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

Abstract

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.

Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes

“…The fact that homoeologous loci (mapped on both A and B subgenomes) were mapped at a fivefold lower frequency than homologous loci (mapped in both AP13 and VS16) indicates that many of the primer sets are genome specific. This agrees with observations made in previous mapping studies [11,14] and supports the contention that switchgrass is an allotetraploid.…”

“…These tracts are found mainly in regions of high linkage disequilibrium and low recombination, and must be present in sufficiently high frequency in the population to sometimes being inherited from both parents by chance. Liu et al [14] attributed homozygosity in switchgrass accession NL94 LYE, the line that was selfed to generate an F 2 mapping population, as the underlying cause to the fact that only four closely linked markers were mapped to LG VII-b. We examined the profiles in AP13, VS16, and their progeny of nine SSRs that had been mapped to LG VII-a in the female parent, AP13, and that gave amplification patterns in which we could account for all major fragments.…”

“…Three genetic maps have been produced in switchgrass [10,11,14]. Missaoui et al [10] used restriction fragment length polymorphism (RFLP) markers in a full-sib progeny population from a cross between a lowland genotype derived from the cultivar Alamo (AP13) and an upland genotype derived from the cultivar Summer (VS16).…”

“…Single-dose microsatellite markers were mapped to generate female and male maps which spanned 1,376 and 1,645 cM, respectively. Recently, Liu and colleagues generated a genetic map in a population obtained by selfing a self-compatible lowland genotype NL94 LYE [14]. The maps comprised 499 SSR loci and spanned 2,085 cM.…”

Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica)

“…To enhance the breeding process, genetic maps have been developed for switchgrass [4][5][6][7][8], and its genome has been sequenced (www.phytozome.net). However, genetic analyses have been hampered by the complexity of the switchgrass genome.…”