A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome

G3-Genes Genomes Genetics (Impact Factor: 2.51). 01/2012; 2(1):43-58. DOI: 10.1534/g3.111.001552
Source: PubMed

ABSTRACT Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.

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    • "genome at a frequency of two markers per chromosome arm (Yu et al. 2012a). These markers were primarily identified on the basis of a uniform distribution across the 26 tetraploid cotton chromosomes (Wang et al. 2013; Blenda et al. 2012; Yu et al. 2012b; Zhao et al. 2012) with additional criteria including purported lack of locus duplication, PCR reproducibility, polymorphism information content (PIC), and source representation. These markers, many of which are single copy, were multiplexed prior to PCR to form 35 sets of reaction bins (Yu et al. 2012a). "
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    ABSTRACT: Key message A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection. Abstract An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.
    Theoretical and Applied Genetics 11/2014; DOI:10.1007/s00122-014-2431-7 · 3.51 Impact Factor
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    • "RFLP markers reported by Rong et al. [32] were not screened due to unavailability of probes, and technical difficulties for RFLP marker analysis. The SSR markers mapped on Chr. 5 and its homeologous Chr.19 were also included because of a known translocation between Chr. 4 and Chr. 5 [45,46]. All together, a total of 921 SSR markers mapped in these four chromosomes were screened for polymorphism between DNA bulks. "
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    ABSTRACT: Background Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li1) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6 mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points. Results Physical and morphological measurements of the Li1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li1 gene. Conclusions The early termination of fiber elongation in the Li1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li1 mutant were identified. Molecular markers closely associated with the Li1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.
    BMC Genomics 06/2013; 14(1):403. DOI:10.1186/1471-2164-14-403 · 4.04 Impact Factor
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    • "As an example, by using SAMtools we identified more than 1000 new allele-SNPs within both allopolyploid genomes of G. hirsutum and G. tomentosum (Figure 6). These allele-SNPs would be the most useful type of SNPs for cotton improvement because they have been bioinformatically discriminated from homoeo-SNPs and because they could be expected to segregate in Mendelian fashion (Van Deynze et al. 2009; Byers et al. 2012; Yu et al. 2012). "
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    ABSTRACT: Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat-a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP's single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. Bisulfite-treated reads have a significant reduction in nucleotide complexity because nucleotide conversion events are confounded with transition substitutions. PolyCat includes special provisions to properly handle bisulfite-treated data. We demonstrate the functionality of PolyCat on allotetraploid cotton, , and create a functional SNP index for efficiently mapping sequence reads to the D-genome sequence of . PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.
    G3-Genes Genomes Genetics 03/2013; 3(3):517-25. DOI:10.1534/g3.112.005298 · 2.51 Impact Factor
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