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Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton

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Abstract

Cotton is a model system for studying polyploidization, genomic organization, and genome-size variation because the allotetraploid was formed 1-2 million years ago, which is old enough for sequence divergence but relatively recent to maintain genome stability. In spite of characterizing random genomic sequences in many polyploidy plants, the cytogenetic and sequence data that decipher homoeologous chromosomes are very limited in allopolyploid species. Here, we reported comprehensive analyses of integrated cytogenetic and linkage maps of homoeologous chromosomes 12A and 12D in allotetraploid cotton using fluorescence in situ hybridization and a large number of bacterial artificial chromosomes that were anchored by simple sequence repeat markers in the corresponding linkage maps. Integration of genetic loci into physical localizations showed considerable variation of genome organization, structure, and size between 12A and 12D homoeologous chromosomes. The distal regions of the chromosomes displayed relatively lower levels of structural and size variation than other regions of the chromosomes. The highest level of variation was found in the pericentric regions in the long arms of the two homoeologous chromosomes. The genome-size difference between A and D sub-genomes in allotetraploid cotton was mainly associated with uneven expansion or contraction between different regions of homoeologous chromosomes. As an attempt for studying on the polyploidy homoeologous chromosomes, these results are of general interest to the understanding and future sequencing of complex genomes in plant species.

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Acknowledgments

We thank Prof. Xiue Wang of Nanjing Agricultural University and Prof. Weichang Yu of Chinese University of Hong Kong for technical assistance in FISH analysis. This work was supported by the National Natural Science Foundation of China (30700510, 30730067), Natural Science Foundation of Jiangsu Province of China (BK2008333), and State Key Laboratory of Crop Genetics and Germplasm Enhancement (010-60066009, 010-60060305-2). The work in the Z. Jeffrey Chen and David M. Stelly labs was supported by the grant from the US National Science Foundation Plant Genome Research grant (DBI0624077).

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, China

    Kai Wang, Wangzhen Guo, Zaijie Yang, Yan Hu, Wenpan Zhang, Baoliang Zhou & Tianzhen Zhang

  2. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA

    David M. Stelly

  3. Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, University of Texas, One University Station, A-4800, Austin, TX, 78712, USA

    Z. Jeffrey Chen

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  1. Kai Wang
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  2. Wangzhen Guo
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  3. Zaijie Yang
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  4. Yan Hu
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Correspondence to Tianzhen Zhang.

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Fig. S1

SSR amplification analysis of the monomorphic- and polymorphic-positive BACs of the SSR primer NAU1237. a Figure shows identification of the BAC r081K08 (lane 3) containing the polymorphic locus of NAU1237-155, and t215O23 (lane 4) containing the monomorphic locus NAU1237-140 between TM-1 and Hai7124 using SSR marker NAU1237. Lanes 1 and 2 are TM-1 and Hai7124, respectively. b BAC r043C02 (green signals, arrows), which is derived from chromosome 12A, was FISHed simultaneously (with150 × Cot-1 DNA blocking) with polymorphic BAC r081K08 (red signals, arrowheads); the results reconfirmed that polymorphic BAC r081K08 is located on chromosome 12A. Bar 10 µm. (DOC 482 kb)

Fig. S2

FISH analysis of homoeologous- and centromere-specific BACs on cotton mitotic chromosomes. Homoeologous-specific BACs t283I16 (a), t208C15 (b), and r070L23 (c) produced two pairs of bright signals (arrows and arrowheads) in FISH. These loci were revealed to be localized on chromosomes 12A (arrows, the larger pair of chromosomes) and 12D (arrowheads, the smaller pair of chromosomes) in the subsequently constructed cytogenetic map. Centromere-specific BAC t097G20 (d) was mapped to the centromeric region of all 26 mitotic chromosomes in tetraploid cotton. Further FISHing based on meiotic metaphase chromosomes showed that all signals were localized on the very top of 26 bivalents (e) and proved its centromere-specific nature. Bars 10 µm. (DOC 326 kb)

Fig. S3

FISH analysis of BAC repetitive sequence content. BACs r075A11 (a) and t107F20 (b) were specific for A subgenome chromosomes and all of the chromosomes of mitotic tetraploid cotton cells stained brightly on FISH analysis, indicating a high content of A or AD subgenome-specific repetitive sequences. Arrowheads indicate the original signals of the corresponding BACs. Bars 10 µm. (DOC 167 kb)

Fig. S4

FISH testing five 12D BACs (t215O23, t081H09, t246C12, t107F20, and r010G17) with A-genome diploid cotton, Gossypium arboreum. Five 12D BACs, t215O23, t081H09, t246C12, t107F20, and r010G17 were hybridized to the G. arboreum chromosome. Two 12A BACs t259M16 and t336G12 were used simultaneously in FISH as control. Signals derived from BACs t259M16 (red, arrow) and t336G12 (green, arrow) could be detected but no other signals from five testing BACs could be detected. Bar 10 µm. (DOC 76 kb)

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Wang, K., Guo, W., Yang, Z. et al. Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma 119, 255–266 (2010). https://doi.org/10.1007/s00412-009-0254-0

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