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Cotton Genetic Resources. a Review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson

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Cotton Genetic Resources. a Review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson Cotton genetic resources. A review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson To cite this version: Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, et al.. Cotton genetic re- sources. A review. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 2012, 32 (2), pp.419-432. 10.1007/s13593-011-0051-z. hal-00930526 HAL Id: hal-00930526 https://hal.archives-ouvertes.fr/hal-00930526 Submitted on 1 Jan 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Agron. Sustain. Dev. (2012) 32:419–432 DOI 10.1007/s13593-011-0051-z REVIEW ARTICLE Cotton genetic resources. A review Mehboob-ur-Rahman & Tayyaba Shaheen & Nabila Tabbasam & Muhammad Atif Iqbal & Muhammad Ashraf & Yusuf Zafar & Andrew H. Paterson Accepted: 29 July 2011 /Published online: 13 October 2011 # INRA and Springer-Verlag, France 2011 Abstract Since 6000 BC, cotton has been cultivated for lint Much of the genetic diversity among G. barbadense cultivars fiber, which now dominates the natural textile industry is attributed to the introgression of G. hirsutum alleles. This worldwide. Common resources such as an integrated web process highlights the importance of introgression of new database, a microsatellite database, and comparative quantita- alleles from accessions of all the Gossypium species into tive trait loci (QTL) resources for Gossypium have accelerated cultivated cotton species. Among the genomic resources, the progress towards quantifying the impact of repeated about 16,162 publicly available SSRs and 312 mapped human dispersals and selection regimes on various gene cotton RFLP sequences containing simple sequence repeat pools of the genus Gossypium. Out of 50 Gossypium species, (SSR), restriction fragment length polymorphism (RFLP), four have been domesticated—two diploids and two tetra- amplified fragment length polymorphism (AFLP), and ploids—for elimination of hard seed coat, improvement in random amplified polymorphic DNA (RAPD) markers have lint percentage of about 40% and fiber length of 22%, larger been surveyed on numerous mapping populations, and boll size, and day-neutral reproductive habit. The major developed about 26 linkage maps (SSR, RFLP, AFLP, and drawback of domestication is the lack of genetic diversity. RAPD). Reports show the identification of DNA markers This lack of genetic diversity is observed more in Gossypium associated with over 29 important traits or QTLs such as hirsutum L. cultivars characterizing upland cotton than in fiber quality and yield, leaf and flower morphology, trichome Gossypium barbadense, typical of Pima and Egyptian cotton. density and their distribution, and disease resistance. In comparative mapping studies, 432 QTLs mapped on 11 different mapping populations were aligned on a high-density reference map containing 3,475 loci. In a meta-analysis study * : : : Mehboob-ur-Rahman: ( ) T. Shaheen N. Tabbasam of over 1,000 QTLs obtained from backcross population and M. A. Iqbal Y. Zafar recombinant inbred line populations derived from the same Plant Genomics and Molecular Breeding Lab, National Institute for Biotechnology and Genetic Engineering (NIBGE), parents, most consistent meta-clusters were reported for fiber P.O. Box 577, Jhang Road, color, fineness, and length. For exploring the function of Faisalabad, Pakistan genes, the targeting induced local lesions in genomes e-mail: [email protected] (TILLING) approach—avoiding gene transfer process was M. Ashraf used for identifying a brassino steroid receptor gene that is Department of Botany, University of Agriculture, involved in fiber development. Lastly, cotton genome has Faisalabad, Pakistan been enriched with genes isolated from distantly related organisms using various transformation methods. For exam- A. H. Paterson Plant Genome Mapping Laboratory, University of Georgia, ple, Cry1Ac, Cry1Ab, and herbicide-resistant genes were Athens, GA 30602, USA transformed in cotton that covered a vast majority of cotton acreage worldwide. Here the authors discuss investigations T. Shaheen for improving the efficacy of transformation and regeneration Department of Bioinformatics and Biotechnology, Government College University, systems, and for searching new genes or silencing the Faisalabad, Pakistan unwanted cotton genes using RNAi technology. We suggest 420 Mehboob-ur-Rahman initiating projects on sequencing the diploid and 4. Dry-lab resources—comparative genomics........7 tetraploid genomes for exploring the extent of genetic variations, developing TILLING populations, initiating 4.1 Transfer of genomic information from model nested association mapping studies, and developing species to cotton.........................7 third generation genetically modified cotton, collective- 4.2 Broader Applications......................9 ly setting the stage for sustaining cotton production 4.2.1 Identification of genes for cotton breed- under continually changing production conditions, ing...............................9 climates, and human needs. 4.2.2 Utilization of αω genetic resources......9 5. Implications................................9 Keywords Gossypium . Genetic diversity. Diploid cotton . Tetraploid cotton . Hybrid cotton . Structural genomic 5.1 Knowledge-based breeding—proactive deci- resources . Functional genomic resources . Dry lab sion...............................9 resources . Translational genomics . Comparative mapping . 5.2 Marker-assisted selection (MAS) for various traits DNA marker . RFLP. RAPD . SSRs . SNPs . QTLs . Marker- of interest..............................10 assisted selection . GM cotton 5.3 Fiber genes—exploring unique genetic path- ways.................................10 Abbreviations 5.4 Translational genomics...................10 AFLP Amplified fragment length polymorphism 5.5 Genetic resource for other species...........10 BC Backcross population 6. Conclusion................................11 CLCuD Cotton leaf curl disease 7. References................................11 GUS gene Beta-glucuronidase gene LD Linkage disequilibrium MAS Marker-assisted selection 1 Introduction MYA Million years ago NAM Nested association mapping Cotton is a world leading natural fiber crop sustaining PCR Polymerase chain reaction one of the world’s largest industries (textiles) with an QTLs Quantitative trait loci annual worldwide economic impact of about $500 RAPD Random amplified polymorphic DNA billion. Genetic resources of cotton encompassing a RFLP Restriction fragment length polymorphism range of germplasm of ∼50 cotton species offers unique RIL Recombinant inbred line opportunities for understanding the evolution of culti- SNPs Single nucleotide polymorphisms vated cotton from wild ancestors which will pave the SSR Simple sequence repeat way for dissecting the evolution of lint fiber and also TILLING Targeting induced local lesions in genomes the role of polyploidy for enhancing the lint production. Other features like understanding the extent of genetic diversity and its utilization in improving sustainability Contents of cotton production and lint quality and also the 1. Introduction................................2 utilization of bio-based alternatives to petrochemicals 2. Spectrum of genetic diversity...................3 are being explored at length. In this article, advances made during the last two 2.1 Genetic diversity at inter-specific level........3 decades have been summarized. For example, progress in 2.2 Genetic diversity at intra-specific level.......3 understanding variations in multiple morphological, 3. Genomic Resources..........................4 physiological, biochemical, and genetically important traits have been discussed. Like other important crop 3.1 Conventional structural genomic resources.....4 species, much emphasis was given on understanding the 3.1.1 Cytogenetic stocks...................4 cotton genome of the genus Gossypium using various 3.1.2 Genetic maps.....................5 cutting edge genomic technologies which substantially 3.1.3 Scope of developing new populations.....5 laid down the foundation for sustaining lint production 3.1.3.1 Utilizing untapped resources........5 worldwide (Rahman et al. 2009). Still there are many 3.1.3.2 New mapping approaches – nested aspects to explore (Chen et al. 2009). Tremendous association mapping............5 domestication has resulted in narrow genetic base of 3.2 Functional Genomic Resources..............7 cotton (Rahman et al. 2008). Conventional genetic 3.2.1 Knock-out populations................7 resources have been utilized over the years; however, a 3.2.2 Opportunities.....................7 decline in cotton production has been seen for last few Cotton genetic resources: a review 421 decades (Helms 2000). It was the need of time to generate Hawaii, and is found in rocky, arid, or clay coastal plains new resources to combat the problems of new era. (http://kalama.doe.hawaii.edu/hern95/pt009/Ann/mcc_ Genomic tools have been deployed extensively for nativeplants.html). Progenies generated after making an improving
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