Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae

Abstract

Bermudagrass ( Cynodon dactylon Pers.) is an important warm-season perennial used extensively for turf, forage, soil conservation and remediation worldwide. However, limited genomic information has hindered the application of molecular tools towards understanding genome evolution and in breeding new cultivars. We genotype a first-generation selfed population derived from the tetraploid (4x = 36) ‘A12359’ using genotyping-by-sequencing. A high-density genetic map of 18 linkage groups (LGs) is constructed with 3,544 markers. Comparative genomic analyses reveal that each of nine homeologous LG pairs of C. dactylon corresponds to one of the first nine chromosomes of Oropetium thomaeum . Two nested paleo-ancestor chromosome fusions (ρ6-ρ9-ρ6, ρ2-ρ10-ρ2) may have resulted in a 12-to-10 chromosome reduction. A segmental dissemination of the paleo-chromosome ρ12 (ρ1-ρ12-ρ1, ρ6-ρ12-ρ6) leads to the 10-to-9 chromosome reduction in C. dactylon genome. The genetic map will assist in an ongoing whole genome sequence assembly and facilitate marker-assisted selection (MAS) in developing new cultivars.

The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis)

“…3 and 4 ). Similarly, another Cynodon species, C. dactylon, was reported to have a high degree of chromosome-level collinearity with two Chloridoideae grasses, including Z. japonica 53 . According to the phylogenetic analysis, C. transvaalensis and Z. japonica diverged from the MRCA ∼23.6 Mya, and they shared an MRCA with the Panicoideae subfamily species ( S. bicolor , S. italica , S. viridis , and Z. mays ) belonging to the “PACMAD” clade ∼40.6 Mya, whereas ∼47.3 Mya, they shared an MRCS with Bambusoideae ( P. edulis ), Oryzoideae ( O. sativa ), and Pooideae subfamily species ( A. tauschii , B. distachyon, H. vulgare ) belonging to the “BOP” clade (Bambusoideae, Oryzoideae, and Pooideae), which is consistent with previous studies 17 , 53 , 54 .…”

Comparative analysis reveals chromosome number reductions in the evolution of African bermudagrass (Cynodon transvaalensisBurtt-Davy)

“…The top hits of SNP marker sequences showing synteny to the genome of Oropetium thomaeum were extracted for comparative analysis. A genomic synteny dot plot was generated using R (version 3.5.2) (R Core Team 2018) with customized scripts based on Fang et al (2020). A Circos plot was generated in R using the circlize package (Gu et al 2014).…”

“…The Cynodon species have a basic chromosome number of nine, with African bermudagrass being a diploid (2n = 2x = 18) species and common bermudagrass predominantly a tetraploid (2n = 4x = 36) species (Forbes and Burton 1963). Although lagging behind other subfamilies, the evolutionary history of the Chloridoideae subfamily has drawn attention in molecular investigations recently (Srinivasachary et al 2007; F. Huang et al 2016;Fang et al 2020). The 12-to-9 chromosome reduction in the Cynodon genus has been an intriguing evolutionary question.…”

“…Comparative mapping studies in zoysiagrass revealed two NCFs (ρ6-ρ9-ρ6 and ρ2-ρ10-ρ2) that explained the reduction of the basic chromosome number from 12 to 10 (F. Huang et al 2016). Recently, a comparative genomic analysis among tetraploid C. dactylon (2n = 4x = 36), Oryza sativa (2n = 2x = 24), and Oropetium thomaeum (2n = 2x = 20) shed light on the mechanism of the 10-to-9 chromosome reduction in Cynodon with two NCFs (ρ1-ρ12-ρ1 and ρ6-ρ12-ρ6) (Fang et al 2020). However, no information is available regarding the chromosome number reduction in diploid African bermudagrass (2n = 2x = 18).…”

Genetic and QTL mapping in African bermudagrass

“…Khanal et al (2017) also reported that most C. transvaalensis LGs corresponded to two C. dactylon LGs and some C. transvaalensis LGs corresponded to either one or three C. dactylon LGs. Cynodon dactylon was considered an allopolyploid tetraploid species (Fang et al, 2020;Gong, Xue, Zhang, & Wang, 2013;Guo, Wu, Anderson, Moss, & Zhu, 2015). More research is needed to definitively characterize the genomic relationship between the two closely related species.…”