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Restriction site‐associated DNA sequencing allows for the rapid identification of simple sequence repeat markers in Echinochloa crus‐galli
Author(s) -
Chen Guoqi,
Zhang Wei,
Fang Jiangpeng,
Dong Liyao
Publication year - 2017
Publication title -
weed biology and management
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.351
H-Index - 36
eISSN - 1445-6664
pISSN - 1444-6162
DOI - 10.1111/wbm.12119
Subject(s) - biology , microsatellite , genetic diversity , genetics , echinochloa crus galli , echinochloa , dna sequencing , population , allele , dna , weed , gene , botany , demography , sociology
Echinochloa crus‐galli is a serious weed worldwide. Microsatellite markers (simple sequence repeats, SSR s) are important molecular markers that are used widely for studying genetic diversity in plants. However, a limited number of SSR s 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 SSR s 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 SSR s were detected, of which 82.2% were dinucleotide motif‐repeats. AT was the most frequent motif, accounting for 35.0% of the SSR s. In order to test the validity of the SSR s that were developed here, eight SSR s that were selected from putative SSR s 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 SSR s that were identified in this study represent a valuable resource for studying the genetic diversity, population biology and evolution of E. crus‐galli .