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They were subjected to preliminary linkage analysis with 83 DNA markers distributed on the whole rice genome (for details, see Materials and methods).
A set of 19 simple sequence repeat (SSR) markers distributed on the 12 chromosomes was genotyped on the 147 Myanmar accessions and the 31 reference set accessions from group 5.
For HWA2 mapping, a total of 84 DNA markers distributed on the whole rice genome were used: the 23 polymorphic indel markers presented in Fig. 2, 59 SSR markers, and two indel markers designed by RGP S21074 and S5865.
The concentrations of primers, template DNA, Master Mix, and annealing temperature was optimized on eight diverse accessions for 156 SSR markers distributed on the 12 chromosomes by modified Taguchi method (Cobb and CIarkson 1994).
For HWA1 mapping, a total of 83 DNA markers distributed on the whole rice genome were used: 24 polymorphic indel markers in Fig. 2, an indel marker named S21074 designed by RGP, another indel marker named Knindel1 (Matsubara et al. 2007), a sequence characterized amplified region (SCAR) marker named d (Ueda et al. 2005), and 56 published SSR markers.
In each generation, genotyping was performed by using MIT markers distributed on the desired chromosome (Fig. 1).
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Twenty-eight RFLP markers distributing on 12 rice chromosomes were selected and used to estimate the subspecies index of rice lines in one double haploid (DH) and one recombinant inbred line (RIL) population.
A single plant of each line was analysed with SSR markers distributing on the 12 chromosomes of rice, and an RHL carrying a heterozygous segment that covers a major portion of the short arm of rice chromosome 6 was selected.
To confirm the chromosomal localization of the Z3 locus, we initially mapped the z3 mutation using 291 F2 plants with the z3 mutant phenotype, 9 simple sequence repeat (SSR) markers, and one sequence-tagged site (STS) marker distributed on chromosome 3. SSR marker information is available in GRAMENE (http://www.gramene.org).org
These microsatellite markers distributed evenly on 24 linkage groups and were genotyped on a 3730xl DNA analyzer (Applied Biosystems) after PCR amplification using fluorescently labeled primers.
The first set was 53 SSR markers distributed evenly on 12 chromosomes and used to infer structure of the population (Additional file 1: Table S2).
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