Yanqi Wu

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

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.

Identification of a Selfing Compatible Genotype and Mode of Inheritance in Switchgrass

Switchgrass (Panicum virgatum L.) is being targeted for use as a dedicated lignocellulosic feedstock crop for producing bioenergy in the United States. The breeding of new switchgrass cultivars with enhanced performance is a research emphasis supporting the targeted use. The species is considered allogamous due to wind facilitated cross-pollination and strong genetic self-incompatibility. Plants typically produce few or no seed when self-fertilized. No attempt has been made to identify selfing-compatible plants that would potentially enable developing inbred lines. Here, using a set of 12 simple sequence repeat-based molecular markers, we identified one lowland plant, ‘NL94 LYE 16 × 13’ (NL94), demonstrating high self-compatibility. A large potted plant of NL94 and a similar size plant of ‘SL93 7 × 15’ were grown in a growth chamber for the purpose of producing a hybrid full-sib mapping population. Marker analyses of 456 progeny from the NL94 plant indicated that 279 (61.2%) and 177 (38.8%) resulted from self- and cross-fertilization, respectively. SSR marker segregation analyses in both the selfed and hybrid progeny populations conclusively indicated disomic inheritance in the two switchgrass parents. Disomic inheritance of switchgrass is significant to the development of switchgrass inbreds as homozygosity is approached much faster via inbreeding under disomic vs. tetrasomic inheritance. Self-compatibility in switchgrass potentially enables the development of inbred lines for use in producing heterotic F1 hybrid cultivars.

Control of floral transition in the bioenergy crop switchgrass

Switchgrass (Panicum virgatum L.), a perennial warm season bunchgrass native to North America, has been a target in the U.S. as a renewable bioenergy crop because of its ability to produce moderate to high biomass yield on marginal soils. Delaying flowering can increase vegetative biomass production by allowing prolonged growth before switching to the reproductive phase. Despite the identification of flowering time as a biomass trait in switchgrass, the molecular regulatory factors involved in controlling floral transition are poorly understood. Here we identified PvFT1, PvAPL1-3 and PvSL1, 2 as key flowering regulators required from floral transition initiation to development of floral organs. PvFT1 expression in leaves is developmentally regulated peaking at the time of floral transition, and diurnally regulated with peak at approximately 2 h into the dark period. Ectopic expression of PvFT1 in Arabidopsis, Brachypodium and switchgrass led to extremely early flowering, and activation of FT downstream target genes, confirming that it is a strong activator of flowering in switchgrass. Ectopic expression of PvAPL1-3 and PvSL1, 2 in Arabidopsis also activated early flowering with distinct floral organ phenotypes. Our results suggest that switchgrass has conserved flowering pathway regulators similar to Arabidopsis and rice.

QTL mapping for reproductive maturity in lowland switchgrass populations

Switchgrass (Panicum virgatum L.) has potential to be a major cellulosic bioenergy crop. Selection for late flowering plants will extend the vegetative growth, likely resulting in larger biomass yields. However, the genetic structure for reproductive maturity in switchgrass is undefined. Accordingly, the major objective of this study was to identify genomic regions associated with reproductive development. Two lowland populations, one consisting of 176 progeny from NL94 (♀) × SL93 (♂) and a first-generation self-fertilized population of 265 progeny from NL94, were field established in a randomized complete block design with three replications at two Oklahoma locations in 2011. Phenotypic data of reproductive maturity in the populations were collected in 2012 and 2013. Significant genetic variation for reproductive maturity was observed within the two populations. Broad-sense heritabilities were 0.46 to 0.77 and 0.28 to 0.74 for the hybrid and selfed populations, respectively. A linkage map with 178 simple sequence repeat (SSR) markers of the hybrid population constructed in this study and a pre-existing linkage map of 439 SSR markers in the selfed population were used for quantitative trait loci (QTL) characterization. QTL analyses revealed that reproductive maturity was controlled by multiple genomic regions. The QTL regions between nfsg-125 and PVE-781/782 on linkage group (LG) 2b, between PVGA-1727/1728 and PVGA-1201/1202 on LG 3b, and between PVCAG-2503/2504 and PVAAG-3253/3254 on LG 7a were associated with reproductive maturity in both populations. The markers linked to the significant QTL could be used to accelerate the development of switchgrass germplasm with later flowering to increase biomass yield.

SSR Marker Development, Linkage Mapping, and QTL Analysis for Establishment Rate in Common Bermudagrass

Common bermudagrass has been widely used as a major warm‐season turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs). A linkage map was constructed using a first‐generation selfed population derived from a genotype A12359 (2n = 4x = 36). A total of 249 polymorphic SSR PPs were mapped to 18 linkage groups (LGs). The total length of the map is 1094.7 cM, with an average marker interval of 4.3 cM. Ninety‐eight out of 252 mapped loci (39%) were found to be distorted from the Mendelian 1:2:1 segregation ratio. Among the other 154 nondistorted loci, 88 coupling vs. 66 repulsion linkage phases were observed to confirm the allopolyploid origin of the parent. Ground coverage (GCR) phenotypic data in the establishment stage were collected in two replicated field trials. Quantitative trait loci mapping identified five genomic regions significantly related to the trait. The findings of this study provide valuable genetic tools and resources for genomic research, genetic improvement, and breeding new cultivars in the species.

Disomic Inheritance and Segregation Distortion of SSR Markers in Two Populations of Cynodon dactylon (L.) Pers. var. dactylon.

Common bermudagrass [C. dactylon (L.) Pers. var. dactylon] is economically and environmentally the most important member among Cynodon species because of its extensive use for turf, forage and soil erosion control in the world. However, information regarding the inheritance within the taxon is limited. Accordingly, the objective of this study was to determine qualitative inheritance mode in common bermudagrass. Two tetraploid (2n = 4x = 36), first-generation selfed (S1) populations, 228 progenies of ‘Zebra’ and 273 from A12359, were analyzed for segregation with 21 and 12 simple sequence repeat (SSR) markers, respectively. It is concluded that the inheritance mode of tetraploid bermudagrass was complete or near complete disomic. It is evident that the two bermudagrass parents had an allotetraploid genome with two distinct subgenomes since 33 SSR primer pairs amplified 34 loci, each having two alleles. Severe transmission ratio distortions occurred in the Zebra population while less so in the A12359 population. The findings of disomic inheritance and segregation ratio distortion in common bermudagrass is significant in subsequent linkage map construction, quantitative trait locus mapping and marker-assisted selection in the species.

Quantitative Trait Loci Mapping for Tillering-Related Traits in Two Switchgrass Populations.

Phenotypic data for six tillering traits related to biomass yield in two populations were assessed in two field trials. Associations between phenotypic data and two preexisting linkage maps were analyzed. Twenty QTL were identified in a hybrid population. Twenty‐six QTL were identified in a selfed population. Two significant QTL were stably expressed in multiple environments in the two populations.