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Cotton genetic resources. A review

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Abstract

Since 6000 BC, cotton has been cultivated for lint fiber, which now dominates the natural textile industry worldwide. Common resources such as an integrated web database, a microsatellite database, and comparative quantitative trait loci (QTL) resources for Gossypium have accelerated the progress towards quantifying the impact of repeated human dispersals and selection regimes on various gene pools of the genus Gossypium. Out of 50 Gossypium species, four have been domesticated—two diploids and two tetraploids—for elimination of hard seed coat, improvement in lint percentage of about 40% and fiber length of 22%, larger boll size, and day-neutral reproductive habit. The major drawback of domestication is the lack of genetic diversity. This lack of genetic diversity is observed more in Gossypium hirsutum L. cultivars characterizing upland cotton than in Gossypium barbadense, typical of Pima and Egyptian cotton. Much of the genetic diversity among G. barbadense cultivars is attributed to the introgression of G. hirsutum alleles. This process highlights the importance of introgression of new alleles from accessions of all the Gossypium species into cultivated cotton species. Among the genomic resources, about 16,162 publicly available SSRs and 312 mapped cotton RFLP sequences containing simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) markers have been surveyed on numerous mapping populations, and developed about 26 linkage maps (SSR, RFLP, AFLP, and RAPD). Reports show the identification of DNA markers associated with over 29 important traits or QTLs such as fiber quality and yield, leaf and flower morphology, trichome 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 of over 1,000 QTLs obtained from backcross population and recombinant inbred line populations derived from the same parents, most consistent meta-clusters were reported for fiber color, fineness, and length. For exploring the function of genes, the targeting induced local lesions in genomes (TILLING) approach—avoiding gene transfer process was used for identifying a brassino steroid receptor gene that is involved in fiber development. Lastly, cotton genome has been enriched with genes isolated from distantly related organisms using various transformation methods. For example, Cry1Ac, Cry1Ab, and herbicide-resistant genes were transformed in cotton that covered a vast majority of cotton acreage worldwide. Here the authors discuss investigations for improving the efficacy of transformation and regeneration systems, and for searching new genes or silencing the unwanted cotton genes using RNAi technology. We suggest initiating projects on sequencing the diploid and tetraploid genomes for exploring the extent of genetic variations, developing TILLING populations, initiating nested association mapping studies, and developing third generation genetically modified cotton, collectively setting the stage for sustaining cotton production under continually changing production conditions, climates, and human needs.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

BC:

Backcross population

CLCuD:

Cotton leaf curl disease

GUS gene:

Beta-glucuronidase gene

LD:

Linkage disequilibrium

MAS:

Marker-assisted selection

MYA:

Million years ago

NAM:

Nested association mapping

PCR:

Polymerase chain reaction

QTLs:

Quantitative trait loci

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

RIL:

Recombinant inbred line

SNPs:

Single nucleotide polymorphisms

SSR:

Simple sequence repeat

TILLING:

Targeting induced local lesions in genomes

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Authors and Affiliations

  1. Plant Genomics and Molecular Breeding Lab, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan

    Mehboob-ur-Rahman, Tayyaba Shaheen, Nabila Tabbasam, Muhammad Atif Iqbal & Yusuf Zafar

  2. Department of Botany, University of Agriculture, Faisalabad, Pakistan

    Muhammad Ashraf

  3. Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA

    Andrew H. Paterson

  4. Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan

    Tayyaba Shaheen

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  1. Mehboob-ur-Rahman
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  2. Tayyaba Shaheen
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  3. Nabila Tabbasam
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  4. Muhammad Atif Iqbal
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  5. Muhammad Ashraf
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  6. Yusuf Zafar
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  7. Andrew H. Paterson
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Correspondence to Mehboob-ur-Rahman.

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Mehboob-ur-Rahman, Shaheen, T., Tabbasam, N. et al. Cotton genetic resources. A review. Agron. Sustain. Dev. 32, 419–432 (2012). https://doi.org/10.1007/s13593-011-0051-z

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