Are you John Jacobs?

Claim your profile

Publications (6)20.06 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Cotton (Gossypium) fiber is the most prevalent natural product used in the textile industry. The two major cultivated species, G. hirsutum (Gh) and G. barbadense (Gb), are allotetraploids with contrasting fiber quality properties. To better understand the molecular basis for their fiber differences, EST pyrosequencing was used to document the fiber transcriptomes at two key development stages, 10 days post anthesis (dpa), representing the peak of fiber elongation, and 22 dpa, representing the transition to secondary cell wall synthesis. The 617,000 high quality reads (89% of the total 692,000 reads) from 4 libraries were assembled into 46,072 unigenes, comprising 38,297 contigs and 7,775 singletons. Functional annotation of the unigenes together with comparative digital gene expression (DGE) revealed a diverse set of functions and processes that were partly linked to specific fiber stages. Globally, 2,770 contigs (7%) showed differential expression (>2-fold) between 10 and 22 dpa (irrespective of genotype), with 70% more highly expressed at 10 dpa, while 2,248 (6%) were differentially expressed between the genotypes (irrespective of stage). The most significant genes with differential DGE at 10 dpa included expansins and lipid transfer proteins (higher in Gb), while at 22 dpa tubulins, cellulose, and sucrose synthases showed higher expression in Gb. DGE was compared with expression data of 10 dpa-old fibers from Affymetrix microarrays. Among 543 contigs showing differential expression on both platforms, 74% were consistent in being either over-expressed in Gh (242 genes) or in Gb (161 genes). Furthermore, the unigene set served to identify 339 new SSRs and close to 21,000 inter-genotypic SNPs. Subsets of 88 SSRs and 48 SNPs were validated through mapping and added 65 new loci to a RIL genetic map. The new set of fiber ESTs and the gene-based markers complement existing available resources useful in basic and applied research for crop improvement in cotton.
    PLoS ONE 01/2012; 7(11):e48855. · 3.53 Impact Factor
  • [Show abstract] [Hide abstract]
    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.
    Theoretical and Applied Genetics 11/2011; 124(4):665-83. · 3.66 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Exploiting genetic variation through inter-specific breeding has improved cotton yield, fibre properties and adaptability. The objectives of this study were to examine heritability and predicted selection response of yield components and fibre properties in a recombinant inbred line (RIL) population from an inter-specific cross between Gossypium hirsutum (Gh) variety Guazuncho 2, and G. barbadense (Gb) line VH8-4602. A population of 93 and 82 RILs was tested in two seasons, with two parents and local controls, Sicot 75 (Gh) and Sipima 280 (Gb) in field experiments. Seed cotton samples hand harvested before and after defoliation were used to measure lint percent, boll weight, 100 seed weight and the lint to measure fibre length, uniformity, short fibre index (SFI), elongation, strength, micronaire, maturity ratio (MR), percent of maturity (PM) and fineness. There was large phenotypic variation for individual traits and transgressive segregation occurred in lint percent, lint weight/seed, fibre no./seed, uniformity, SFI, elongation, MR and PM. Narrow sense heritabilities were moderate for yield components (34.3–41.2%) and for key fibre properties, length, strength, micronaire and fineness (38.3–42.1%), which led to a predicted selection response of 6.7–24.0% for yield components and 3.9–10.9% for key fibre properties under a selection intensity of 10%. Favourable associations were found between key fibre properties, but an adverse association between lint percent and each of these fibre properties. Only five RILs were identified with desirable combinations. The results demonstrated the value of exploiting inter-specific variation to develop cotton germplasm and how breeding strategies can be improved. KeywordsInter-specific breeding–Heritability–Predicted selection response–Phenotypic correlation–Recombinant inbred lines– Gossypium hirsutum L.– Gossypium barbadense L.
    Euphytica 01/2011; 178(3):309-320. · 1.64 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Cotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh x Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years. The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3. Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.
    BMC Plant Biology 01/2010; 10:132. · 4.35 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.
    BMC Genomics 02/2006; 7:132. · 4.40 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Two major cultivated cotton species, Gossypium hirsutum (Gh) and G. barbadense (Gb) contribute to the bulk of cotton fiber production worldwide (95%). These species are largely inter-fertile and each displays a series of distinctive characteristics in terms of numerous botanical features and, more importantly, in their agronomic performance, adaptability and overall fiber quality. A recombinant inbred line (RIL) population derived from an inter-specific cross between Gh and Gb, used previously for QTL mapping of fiber quality characteristics, has also been evaluated over 6 sites and 2 years for various plant morphological, phenological and yield component traits. A total of 27 traits were assessed across a varying number of locations (up to 6 locations, in Australia, USA, Brazil, Cameroon, Belgium and France) and years, representing up to 10 different combinations. Variability in many of these traits was observed among the RILs and they frequently showed transgression. One hundred and sixty six significant QTLs, covering the 27 traits, were detected by composite interval mapping when using individual datasets. Cases of confirmation of localizations of individual QTLs from different data sets were detected in 27 instances, indicating that the 166 individual QTLs in this study could be represented by a maximum of 121 chromosome positions. QTL were shared between traits related to hairiness (22 individual QTLs), plant morphology of vegetative (29 QTLs) and reproductive (37 QTLs) parts, phenology (17 QTLs), and yield-related traits (61 QTLs). This is the first report of QTL mapping in cotton for various within-boll yield-related traits assessed on a per-seed basis, including fiber mass per unit of seed surface area (5 QTLs), calculated number of fibers per seed (2 QTLs) or per unit of seed surface area (1 QTL). This report confirms the importance of considering such basic yield components in selection for better yielding cotton varieties.
    Field Crops Research 144:256–267. · 2.47 Impact Factor