A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

Publication Overview
TitleA combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)
AuthorsHinchliffe DJ, Turley RB, Naoumkina M, Kim HJ, Tang Y, Yeater KM, Li P, Fang DD
TypeJournal Article
Journal NameBMC genomics
Year2011
CitationHinchliffe DJ, Turley RB, Naoumkina M, Kim HJ, Tang Y, Yeater KM, Li P, Fang DD. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). BMC genomics. 2011. 12-445
Publication CodeBMCGN-12-445

Abstract

Background: Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li2) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation. Results: Two near-isogenic lines of Ligon lintless-2 (Li2) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC5). An F2 population was developed from a cross between the two Li2 near-isogenic lines and used to develop a linkage map of the Li2 locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the Li2 locus region with two of the markers flanking the Li2 locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the Li2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li2 locus. Conclusions: In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li2 locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the Li2 gene.
Image
File NameLegend
Li2_BMCGN-12-445_F1.jpgComparison of Li2 mutant and WT fibers and ovules during development. [Image from Hinchliffe et al., 2011, BMCGN-12-445]
Li2_BMCGN-12-445_F2.jpgSEM analysis of developing Li2 mutant and WT fibers and ovules. [Image from Hinchliffe et al., 2011, BMCGN-12-445]
Features
This publication contains information about 20 features:
Feature NameUniquenameType
USDA_CFB_Ghi.2036.1.S1_s_atUSDA_CFB_Ghi.2036.1.S1_s_atgenetic_marker
USDA_CFB_Gra.2547.1.S1_s_atUSDA_CFB_Gra.2547.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.2039.1.S1_x_atUSDA_CFB_Ghi.2039.1.S1_x_atgenetic_marker
USDA_CFB_Ghi.6061.1.S1_atUSDA_CFB_Ghi.6061.1.S1_atgenetic_marker
USDA_CFB_Ghi.1314.1.S1_x_atUSDA_CFB_Ghi.1314.1.S1_x_atgenetic_marker
USDA_CFB_GraAffx.30567.2.S1_s_atUSDA_CFB_GraAffx.30567.2.S1_s_atgenetic_marker
USDA_CFB_GhirRNA.4.1.S1_s_atUSDA_CFB_GhirRNA.4.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.1711.1.S1_s_atUSDA_CFB_Ghi.1711.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.3235.1.A1_atUSDA_CFB_Ghi.3235.1.A1_atgenetic_marker
USDA_CFB_Ghi.4377.1.A1_atUSDA_CFB_Ghi.4377.1.A1_atgenetic_marker
USDA_CFB_Ghi.6551.1.S1_atUSDA_CFB_Ghi.6551.1.S1_atgenetic_marker
USDA_CFB_Ghi.7279.1.S1_atUSDA_CFB_Ghi.7279.1.S1_atgenetic_marker
USDA_CFB_Ghi.7450.1.S1_s_atUSDA_CFB_Ghi.7450.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.7724.1.S1_atUSDA_CFB_Ghi.7724.1.S1_atgenetic_marker
USDA_CFB_Ghi.8115.1.S1_s_atUSDA_CFB_Ghi.8115.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.8501.1.A1_atUSDA_CFB_Ghi.8501.1.A1_atgenetic_marker
USDA_CFB_Ghi.8665.1.S1_s_atUSDA_CFB_Ghi.8665.1.S1_s_atgenetic_marker
USDA_CFB_Ghi.9209.1.S1_atUSDA_CFB_Ghi.9209.1.S1_atgenetic_marker
USDA_CFB_Ghi.9236.1.S1_atUSDA_CFB_Ghi.9236.1.S1_atgenetic_marker
USDA_CFB_Gra.2056.1.A1_s_atUSDA_CFB_Gra.2056.1.A1_s_atgenetic_marker
Germplasm
This publication contains information about 2 stocks:
Stock NameUniquenameType
cdbgm_014753Li2genetic_stock
cdbpop_000122Li2 x DP5690, F2population
Featuremaps
This publication contains information about 1 maps:
Map Name
Li2 x DP5690, F2 (2011)
Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
URLhttp://dx.doi.org/10.1186/1471-2164-12-445
Language Abbreng
Publication Date2011
Publication Model[electronic resource].
Published Location|||
Publication CodeBMCGN-12-445
Keywordsexpressed sequence tags, microsatellite repeats, genetic markers, linkage (genetics), chromosome mapping, homozygosity, Gossypium hirsutum
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4618504
PMID: PubMedPMID:21902843