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Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.

Wang H, Jin X, Zhang B, Shen C, Lin Z - DNA Res. (2015)

Bottom Line: A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population.Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed.This map can be used for molecular marker-assisted selection in cotton.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

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Characteristics and distribution of InDels and SNPs in two RAD libraries. (a) Distribution of insertions (+) and deletions (−). (b) Transitions and transversions occurring within the mined SNPs.
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DSU047F6: Characteristics and distribution of InDels and SNPs in two RAD libraries. (a) Distribution of insertions (+) and deletions (−). (b) Transitions and transversions occurring within the mined SNPs.

Mentions: InDel calling showed there to be 3,558 InDels after mapping DH962 reads to Jimian5 assembled contigs (D/J-I) and 3,240 InDels after mapping Jimian5 reads to DH962 assembled contigs (J/D-I). The called results that conformed to any one of the conditions {MQ0 ≥ 4 [[MQ0/(1.0 * DP)] > 0.1]; MQ < 30.0; QUAL < 50; DP < 5} were removed. After filtering, the mapping of D/J-I included 3,119 InDels, and the mapping of J/D-I included 2,869 InDels. The frequency of InDels was 1/18.46 kb. Among the 3,119 InDels of D/J-I, 1,355 were insertions and 1,764 were deletions, with the average length of the InDels being 1.4 bp (Fig. 6a). Among the 2,869 InDels of J/D-I, 1,301 were insertions, and 1,568 were deletions. The average length of the InDels was 1.3 bp (Fig. 6a). After BLAST of the flanking sequences of InDels, 1,686 InDels were found to appear only in D/J-I (Supplementary Table S3a), and 1,477 InDels appeared only in J/D-I (Supplementary Table S3b), with 675 InDels appearing in both (Supplementary Table S3c). Among the 675 sites, there were 121 sites between DH962 and Jimian5 that were homozygous and polymorphic (Supplementary Table S3d). A total of 3,838 InDel primer pairs were obtained (Fig. 1).Figure 6.


Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.

Wang H, Jin X, Zhang B, Shen C, Lin Z - DNA Res. (2015)

Characteristics and distribution of InDels and SNPs in two RAD libraries. (a) Distribution of insertions (+) and deletions (−). (b) Transitions and transversions occurring within the mined SNPs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401325&req=5

DSU047F6: Characteristics and distribution of InDels and SNPs in two RAD libraries. (a) Distribution of insertions (+) and deletions (−). (b) Transitions and transversions occurring within the mined SNPs.
Mentions: InDel calling showed there to be 3,558 InDels after mapping DH962 reads to Jimian5 assembled contigs (D/J-I) and 3,240 InDels after mapping Jimian5 reads to DH962 assembled contigs (J/D-I). The called results that conformed to any one of the conditions {MQ0 ≥ 4 [[MQ0/(1.0 * DP)] > 0.1]; MQ < 30.0; QUAL < 50; DP < 5} were removed. After filtering, the mapping of D/J-I included 3,119 InDels, and the mapping of J/D-I included 2,869 InDels. The frequency of InDels was 1/18.46 kb. Among the 3,119 InDels of D/J-I, 1,355 were insertions and 1,764 were deletions, with the average length of the InDels being 1.4 bp (Fig. 6a). Among the 2,869 InDels of J/D-I, 1,301 were insertions, and 1,568 were deletions. The average length of the InDels was 1.3 bp (Fig. 6a). After BLAST of the flanking sequences of InDels, 1,686 InDels were found to appear only in D/J-I (Supplementary Table S3a), and 1,477 InDels appeared only in J/D-I (Supplementary Table S3b), with 675 InDels appearing in both (Supplementary Table S3c). Among the 675 sites, there were 121 sites between DH962 and Jimian5 that were homozygous and polymorphic (Supplementary Table S3d). A total of 3,838 InDel primer pairs were obtained (Fig. 1).Figure 6.

Bottom Line: A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population.Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed.This map can be used for molecular marker-assisted selection in cotton.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

Show MeSH