Weed Biology and Management (2017) 17, 68-76

Guoqi Chen, Wei Zhang, Jiangpeng Fang and Liyao Dong (2017)
Restriction site-associated DNA sequencing allows for the rapid identification of simple sequence repeat markers in Echinochloa crus-galli
Weed Biology and Management 17 (2), 68-76
Abstract: Echinochloa crus-galli is a serious weed worldwide. Microsatellite markers (simple sequence repeats, SSRs) are important molecular markers that are used widely for studying genetic diversity in plants. However, a limited number of SSRs is available for E. crus-galli. The restriction site-associated DNA (RAD) sequencing approach was combined with Illumina DNA sequencing for the rapid and mass detection of SSRs in E. crus-galli. The RAD tags were generated from the genomic DNA of E. crus-galli and were sequenced in order to produce 6921.6 Mb of high-quality sequences with 45.1% guanine–cytosine content. In total, 3081 putative SSRs were detected, of which 82.2% were dinucleotide motif-repeats. AT was the most frequent motif, accounting for 35.0% of the SSRs. In order to test the validity of the SSRs that were developed here, eight SSRs that were selected from putative SSRs were used to study the genetic diversity and structures of 20 E. crus-galli populations that had been collected from rice fields in eastern China. Ninety-seven alleles were amplified from the eight microsatellite loci among the 20 E. crus-galli populations. These populations showed low genetic diversity and were classified on the basis of their genetic structures into three distinct groups that corresponded to the three regions of population sampling. The SSRs that were identified in this study represent a valuable resource for studying the genetic diversity, population biology and evolution of E. crus-galli.
(The abstract is excluded from the Creative Commons licence and has been copied with permission by the publisher.)
Link to article at publishers website
Database assignments for author(s): Liyao Dong

Research topic(s) for pests/diseases/weeds:
molecular biology - genes

---

Pest and/or beneficial records:

Beneficial	Pest/Disease/Weed	Crop/Product	Country	Quarant.
	Echinochloa crus-galli (weed)	Rice (Oryza)	China (NE)