ranged from 0.582 (between G. herbaceum and G. trilobum) up to 0.969 (between G. arboreum and G. herbaceum). Phylogenetic trees based on genetic similarities were consistent with known taxonomic relationships. The results also indicated that G. raimondii is the closest living relative of the ancestral D-genome donor of tetraploid species and the A-genome donor is much similar to the present-day G. herbaceum and G. arboreum. Ancient tetraploid cotton species were formed by hybridizing and chromosome doubling between them, then different tetraploid cotton species appeared by further geographical and genetic isolation and separating differentiation. The results showed that SSRs could be an ideal means for the identification of the genetic diversity and relationship of cotton resources at the genomic level.