Ammad ABBAS, Muhammad Atif IQBAL, Mehboob-ur RAHMAN, Andrew H PATERSON

Estimating genetic diversity among selected cotton genotypes and the identificationof DNA markers associated with resistance to cotton leaf curl disease

To the extent of our knowledge, applications of DNA markers in marker-assisted breeding of cotton are handicapped due to low genetic diversity in cotton germplasm. Cotton leaf curl disease, a disease of viral origin, has substantially depressed cotton production in Pakistan, and this disease is also an emerging threat to the neighboring cotton-growing countries like China and India. The present study was designed to identify DNA markers, predominately simple sequence repeats (SSRs), associated with tolerance and/or resistance to the disease. Based upon 2 years of disease-screening field experiments, a total of 10 cotton genotypes (five highly tolerant, four highly susceptible, and one immune) of diverse origin were selected from the available cotton germplasm (~1200 accessions) of the National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. In total, 322 SSRs derived from bacterial artificial chromosome end sequences of Gossypium raimondii (one of the progenitor species of cultivated tetraploid cotton) were screened. Out of these, 65 primer pairs were found polymorphic, and the extent of genetic similarity was in the range of 81.7% to 98.7%. A similarity matrix was used for studying their phylogenetic relationship using unweighted pair-group method with arithmetic means (UPGMA) analysis. The dendrogram showed the grouping of the genotypes into two distinct clusters comprising tolerant and susceptible genotypes, respectively. Out of the polymorphic markers, two SSR markers, PR-91 and CM-43, that were amplified only in tolerant genotypes showed significant association with resistance to the disease. These preliminary results set the stage for initiating in-depth marker-trait association studies, which will be instrumental for initiating marker-assisted breeding in cotton.

Anahtar Kelimeler:

Gossypium, simple sequence repeats, tetraploid cotton, cotton leaf curl disease, genetic diversity, DNA marker, resistance

Estimating genetic diversity among selected cotton genotypes and the identificationof DNA markers associated with resistance to cotton leaf curl disease

Keywords:

Gossypium, simple sequence repeats, tetraploid cotton, cotton leaf curl disease, genetic diversity, DNA marker, resistance,

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Abdurakhmonov IY, Buriev ZT, Saha S, Pepper AE, Musaev JA, Almatov A, Shermatov SE, Kushanov FN, Mavlonov GT, Reddy UK et al. (2007). Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum. Euphytica 156: 141–156.
Bardak A, Bolek Y (2012). Genetic diversity of diploid and tetraploid cottons determined by SSR and ISSR markers. Turk J Field Crops 17: 139–144.
Becerra Lopez-Lavalle L, Matheson B, Brubaker CL (2011). A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton. Genome 54: 779–794.
Bertini CH, Schuster I, Sediyama T, Barros EGD, Moreira MA (2006). Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genet Mol Biol 29: 321–329.
Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P et al. (2006). CMD: A cotton microsatellite database resource for Gossypium genomics. BMC Genomics 7: 132.
Briddon RW (2003). Cotton leaf curl disease, a multicomponent begomovirus complex. Mol Plant Pathol 4: 427–434. Briddon RW, Markham PG (2000). Cotton leaf curl virus disease. Virus Res 71: 151–159.
Brubaker CL, Wendel JF (1994). Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). Am J Bot 81: 1309–1326.
Cai C, Ye W, Zhang T, Guo W (2014). Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). J Integr Plant Biol 56: 51–62.
Cai JH, Xie K, Lin L, Qin BX, Chen BS, Meng JR, Liu YL (2010). Cotton leaf curl Multan virus newly reported to be associated with cotton leaf curl disease in China. Plant Pathol 59: 794–795.
Doğan B, Ünal M, Özgökçe F, Martin E, Kaya A (2011). Phylogenetic relationships between Malcolmia, Strigosella, Zuvanda, and some closely related genera (Brassicaceae) from Turkey revealed by inter-simple sequence repeat amplification. Turk J Bot 35: 17–23.
Farooq A, Farooq J, Mahmood A, Shakeel A, Rehman KA, Batool A, Riaz M, Shahid MTH, Mehboob S (2011). An overview of cotton leaf curl virus disease (CLCuD) a serious threat to cotton productivity. Aust J Crop Sci 5: 1823–1831.
Ghaffari S, Hasnaoui N (2013). Microsatellite amplification in plants: optimization procedure of major PCR components. In: Kantartzi SK, editor. Microsatellites: Methods and Protocols. New York, NY, USA: Humana Press, pp. 139–146.
Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK (2010). Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13: 167–173.
Government of Pakistan (2014). Economic Survey of Pakistan: Finance Division. Islamabad, Pakistan: Government of Pakistan.
Guang C, Xiong-Ming DU (2006). Genetic diversity of source germplasm of Upland cotton in China as determined by SSR marker analysis. Acta Genetica Sinica 33: 733–745.
Hall D, Tegstrom C, Ingvarsson PK (2010). Using association mapping to dissect the genetic basis of complex traits in plants. Brief Funct Genomics 9: 157–165.
Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006). Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112: 430–439.
He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W (2007). QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153: 181–197.
Hinze LL, Dever JK, Percy RG (2012). Molecular variation among and within improved cultivars in the US cotton germplasm collection. Crop Sci 52: 222–230.
Iqbal MJ, Aziz N, Saeed NA, Zafar Y, Malik KA (1997). Genetic diversity evaluation of some elite cotton varieties by RAPD analysis. Theor Appl Genet 94: 139–144.
Khan AI, Fu YB, Khan IA (2009). Genetic diversity of Pakistani cotton cultivars as revealed by simple sequence repeat markers. Communications in Biometry and Crop Science 4: 21–30.
Michelmore RW, Paran I, Kesseli RV (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. P Natl Acad Sci USA 88: 9828–9832.
Nei M, Li WH (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. P Natl Acad Sci USA 76: 5269–5273.
Paran I, Michelmore RW (1993). Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85: 985–993.
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J et al. (2012).
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423–427.
Prioul JL, Quarrie S, Causse M, de Vienne D (1997). Dissecting complex physiological functions through the use of molecular quantitative genetics. J Exp Bot 48: 1151–1163.
Rahman M, Hussain D, Malik TA, Zafar Y (2005). Genetics of resistance to cotton leaf curl disease in Gossypium hirsutum. Plant Pathol 54: 764–772.
Rahman M, Hussain D, Zafar Y (2002). Estimation of genetic divergence among elite cotton cultivars-genotypes by DNA fingerprinting technology. Crop Sci 42: 2137–2144.
Rahman M, Rahmat Z, Mahmood A, Abdullah K, Zafar Y (2014). Cotton germplasm of Pakistan. In: Abdurakhmonov IY, editor. World Cotton Germplasm Resources. Rijeka, Croatia: InTech. DOI: 10.5772/58620.
Rahman M, Shaheen T, Tabbasam N, Iqbal MA, Ashraf M, Zafar Y, Paterson AH (2012). Cotton genetic resources. A review. Agron Sustain Dev 32: 419–432.
Rahman M, Ullah I, Ahsraf M, Stewart JM, Zafar Y (2008). Genotypic variation for drought tolerance in cotton. Agron Sustain Dev 28: 439–447.
Rahman M, Yasmin T, Tabbasam N, Ullah I, Asif M, Zafar Y (2007). Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting. Genet Resour Crop Ev 55: 331–339.
Rahman M, Zafar Y (2007). Registration of NIBGE-115 cotton. Journal of Plant Registrations 1: 51–52.
Rahman M, Zafar Y (2012). Registration of NN-3 cotton. Journal of Plant Registrations 6: 342–347.
Saeed M, Wangzhen G, Tianzhen Z (2014). Association mapping for salinity tolerance in cotton (Gossypium hirsutum L.) germplasm from US and diverse regions of China. Aust J Crop Sci 8: 338–346.
Shen X, Guo W, Lu Q, Zhu X, Yuan Y, Zhang T (2007). Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155: 371–380.
Sneath PH, Sokal RR (1973). Numerical Taxonomy. The Principles and Practice of Numerical Classification. 1st ed. London, UK: W.H. Freeman & Co.
Surgun Y, Çöl B, Bürün B (2012). Genetic diversity and identification of some Turkish cotton genotypes (Gossypium hirsutum L.) by RAPD-PCR analysis. Turk J Biol 36: 143–150.
Thormann CE, Ferreira ME, Camargo LEA, Tivang JG, Osborn TC (1994). Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor Appl Genet 88: 973–980.
Tuberosa R, Salvi S, Sanguineti MC, Landi P, Maccaferri M, Conti S (2002). Mapping QTLs regulating morpho‐physiological traits and yield: case studies, shortcomings and perspectives in drought‐stressed maize. Ann Bot 89: 941–963.
Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V (2014). Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 127: 283–295.
Wu J, Gutierrez OA, Jenkins JN, McCarty JC, Zhu J (2009). Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton. Euphytica 165: 231–245.
Zhao Y, Wang H, Chen W, Li Y (2014). Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One 9: e86308.
Zhu Y, Chen H, Fan J, Wang Y, Li Y, Chen J, Fan JX, Yang S, Hu L, Leung H (2000). Genetic diversity and disease control in rice. Nature 406: 718–722.