Sequence‐tagged high‐density genetic maps of Zoysia japonica provide insights into genome evolution in Chloridoideae

Abstract

Summary Zoysiagrass (Zoysia spp.), belonging to the genus Zoysia in the subfamily Chloridoideae, is widely used in domestic lawns, sports fields and as forage. We constructed high‐density genetic maps of Zoysia japonica using a restriction site‐associated DNA sequencing (RAD‐Seq) approach and an F1 mapping population derived from a cross between ‘Carrizo’ and ‘El Toro’. Two linkage maps were constructed, one for each of the parents. A map consisting of 2408 RAD markers distributed on 21 linkage groups was constructed for ‘Carrizo’. Another map with 1230 RAD markers mapped on 20 linkage groups was constructed for ‘El Toro’. The average distance between adjacent markers of the two maps was at 0.56 and 1.4 cM, respectively. Comparative genomics analysis was carried out among zoysiagrass, rice and sorghum genomes and a highly conserved collinearity in the gene order was observed among the three genomes. Chromosome collinearity was disrupted at centromeric regions for each chromosome pair between zoysiagrass and sorghum genomes. However, no obvious synteny gaps were observed across the centromeric regions between zoysiagrass and rice genomes. Two homologous chromosomes for each of the 10 sorghum chromosomes were found in the zoysiagrass genome, indicating an allotetraploid origin for zoysiagrass. The reduction of the basic chromosome number from 12 to 10 in chloridoids and panicoids took place via independent single‐step nested chromosome fusion events after the two subfamilies diverged from a common ancestor. The genetic maps will assist in genome sequence assembly, targeted gene isolation and comparative genomic analyses among grasses.

Sequencing and comparative analyses of the genomes of zoysiagrasses

“…The authenticity of the assembled genome sequences was further evaluated by comparing the genome sequence of ‘Nagirizaki’ and the published Z. japonica linkage map of RAD markers. 8 We compared 1,230 marker-associated sequences on the Z. japonica ‘ El Toro’ linkage map developed by Wang et al 8 with the scaffold sequences of Zjn_r1.1 and found that 1,224 (99.5%) of the sequences were successfully located on Zjn_r1.1. The 135 scaffolds in Zjn_r1.1 were each anchored by three or more markers in the ‘El Toro’ linkage groups and the order of most of the markers was in good agreement with their physical positions on the scaffolds.…”

“…To confirm the genome coverage and the accuracy of the assembled genome sequences, the core eukaryotic genes were mapped using CEGMA, v2.5. 26 The quality of the assembled genome sequences was also confirmed using published DNA markers developed by Wang et al 8 The marker sequences of Z. japonica ‘El Toro’ linkage groups were mapped onto the genome sequences of ‘Nagirizaki’ using BLASTN 27 with an E-value cut-off of 1E−4 considering the length (95 bp) of the marker sequences.…”

“… 4 , 6 , 7 Moreover, sequence-tagged high-density genetic maps of Z. japonica were constructed and compared with those of Oryza sativa and Sorghum bicolor , revealing a highly conserved collinearity in the gene order of these genomes. 8 In parallel with the construction of genetic maps, transcriptome analyses have been used to identify abiotic stress-related genes 9 , 10 and genes that control tissue-specific anthocyanin pigmentation in Z. japonica . 11 A complete sequence of the chloroplast genome of Z. matrella L. Merr has also been published.…”

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

“…Akin to GBS, it also reduces the genome complexity by subsampling the restriction site of specific enzymes and can provide genomics-scale insights for orphan crops with no prior genomic information available. Many SNP-based genetic maps and association studies have been reported using a RAD sequencing platform in understudied grasses (Chutimanitsakun et al, 2011; Hegarty et al, 2013; Wang et al, 2013; Slavov et al, 2014; Varshney, 2015; Wang F. et al, 2015). …”

“…The Illumina GoldenGate has been the most widely used platform for SNP genotyping, while Sequenom MassARRAY platform-based SNP-typing assays are becoming popular as well (Oliver et al, 2011; Chagné et al, 2015). SNP-based high density linkage and transcriptome map construction using NGS data has been successful in wheat (Wu et al, 2015; Holtz et al, 2016), rice (Xie et al, 2010; Zhang et al, 2015), maize (Liu et al, 2010; Mahuku et al, 2016), barley (Chutimanitsakun et al, 2011; Obsa et al, 2016), perennial ryegrass (Pfender et al, 2011; Paina et al, 2016; Velmurugan et al, 2016), orchardgrass (Zhao et al, 2016), intermediate wheatgrass (Kantarski et al, 2017), and zoysia grass ( Zoysia japonica ) (Wang F. et al, 2015). NGS-derived SNP-based genetic maps are useful for comparative mapping and have great potential for cool-season perennial grasses with limited genomic information available.…”