Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium)

Mei, Mengjun; Syed, Naeem H.; Gao, Wenxiang; Thaxton, P. M.; Smith, C. Wayne; Stelly, David M.; Chen, Zengjian J

doi:10.1007/s00122-003-1433-7

Cited by 217 publications

(161 citation statements)

References 53 publications

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“…Alternatively, EcoR I and its primers may be replaced with another restriction enzyme such as Hind III or Dra I. EcoR I activity is sensitive to DNA methylation, which may affect the genomic AFLP results. However, data obtained from our lab and others indicate that similar polymorphism levels of the fingerprints may be obtained using restriction enzymes other than EcoR I (Mei et al, 2004).…”

supporting

confidence: 68%

“…The method can be used to analyze simultaneously different DNA regions throughout the entire genome regardless of its origin or complexity (Mei et al, 2004). A modification of the method using complementary DNA (cDNA) samples in the analysis, known as AFLP-cDNA or cDNA-AFLP display, allows the characterization of tissue-specific gene expression patterns (Bachem et al, 1996) and detection of gene expression differences in allopolyploids (Comai et al, 2000;Lee and Chen, 2001;Madlung et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

Wang

Lee²,

Tian³

et al. 2005

Methods in Enzymology

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Polyploidy is an evolutionary innovation, providing extra sets of genetic material for phenotypic variation and adaptation. It is predicted that changes of gene expression by genetic and epigenetic mechanisms are responsible for novel variation in nascent and established polyploids (Liu and Wendel, 2002;Osborn et al., 2003;Pikaard, 2001). Studying gene expression changes in allopolyploids is more complicated than in autopolyploids, because allopolyploids contain more than two sets of genomes originating from divergent, but related, species. Here we describe two methods that are applicable to the genome-wide analysis of gene expression differences resulting from genome duplication in autopolyploids or interactions between homoeologous genomes in allopolyploids. First, we describe an amplified fragment length polymorphism (AFLP)-complementary DNA (cDNA) display method that allows the discrimination of homoeologous loci based on restriction polymorphisms between the progenitors. Second, we describe microarray analyses that can be used to compare gene expression differences between the allopolyploids and respective progenitors using appropriate experimental design and statistical analysis. We demonstrate the utility of these two complementary methods and discuss the pros and cons of using the methods to analyze gene expression changes in autopolyploids and allopolyploids. Furthermore, we describe these methods in general terms to be of wider applicability for comparative gene expression in a variety of evolutionary, genetic, biological, and physiological contexts.

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supporting

confidence: 68%

Section: Introductionmentioning

confidence: 99%

Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

Wang

Lee²,

Tian³

et al. 2005

Methods in Enzymology

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“…The 450 SSR primer pairs that showed polymorphisms between the two mapping parents were used to genotype 173 individuals from the F 2 population. The procedure for SSR analysis was that described by Mei et al [24].…”

Section: Dna Extraction and Genotype Analysismentioning

confidence: 99%

Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

Liang

Hua

et al. 2013

Chin. Sci. Bull.

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With the development in spinning technology, the improvement of cotton fiber quality is becoming more and more important. The main objective of this research was to construct a high-density genetic linkage map to facilitate marker assisted selection for fiber quality traits in upland cotton (Gossypium hirsutum L.). A genetic linkage map comprising 421 loci and covering 3814.3 cM, accounting for approximately 73.35% of the cotton genome, was constructed using an F 2 population derived from cross GX1135 (P 1 )×GX100-2 (P 2 ). Forty-four of 49 linkage groups were assigned to the 26 chromosomes. Fiber quality traits were investigated in F 2 population sampled from individuals, and in F 2:3 , and F 2:4 generations sampled by lines from two sites and one respectively, and each followed a randomized complete block design with two replications. Thirty-nine quantitative trait loci were detected for five fiber quality traits with data from single environments (separate analysis each): 12 for fiber length, five for fiber uniformity, nine for fiber strength, seven for fiber elongation, and six for fiber micronaire, whereas 15 QTLs were found in combined analysis (data from means of different environments in F 2:3 generation). Among these QTLs, qFL-chr5-2 and qFL-chr14-2 for fiber length were detected simultaneously in three generations (four environments) and verified further by combined analysis, and these QTLs should be useful for marker assisted selection to improve fiber quality in upland cotton.upland cotton (Gossypium hirsutum L.), fiber quality traits, genetic linkage map, marker assisted selection, QTLs Citation:Liang Q Z, Hu C, Hua H, et al. Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.). Chin Sci Bull, 2013, 58: 32333243,

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“…The SSRs did not amplify distinctive fragments with genomic DNA of A-genome species but produced clear bands in the D-and AD-genome species were placed on D-subgenome of allotetraploid cotton (Lacape et al 2003;Mei et al 2004). Only (12) markers were D-genome specific reflecting substantial divergence of D-genome species from D-subgenome of allotetraploid cotton (Brubaker et al 1999;Adams and Wendel 2004;Guo et al 2006;Wu et al 2007).…”

Section: Performance Of Microsatellite Between a D And Ad-genome Spementioning

confidence: 99%

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

2013

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The genus Gossypium is comprised of 50 diverse cotton species representing eight different genomes (A through G and K), however, phylogenetic relationship using various DNA marker types such as RAPD and SSRs was determined on limited number of cotton species. In this report, we have demonstrated the application of genomic SSRs (gSSRs) and EST-SSRs, and after combining both the data sets, for resolving the phylogenies of 36 cotton species including seven races. Out of the 100 primer pairs surveyed (50 for gSSRs and 50 for ESTSSRs), 75 produced scorable amplification products in all species. Out of these, 73 were found to be polymorphic and amplified 135 alleles ranging from 1 to 5 alleles per SSR marker (average 2.87 alleles per marker). The gSSRs amplified higher number of alleles (72) compared to the EST-SSRs (63). In total 22 highly informative SSRs with PIC values C0.5 were identified. Genomic SSRs containing di-while EST-SSRs containing tri-nucleotide repeats exhibited high polymorphism compared to the other nucleotide repeats containing gSSRs/EST-SSRs. Number of tandem repeats and polymorphism were positively correlated. Neither the type of chromosome nor the location of the SSRs showed association with the polymorphism. Gossypium herbaceum var. africanum (Watt) Hutch. ex and Ghose and Gossypium robinsonii F. Muell. were found the most genetically diverse, while among races of Gossypium hirsutum L. ''yucatanense'' and G. hirsutum ''punctatum'' were found genetically diverse. Of the three data sets, clustering analysis based on EST-SSRs and combined data sets, revealed parallel results reported in earlier studies. This study further confirmed that Gossypium darwinii Watt has close relationship with Gossypium barbadense L. Moreover, Gossypium raimondii Ulbr. and G. herbaceum/Gossypium arboreum L. are close living relatives of the ancestor allotetraploid species. Our studies suggest that for resolving phylogenetic relationship among the various plant species EST-SSRs could be a better choice. This information can be instrumental in transferring novel alleles or loci from the wild species into the cultivated cotton species which would set a stage for cultivating genetically diverse cultivars-a way to achieve sustainable cotton production in changing climate.

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Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium)

Cited by 217 publications

References 53 publications

Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

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