Eremochloa ophiuroides strain:TifBlair
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA275556 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1811564_1.fastq.gz | Fastqsanger.gz | |||
| SRR1811564_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Genetic diversity is the heritable variation within and among populations, and in the context of this paper describes the heritable variation among the germplasm resources of centipedegrass. Centipedegrass is an important warm-season perennial C4 grass belonging to the Poaceae family in the subfamily Panicoideae and genus Eremochloa. It is the only species cultivated for turf among the eight species in Eremochloa. The center of origin for this species is southern to central China. Although centipedegrass is an excellent lawn grass and is most widely used in the southeastern United States, China has the largest reserve of centipedegrass germplasm in the world. Presently, the gene bank in China holds ~200 centipedegrass accessions collected from geographical regions that are diverse in terms of climate and elevation. This collection appears to have broad variability with regard to morphological and physiological characteristics. To efficiently develop new centipedegrass varieties and improve cultivated species by fully utilizing this variability, multiple approaches have been implemented in recent years to detect the extent of variation and to unravel the patterns of genetic diversity among centipedegrass collections. In this review, we briefly summarize research progress in investigating the diversity of centipedegrass using morphological, physiological, cytological, and molecular biological approaches, and present the current status of genomic studies in centipedegrass. Perspectives on future research on genetics and genomics and modern breeding of centipedegrass are also discussed.
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Project description:Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is a perennial, warm-season C4 grass species that shows great potential for use as a low-maintenance turfgrass species in tropical and subtropical regions. However, limited genetic and genomic information is available for this species, which has impeded systematic studies on the enhancement of its turf quality and resistance against biotic and abiotic stress. In this study, Illumina HiSeq high-throughput sequencing technology was performed to generate centipedegrass transcriptome sequences. A total of 352,513 assembled sequences were used to search for simple sequence repeat (SSR) loci, and 64,470 SSR loci were detected in 47,638 SSR containing sequences. The tri-nucleotides were the most frequent repeat motif, followed by di-nucleotides, tetra-nucleotides hexnucleotides, and pentanucleotides. A total of 48,061 primer pairs were successfully designed in the flanking sequences of the SSRs, and 100 sets of primers were randomly selected for the initial validation in four centipedegrass accessions. In total, 56 (56.0%) of the 100 primer pairs tested successfully amplified alleles from all four centipedegrass accessions, while 50 were identified as polymorphic markers and were then used to assess the level of genetic diversity among 43 centipedegrass core collections. The genetic diversity analysis exhibited that the number of alleles (Na) per locus ranged from 3 to 13, and the observed heterozygosity (Ho) ranged from 0.17 to 0.83. The polymorphism information content (PIC) value of the markers ranged from 0.15 to 0.78, and the genetic distances (coefficient Nei72) between the accessions varied from 0.07 to 0.48. The UPGMA-based dendrogram clustered all 43 core collections into two main groups and six subgroups, which further validated the effectiveness of these newly developed SSR markers. Hence, these newly developed SSR markers will be valuable and potentially useful for future genetic and genomic studies of E. ophiuroides.
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