Dataset Information

Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton.

ABSTRACT: BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis.

SUBMITTER: Lai D

PROVIDER: S-EPMC3232235 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton.

Lai Deyong D Li Huaizhu H Fan Shuli S Song Meizhen M Pang Chaoyou C Wei Hengling H Liu Junjie J Wu Dong D Gong Wenfang W Yu Shuxun S

PloS one 20111206 12

<h4>Background</h4>Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare.<h4>Methodology/principal findings</h4>To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were ge ...[more]

PMID: 22163052

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Project description:Marker-assisted selection (MAS) helps to shorten breeding time as well as reduce breeding resources and efforts. In our MAS program, we have targeted one of previously reported LD-blocks with its simple sequence repeat (SSR) marker(s), putatively associated with, at least, four different fibre quality QTLs such as fibre length, strength, micronaire and uniformity. In order to transfer targeted QTLs from a donor genotype to a cultivar of choice, we selected G. hirsutum donor genotypes L-141 and LN-1, possessing a fibre quality trait-associated LD-block from the chromosome 7/16. We crossed the donor lines with local elite G. hirsutum cultivars 'Andijan-35' and 'Mekhnat' as recipients. As a result, two segregating populations on LD-block of interest containing fibre QTLs were developed through backcrossing (BC) of F1 hybrids with their relative recipients (used as recurrent parents) up to five generations. In each BC and segregating BC1-5F1 populations, a transfer of targeted LD-block/QTLs was monitored using a highly polymorphic SSR marker, BNL1604 genotype. The homozygous cultivar genotypes with superior fibre quality and agronomic traits, bearing a targeted LD-block of interest, were individually selected from self-pollinated BC5F1 (BC5F2-5) population plants using the early-season PCR screening analysis of BNL1604 marker locus and the end-of-season fibre quality parameters. Only improved hybrids with superior fibre quality compared to original recipient parent were used for the next cycle of breeding. We successfully developed two novel MAS-derived cotton cultivars (named as 'Ravnaq-1' and 'Ravnaq-2') of BC5F5 generations. Both novel MAS cultivars possessed stronger and longer fibre as well as improved fibre uniformity and micronaire compared to the original recurrent parents, 'Andijan-35' and 'Mekhnat'. Our efforts demonstrated a precise transfer of the same LD-block with, at least, four superior fibre QTLs in the two independent MAS breeding experiments exploiting different parental genotypes. Results exemplify the feasibility of MAS in cotton breeding.

Project description:BACKGROUND: Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers. RESULTS: A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (< or =1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with > or = 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes and their expression profile showed predominance in specific stress-challenged libraries. CONCLUSION: Generated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species.

Dataset Information

Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton.

Publications

Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton.

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