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The International Cotton Genome Initiative (ICGI) was launched to facilitate the development of a saturated and fully integrated genetic and physical map of cotton [ 1].
To achieve a maximum number of anchor points, a 13-linkage-group consensus map of cotton, constructed by integration of At, Dt, and D genome genetic maps [ 14] was used to anchor contigs.
With an endless effort to construct a high-density genetic map of cotton in our laboratory, we have tried RAPDs, SRAPs, and SSRs when no sufficient easy-to-use markers such as SSRs in cotton were available [ 5, 23].
Since the first genetic map of cotton was published in 1994 [ 14], several high-density genetic maps composed of more than 2,000 loci have been released [ 15- 18].
The approach used in this study should prove useful in the construction of genome-wide physical maps for other polyploid plant genomes including Upland cotton; EST unigenes could be integrated into the BAC contig map to construct transcript map of cotton by overgo hybridization and sequence comparison, and thus gene-rich islands could be identified for function genomics.
Similar(54)
Comparable with a linkage map of rice based on population sequencing with 15,795 SNPs (Xie et al. 2010) and a Brassica genetic map of 13,551 sequence-related amplified polymorphism markers (Sun et al. 2007), this map may facilitate fine mapping, gene cloning, global association mapping of cotton genes and traits, and other genomic studies.
BAC-end sequences from these contigs also were used to blast against all the STSs mapped in the integrated genetic and physical map of tetraploid cotton at an expected value of 1e−30.
BAC DNA isolation, fingerprinting, contig assembly were same as [50] except that DNA fingerprinting raw data were edited using "GenoProfiler" [51] which is different from the one (ABI-to-FPC, unpublished) used for whole genome physical map of tetraploid cotton.
In the current integrated genetic and physical map of tetraploid cotton, there are 10,416 STS markers, including 3,614 BAC-end sequences, 6,152 genetic loci with whole fragment sequences, and 750 sub-clone sequences (Xu et al., under preparation).
To refine our previously-constructed genetic linkage map of tetraploid cotton, we screened more than 2000 primer pairs.
In this study, 535 polymorphic loci were identified, and a genetic map of upland cotton containing 1,013 loci was constructed.
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