A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass

Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma 74078.
G3-Genes Genomes Genetics (Impact Factor: 3.2). 03/2012; 2(3):357-70. DOI: 10.1534/g3.111.001503
Source: PubMed


Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.

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Available from: Yunwen Wang, Oct 06, 2014
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    • "Subsequently, further markers were added to the linkage map. The aforementioned approach has been effectively used in previous studies (Liu et al. 2012; Okada et al. 2010; Wu & Huang 2006). Genetic maps were drawn using MapChart V.2.2 (Voorrips 2002). "
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    ABSTRACT: Genetic linkage maps are deployed to locate quantitative trait loci (QTL) of traits of interest and speed up breeding programs. In this study, we used two Vicia faba L. backcross families (BCFams). Genetic linkage maps were constructed with 193 and 288 polymorphic amplified fragment length polymorphism (AFLP) markers using 131 and 132 individuals for BCFam1 and BCFam2, respectively. The BCFam1 linkage map consisted of 18 linkage groups (LGs) encompassing 1134.7 cM, with a mean inter-marker distance of 11.94 cM. The BCFam.2 linkage map consisted of 19 LGs encompassing 1235 cM with a mean inter-marker distance of 9.29 cM. A set of 13 AFLP markers was homologous among maps of BCFam1 and BCFam2 as well as faba bean consensus map. These linkage maps will be beneficial for genetic analyses and diversity studies as well as for comparative mapping of faba bean and related species.
    Journal of Crop Improvement 07/2015; 29(4):474-490. DOI:10.1080/15427528.2015.1053012
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    • "In recent years, molecular markers have been extensively used to examine variation in switchgrass germplasm [5,8-13]. Switchgrass genetic linkage map has been established [14,15]. Three bacterial artificial chromosome (BAC) libraries have been generated [16,17]. "
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    ABSTRACT: Global warming predictions indicate that temperatures will increase by another 2-6[degree sign]C by the end of this century. High temperature is a major abiotic stress limiting plant growth and productivity in many areas of the world. Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop, due to its rapid growth rate, reliable biomass yield, minimal requirements of water and nutrients, adaptability to grow on marginal lands and widespread distribution throughout North America. The effect of high temperature on switchgrass physiology, cell wall composition and biomass yields has been reported. However, there is void in the knowledge of the molecular responses to heat stress in switchgrass. We conducted long-term heat stress treatment (38o/30[degree sign]C, day/night, for 50 days) in the switchgrass cultivar Alamo. A significant decrease in the plant height and total biomass was evident in the heat stressed plants compared to controls. Total RNA from control and heat stress samples were used for transcriptome analysis with switchgrass Affymetrix genechips. Following normalization and pre-processing, 5365 probesets were identified as differentially expressed using a 2-fold cutoff. Of these, 2233 probesets (2000 switchgrass unigenes) were up-regulated, and 3132 probesets (2809 unigenes) were down-regulated. Differential expression of 42 randomly selected genes from this list was validated using RT-PCR. Rice orthologs were retrieved for 78.7% of the heat stress responsive switchgrass probesets. Gene ontology (GOs) enrichment analysis using AgriGO program showed that genes related to ATPase regulator, chaperone binding, and protein folding was significantly up-regulated. GOs associated with protein modification, transcription, phosphorus and nitrogen metabolic processes, were significantly down-regulated by heat stress. Plausible connections were identified between the identified GOs, physiological responses and heat response phenotype observed in switchgrass plants. Comparative transcriptome analysis in response to heat stress among four monocots -- switchgrass, rice, wheat and maize identified 16 common genes, most of which were associated with protein refolding processes. These core genes will be valuable biomarkers for identifying heat sensitive plant germplasm since they are responsive to both short duration as well as chronic heat stress treatments, and are also expressed in different plant growth stages and tissue types.
    BMC Plant Biology 10/2013; 13(1):153. DOI:10.1186/1471-2229-13-153 · 3.81 Impact Factor
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    • "Marker studies helped delineate upland and lowland variation and are useful in developing germplasm conservation and breeding programs [96]. Genetic linkage maps have been constructed using single dose restriction fragments (SDRFs), SSRs, sequence-tagged sites (STS) markers, expressed sequence tags (EST)-derived SSRs, gene-derived STS markers, and diversity array technology (DArT) markers [97-101]. Linkage maps will aid in the identification of quantitative trait loci linked with biomass yield, plant composition and other important agronomic traits, providing a genetic framework to facilitate marker-assisted breeding and genomics research in switchgrass. "
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    ABSTRACT: Switchgrass (Panicum virgatum L.) is a C4 perennial warm season grass indigenous to the North American tallgrass prairie. A number of its natural and agronomic traits, including adaptation to a wide geographical distribution, low nutrient requirements and production costs, high water use efficiency, high biomass potential, ease of harvesting, and potential for carbon storage, make it an attractive dedicated biomass crop for biofuel production. We believe that genetic improvements using biotechnology will be important to realize the potential of the biomass and biofuel-related uses of switchgrass. Tissue culture techniques aimed at rapid propagation of switchgrass and genetic transformation protocols have been developed. Rapid progress in genome sequencing and bioinformatics has provided efficient strategies to identify, tag, clone and manipulate many economically-important genes, including those related to higher biomass, saccharification efficiency, and lignin biosynthesis. Application of the best genetic tools should render improved switchgrass that will be more economically and environmentally sustainable as a lignocellulosic bioenergy feedstock.
    Biotechnology for Biofuels 05/2013; 6(1):77. DOI:10.1186/1754-6834-6-77 · 6.04 Impact Factor
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