Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting

Rahman, Mehboob-ur; Yasmin, Tahira; Tabbasam, Nabila; Ullah, Ihsan; Asif, Muhammad; Zafar, Yusuf

doi:10.1007/s10722-007-9238-1

Cited by 41 publications

(4 citation statements)

References 22 publications

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“…However, a vast genetic base was found that differed considerably from that uncovered through research using random-amplified polymorphic DNA and SSRs, in which the genetic diversity was narrow. Mehboo-ur-Rahman (2008) analyzed genetic diversity among 30 cultivars of G. arboreum based on random-amplified polymorphic DNA markers and revealed a limited diversity base. Sun et al (2009) analyzed 61 colored-cotton lines using SSR markers and showed that the genetic background of colored cotton with elite properties was narrow.…”

Section: Discussionmentioning

confidence: 99%

Construction of a primary DNA fingerprint database for cotton cultivars

Zhang

Kuang²,

Yang³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Forty core primers were used to construct a DNA fingerprint database of 132 cotton species based on multiplex fluorescence detection technology. A high first successful ratio of 99.04% was demonstrated with tetraplex polymerase chain reaction. Forty primer pairs amplified a total of 262 genotypes among 132 species, with an average of 6.55 per primer and values of polymorphism information content varying from 0.340 to 0.882. Conflicting DNA homozygous ratios were found in various species. The highest DNA homozygous ratio was found in landrace standard cultivars, which had an 81.46% DNA homozygous ratio. The lowest occurred in a group of 2010 leading cultivars with a homozygous ratio of 63.04%. Genetic diversity of the 132 species was briefly analyzed using unweighted pair-group method with arithmetic means.

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Section: Discussionmentioning

confidence: 99%

Construction of a primary DNA fingerprint database for cotton cultivars

Zhang

Kuang²,

Yang³

et al. 2013

Genet. Mol. Res.

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“…The poor reproducibility of RAPD profiles within and between laboratories can be attributed to various factors like quality of DNA, composition of PCR reaction mixture, nature of DNA polymerase and the skills of the working person, to quote a few. RAPDs have been used for diversity, genome mapping and phylogenetic studies in cotton (Rahman et al, 2002b;Zhang et al, 2002;He et al, 2007;Rahman et al, 2008b;Rana and Bhat 2004). RAPDs are not popular for genetic mapping and gene tagging studies in cotton because of their low informativeness and non-locus specific nature.…”

Section: Random Amplified Polymorphic Dna (Rapd)mentioning

confidence: 99%

“…SNP analysis is useful for cultivar discrimination in crops where it is difficult to find polymorphism. These DNA markers have also been used in cotton for fingerprinting (Rahman et al, 2002b(Rahman et al, , 2008b, linkage map construction (Reinisch et al, 1994;Zhang et al, 2002;Lacape et al, 2003;Mei et al, 2004;Rong et al, 2004), gene mapping (Shappley et al, 1998;Ulloa and Meredith, 2000) and genetic diversity studies (Rahman et al, 2002b(Rahman et al, , 2008b.…”

Section: Single Nucleotide Polymorphism (Snps)mentioning

confidence: 99%

Genetic improvement of Gossypium arboreum L. using molecular markers: Status and development needs

Sethi¹,

Siwach²,

Verma³

2014

Afr. J. Agric. Res.

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The genus Gossypium has 45-50 species, of which only four (two allotetraploids and two diploids) enjoy the status of cultivated cotton. Among the four cultivated ones, Gossypium arboreum holds a special place because of the inherent ability to withstand drought, salinity and remarkable resistance to sucking pests and leaf curl virus. However, the species suffer with poor fiber quality traits, low yield and has certain undesirable plant and boll features. Improvement of fiber quality traits of G. arboreum, without disturbing its unique characteristics, has been a long sought after dream of scientists world over. For conservation, evaluation and documentation of existing accessions, gene banks of diploid cultivated cotton has been established by different countries, of which India holds the highest number of G. arboreum collections. Traditional breeding efforts made to improve fiber quality of G. arboreum have met with limited success due to paucity of polymorphic phenotypic markers and polygenic nature of the desired traits. Genetic engineering approach is highly genotype dependent and much success has not been achieved by this way also. Molecular breeding approach, based on the strength of breeding with high polymorphic nature of molecular markers, has yielded significant results in the improvement of G. arboreum. A number of molecular markers have been developed and used in various cotton improvement programs but dominantly these efforts have been made for the allotetraploid species G. hirsutum. Some efforts have been made for generating fingerprint database of G. arboreum germplasm, though much more efforts are needed in this direction. Linkage maps of G. arboreum have been generated using different markers systems which has enabled the mapping of gene/QTLs of desired traits on the chromosome of G. arboreum. More research inputs need to be devoted to produce consensus and saturated genomic maps, if the aim of 'breeding by design', by retaining suitable features and improving the undesirable ones, is to be realized for G. arboreum.

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“…The DNA-based markers used for determining genetic diversity in cotton include restriction fragment length polymorphisms (RFLPs) [29], random amplified polymorphic DNA (RAPD) [30,31,32], amplified fragment length polymorphisms (AFLPs) [33], simple sequence repeat (SSR) [9,34,35,36], expressed sequence tags (ESTs) [37], inter-simple sequence repeat (ISSR) [38,39], and single nucleotide polymorphisms (SNPs) [40]. Compared with other biomarkers, SSR has advantages that include more reproducibility, co-dominant inheritance, distribution throughout the genome, and its being highly transferable, informative, and reliable [41].…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

Ditta

Zhou

Cai

et al. 2018

IJMS

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This study evaluated the genetic diversity and population structures in a novel cotton germplasm collection comprising 132 diploids, including Glossypium klotzschianum and allotetraploid cotton accessions, including Glossypium barbadense, Glossypium darwinii, Glossypium tomentosum, Glossypium ekmanianum, and Glossypium stephensii, from Santa Cruz, Isabella, San Cristobal, Hawaiian, Dominican Republic, and Wake Atoll islands. A total of 111 expressed sequence tag (EST) and genomic simple sequence repeat (gSSR) markers produced 382 polymorphic loci with an average of 3.44 polymorphic alleles per SSR marker. Polymorphism information content values counted 0.08 to 0.82 with an average of 0.56. Analysis of a genetic distance matrix revealed values of 0.003 to 0.53 with an average of 0.33 in the wild cotton collection. Phylogenetic analysis supported the subgroups identified by STRUCTURE and corresponds well with the results of principal coordinate analysis with a cumulative variation of 45.65%. A total of 123 unique alleles were observed among all accessions and 31 identified only in G. ekmanianum. Analysis of molecular variance revealed highly significant variation between the six groups identified by structure analysis with 49% of the total variation and 51% of the variation was due to diversity within the groups. The highest genetic differentiation among tetraploid populations was observed between accessions from the Hawaiian and Santa Cruz regions with a pairwise FST of 0.752 (p < 0.001). DUF819 containing an uncharacterized gene named yjcL linked to genomic markers has been found to be highly related to tryptophan-aspartic acid (W-D) repeats in a superfamily of genes. The RNA sequence expression data of the yjcL-linked gene Gh_A09G2500 was found to be upregulated under drought and salt stress conditions. The existence of genetic diversity, characterization of genes and variation in novel germplasm collection will be a landmark addition to the genetic study of cotton germplasm.

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Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting

Cited by 41 publications

References 22 publications

Construction of a primary DNA fingerprint database for cotton cultivars

Construction of a primary DNA fingerprint database for cotton cultivars

Genetic improvement of Gossypium arboreum L. using molecular markers: Status and development needs

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

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