Limits...
Molecular Mapping of Restriction-Site Associated DNA Markers In Allotetraploid Upland Cotton.

Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H, Ai N, Guo W, Zhang T - PLoS ONE (2015)

Bottom Line: Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton.Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result.It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.

ABSTRACT
Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.

No MeSH data available.


Related in: MedlinePlus

QTLs for fiber strength in two maps.Three QTLs for fiber strength, qFS-D3-1, qFS-A9-1, qFS-A7-1 were identified on both maps, with the different colors indicating different 2-LOD intervals for each QTL. Maps were constructed with RAD markers plus SSR markers, and with SSR markers alone. Lines connecting the same markers in these two maps correlated the trait: these markers are colored brown.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4403916&req=5

pone.0124781.g002: QTLs for fiber strength in two maps.Three QTLs for fiber strength, qFS-D3-1, qFS-A9-1, qFS-A7-1 were identified on both maps, with the different colors indicating different 2-LOD intervals for each QTL. Maps were constructed with RAD markers plus SSR markers, and with SSR markers alone. Lines connecting the same markers in these two maps correlated the trait: these markers are colored brown.

Mentions: The newly constructed enhanced RAD genetic map was used to tag QTLs for fiber strength and VW resistance. Thirteen non-redundant QTLs for fiber strength and ten non-redundant QTLs for VW resistance were detected (Table 4). Most of these QTLs were also detected by Ning et al. using the SSR genetic map, including qFS-D3-1, qFS-A9-1, and qFS-A7-1 for fiber strength, and qVW-D9-1, qVW-A9-1, qVW-D2-1, and qVW-A1-1 for VW resistance (Figs 2 and 3).


Molecular Mapping of Restriction-Site Associated DNA Markers In Allotetraploid Upland Cotton.

Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H, Ai N, Guo W, Zhang T - PLoS ONE (2015)

QTLs for fiber strength in two maps.Three QTLs for fiber strength, qFS-D3-1, qFS-A9-1, qFS-A7-1 were identified on both maps, with the different colors indicating different 2-LOD intervals for each QTL. Maps were constructed with RAD markers plus SSR markers, and with SSR markers alone. Lines connecting the same markers in these two maps correlated the trait: these markers are colored brown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403916&req=5

pone.0124781.g002: QTLs for fiber strength in two maps.Three QTLs for fiber strength, qFS-D3-1, qFS-A9-1, qFS-A7-1 were identified on both maps, with the different colors indicating different 2-LOD intervals for each QTL. Maps were constructed with RAD markers plus SSR markers, and with SSR markers alone. Lines connecting the same markers in these two maps correlated the trait: these markers are colored brown.
Mentions: The newly constructed enhanced RAD genetic map was used to tag QTLs for fiber strength and VW resistance. Thirteen non-redundant QTLs for fiber strength and ten non-redundant QTLs for VW resistance were detected (Table 4). Most of these QTLs were also detected by Ning et al. using the SSR genetic map, including qFS-D3-1, qFS-A9-1, and qFS-A7-1 for fiber strength, and qVW-D9-1, qVW-A9-1, qVW-D2-1, and qVW-A1-1 for VW resistance (Figs 2 and 3).

Bottom Line: Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton.Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result.It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.

ABSTRACT
Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.

No MeSH data available.


Related in: MedlinePlus