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Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton

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Abstract

The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.

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Acknowledgments

The authors thank the Office of International Research Programs, U. S. Department of Agriculture (USDA) for providing funds for this study under research grant UZB2-31016-TA-09 and U.S. Civilian Research & Development Foundation (CRDF) and Cotton Incorporated, USA. We thank the Academy of Sciences of Uzbekistan for supporting this joint study within USDA-Uzbekistan cooperative programs. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture. The U. S. Department of Agriculture is equal opportunity provider and employer. We acknowledge joint publication of USDA/ARS, and Mississippi Agricultural and Forestry Experiment Station, approved for publication as Journal Article of the Mississippi Agricultural and Forestry Experiment Station. We thank all of the public and private cotton breeders who provided seeds for this study. We would specifically like to acknowledge the help of Dr. Jack C. McCarty, Dr. Wayne Smith, Dr. Bill Meredith, Dr. Gerald O. Myers, Dr. Ted Wallace, Dr. Fred Bourland, Dr. Jack Jones, and Dr. Dick L. Auld for their help in this study by providing seeds of their released germplasm. Without their help and support we could not accomplished the goals of this research project. We also thank Dr. B. Todd Campbell and Dr. Mauricio Ulloa for their help in reviewing the manuscript.

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    1. Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215

      Sharof S. Egamberdiev, Ilkhom Salakhutdinov & Ibrokhim Y. Abdurakhmonov

    2. Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA

      Sukumar Saha, Johnie N. Jenkins & Dewayne Deng

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    1. Sharof S. Egamberdiev
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    Sharof S. Egamberdiev and Sukumar Saha equally credited as the first author for their contribution in this research.

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    Egamberdiev, S.S., Saha, S., Salakhutdinov, I. et al. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton. Genetica 144, 289–306 (2016). https://doi.org/10.1007/s10709-016-9898-x

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