cDNA-AFLP-based genetical genomics in cotton fibers

Abstract

Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum × G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD> 3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton.

Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton

“…Usually, transcriptome maps are constructed using cDNAAFLPs since direct mapping of transcripts with the cDNA-AFLP technique is a rapid and practical method of direct mapping of expressed genes (Brugmans et al 2002). Transcriptome maps have been successfully constructed in Arabidopsis and potato (Brugmans et al 2002;Ritter et al 2008) as well as in cotton (Liu et al , 2011Claverie et al 2012) by cDNA-AFLP. The cDNA-AFLP technique is highthroughput, however, the procedure is complex.…”

“…A total of 302 TDFs were mapped onto 26 linkage groups, and 71 QTLs for yield and yield component traits were detected, based on four environments, with 13 QTLs identified in at least two environments. Claverie et al (2012) used quantitative cDNA-AFLP to monitor variation in the expression level of cotton fibre elongation and secondary cell wall thickening transcripts in a population of interspecific G. hirsutum × G. barbadense recombinant inbred lines (RILs). Two-thirds of the normalized intensity ratios of TDFs were mapped between 1 and 6 eQTLs.…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…They are being continuously used in cotton genomic investigations [15]. In the recent past, AFLP markers have been used in monitoring the differential expression of cotton fiber transcripts during elongation and secondary cell wall thickening in interspecific (G. hirsutum × G. barbadense) RI lines [16].…”

Differential transcript profiling alters regulatory gene expression during the development of Gossypium arboreum, G.stocksii and somatic hybrids

“…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 31 and the detection of gene expression differences in allopolyploids 32–34 . The cDNA-AFLP method is an extremely efficient and sensitive mRNA fingerprinting technique for identifying both common and rare or unknown transcripts 35–37 and is an open architecture technology for global transcriptional analysis in a non-model plant species 14, 38, 39 . This technique is a robust and high-throughput tool for the analysis of genome-wide gene expression, and it can be used to identify genes that are differentially expressed in allopolyploids.…”

“…This technique is a robust and high-throughput tool for the analysis of genome-wide gene expression, and it can be used to identify genes that are differentially expressed in allopolyploids. Quantitative cDNA-AFLP was used to monitor variation in the expression levels of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum  ×  G. barbadense recombinant inbred lines (RILs), proving to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling 39 . cDNA-AFLP has been used previously in cotton to compare the transcriptomes of two cotton lines (one fertile and the other male sterile) 40 , to identify genes involved in somatic embryogenesis 41 and to study gene silencing 42 , and to construct genetic maps 39, 43 .…”