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Khidirov MT, Ernazarova DK, Rafieva FU, Ernazarova ZA, Toshpulatov AK, Umarov RF, Kholova MD, Oripova BB, Kudratova MK, Gapparov BM, Khidirova MM, Komilov DJ, Turaev OS, Udall JA, Yu JZ, Kushanov FN. Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton ( Gossypium) Species. Plants (Basel) 2023; 12:4184. [PMID: 38140511 PMCID: PMC10748080 DOI: 10.3390/plants12244184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.
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Affiliation(s)
- Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ziraatkhan A. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Abdulqahhor Kh. Toshpulatov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ramziddin F. Umarov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | | | - Doniyor J. Komilov
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Joshua A. Udall
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
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Kushanov FN, Komilov DJ, Turaev OS, Ernazarova DK, Amanboyeva RS, Gapparov BM, Yu JZ. Genetic Analysis of Mutagenesis That Induces the Photoperiod Insensitivity of Wild Cotton Gossypium hirsutum Subsp. purpurascens. Plants (Basel) 2022; 11:3012. [PMID: 36432741 PMCID: PMC9698681 DOI: 10.3390/plants11223012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a genetic analysis of morphological, cytological, and genomic changes from radiation-mediated mutagenesis that induced plant photoperiod insensitivity in the wild cotton of Gossypium hirsutum. Several morphological and agronomical traits were found to be highly inheritable using the progeny between the wild-type G. hirsutum subsp. purpurascens (El-Salvador) and its mutant line (Kupaysin). An analysis of pollen mother cells (PMCs) revealed quadrivalents that had an open ring shape and an adjoining type of divergence of chromosomes from translocation complexes. Using 336 SSR markers and 157 F2 progenies that were grown with parental genotypes and F1 hybrids in long day and short night conditions, five quantitative trait loci (QTLs) associated with cotton flowering were located on chromosomes At-05, At-11, and Dt-07. Nineteen candidate genes related to the flowering traits were suggested through molecular and in silico analysis. The DNA markers associated with the candidate genes, upon future functional analysis, would provide useful tools in marker-assisted selection (MAS) in cotton breeding programs for early flowering and maturity.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
| | - Doniyor J. Komilov
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray District, Tashkent 111215, Uzbekistan
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Faculty of Natural Sciences, Gulistan State University, 4th Microregion, Gulistan 120100, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). Front Plant Sci 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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Kushanov FN, Buriev ZT, Shermatov SE, Turaev OS, Norov TM, Pepper AE, Saha S, Ulloa M, Yu JZ, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt. PLoS One 2017; 12:e0186240. [PMID: 29016665 PMCID: PMC5633191 DOI: 10.1371/journal.pone.0186240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023] Open
Abstract
Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Zabardast T. Buriev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Shukhrat E. Shermatov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Tokhir M. Norov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, Texas, United States of America
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture-Agricultural Research Services, Lubbock, Texas, United States of America
| | - John Z. Yu
- Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Abdusattor Abdukarimov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- * E-mail:
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Kushanov FN, Pepper AE, Yu JZ, Buriev ZT, Shermatov SE, Saha S, Ulloa M, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BMC Genet 2016; 17:141. [PMID: 27776497 PMCID: PMC5078887 DOI: 10.1186/s12863-016-0448-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies. CONCLUSION This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, TX 77843 USA
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845 USA
| | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Shukhrat E. Shermatov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Mauricio Ulloa
- USDA-ARS, Plant Stress and Germplasm Development Research, 3810 4th Street, Lubbock, TX 79415 USA
| | - Johnie N. Jenkins
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
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Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Salakhutdinov IB, Buriev ZT, Saha S, Scheffler BE, Jenkins JN, Abdukarimov A. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 2008; 92:478-87. [PMID: 18801424 DOI: 10.1016/j.ygeno.2008.07.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 06/23/2008] [Accepted: 07/29/2008] [Indexed: 02/05/2023]
Abstract
The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.
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Affiliation(s)
- I Y Abdurakhmonov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 702151, Uzbekistan
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Abdurakhmonov IY, Devor EJ, Buriev ZT, Huang L, Makamov A, Shermatov SE, Bozorov T, Kushanov FN, Mavlonov GT, Abdukarimov A. Small RNA regulation of ovule development in the cotton plant, G. hirsutum L. BMC Plant Biol 2008; 8:93. [PMID: 18793449 PMCID: PMC2564936 DOI: 10.1186/1471-2229-8-93] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 09/16/2008] [Indexed: 02/08/2023]
Abstract
BACKGROUND The involvement of small RNAs in cotton fiber development is under explored. The objective of this work was to directly clone, annotate, and analyze small RNAs of developing ovules to reveal the candidate small interfering RNA/microRNAs involved in cotton ovule and fiber development. RESULTS We cloned small RNA sequences from 0-10 days post anthesis (DPA) developing cotton ovules. A total of 6691 individual colonies were sequenced from 11 ovule small RNA libraries that yielded 2482 candidate small RNAs with a total of 583 unique sequence signatures. The majority (362, 62.1%) of these 583 sequences were 24 nt long with an additional 145 sequences (24.9%) in the 21 nt to 23 nt size range. Among all small RNA sequence signatures only three mirBase-confirmed plant microRNAs (miR172, miR390 and ath-miR853-like) were identified and only two miRNA-containing clones were recovered beyond 4 DPA. Further, among all of the small RNA sequences obtained from the small RNA pools in developing ovules, only 15 groups of sequences were observed in more than one DPA period. Of these, only five were present in more than two DPA periods. Two of these were miR-172 and miR-390 and a third was identified as 5.8S rRNA sequence. Thus, the vast majority of sequence signatures were expressed in only one DPA period and this included nearly all of the 24 nt sequences. Finally, we observed a distinct DPA-specific expression pattern among our clones based upon sequence abundance. Sequences occurring only once were far more likely to be seen in the 0 to 2 DPA periods while those occurring five or more times were the majority in later periods. CONCLUSION This initial survey of small RNA sequences present in developing ovules in cotton indicates that fiber development is under complex small RNA regulation. Taken together, the results of this initial small RNA screen of developing cotton ovules is most consistent with a model, proposed by Baulcombe, that there are networks of small RNAs that are induced in a cascade fashion by the action of miRNAs and that the nature of these cascades can change from tissue to tissue and developmental stage to developmental stage.
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Affiliation(s)
- Ibrokhim Y Abdurakhmonov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Eric J Devor
- Molecular Genetics, Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Zabardast T Buriev
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Lingyan Huang
- Molecular Genetics, Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Abdusalom Makamov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Shukhrat E Shermatov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Tohir Bozorov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Fakhriddin N Kushanov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Gafurjon T Mavlonov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
| | - Abdusattor Abdukarimov
- Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent district, 111226 Uzbekistan
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Abdurakhmonov IY, Kushanov FN, Djaniqulov F, Buriev ZT, Pepper AE, Fayzieva N, Mavlonov GT, Saha S, Jenkins JN, Abdukarimov A. The role of induced mutation in conversion of photoperiod dependence in cotton. J Hered 2007; 98:258-66. [PMID: 17406024 DOI: 10.1093/jhered/esm007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Wild cotton germplasm resources are largely underutilized because of photoperiod-dependent flowering of "exotic" cottons. The objectives of this work were to explore the genome-wide effect of induced mutation in photoperiod-converted induced cotton mutants, estimating the genetic change between mutant and wild-type cottons using simple sequence repeats (SSRs) as well as understand the pattern of SSR mutation in induced mutagenesis. Three groups of photoperiod-converted radiomutants ((32)P) including their wild-type parental lines, A- and D-genome diploids, and typically grown cotton cultivars were screened with 250 cotton SSR primer pairs. Forty SSRs revealed the same SSR mutation profile in, at least, 2 independent mutant lines that were different from the original wild types. Induced mutagenesis both increased and decreased the allele sizes of SSRs in mutants with the higher mutation rate in SSRs containing dinucleotide motifs. Genetic distance obtained based on 141 informative SSR alleles ranged from 0.09 to 0.60 in all studied cotton genotypes. Genetic distance within all photoperiod-converted induced mutants was in a 0.09-0.25 range. The genetic distance among photoperiod-converted mutants and their originals ranged from 0.28 to 0.50, revealing significant modification of mutants from their original wild types. Typical Gossypium hirsutum cultivar, Namangan-77, revealed mutational pattern similar to induced radiomutants in 40 mutated SSR loci, implying possible pressure to these SSR loci not only in radiomutagenesis but also during common breeding process. Outcomes of the research should be useful in understanding the photoperiod-related mutations, and markers might help in mapping photoperiodic flowering genes in cotton.
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Affiliation(s)
- Ibrokhim Y Abdurakhmonov
- Laboratory of Genetic Engineering and Biotechnology, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Yuqori Yuz, Qibray Region Tashkent District, 702151 Uzbekistan.
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