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Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM - G3 (Bethesda) (2015)

Bottom Line: Hutchinson and Lee.The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines.The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843.

No MeSH data available.


Dot plot of the syntenic positions of SNP markers in the allotetraploid linkage maps vs. the JGI G. raimondii reference genome. The 26 allotetraploid chromosomes are shown on the y-axis and the 13 chromosomes of G. raimondii are shown on the x-axis. Red arrows indicate translocation events relative to G. raimondii. (A) Intraspecific linkage map displaying positions of 4521 mapped SNP in G. hirsutum with alignments to G. raimondii. (B) Interspecific linkage map (G. barbadense line 3-79 by G. hirsutum genetic standard line Texas Marker -1) displaying positions of 12,027 mapped SNP with alignments to G. raimondii.
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fig9: Dot plot of the syntenic positions of SNP markers in the allotetraploid linkage maps vs. the JGI G. raimondii reference genome. The 26 allotetraploid chromosomes are shown on the y-axis and the 13 chromosomes of G. raimondii are shown on the x-axis. Red arrows indicate translocation events relative to G. raimondii. (A) Intraspecific linkage map displaying positions of 4521 mapped SNP in G. hirsutum with alignments to G. raimondii. (B) Interspecific linkage map (G. barbadense line 3-79 by G. hirsutum genetic standard line Texas Marker -1) displaying positions of 12,027 mapped SNP with alignments to G. raimondii.

Mentions: All of the 70,000 putative SNP markers that were used for production of the CottonSNP63K array were aligned to the D5 reference genome using BWA in Galaxy; 59.7% of the markers produced alignments to the reference. Synteny was detected for a total of 4521 and 12,027 mapped SNPs for the intraspecific and interspecific maps, respectively. Dot plots of the linkage maps vs. the D5 reference genome show high collinearity across linkage groups and chromosomes as expected, except for four A-subgenome chromosomes, which are known to contain translocations relative to D-chromosomes. Translocations involving chromosomes 2, 3, 4, and 5 were identified in both maps and are indicated in Figure 9, A and B.


Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM - G3 (Bethesda) (2015)

Dot plot of the syntenic positions of SNP markers in the allotetraploid linkage maps vs. the JGI G. raimondii reference genome. The 26 allotetraploid chromosomes are shown on the y-axis and the 13 chromosomes of G. raimondii are shown on the x-axis. Red arrows indicate translocation events relative to G. raimondii. (A) Intraspecific linkage map displaying positions of 4521 mapped SNP in G. hirsutum with alignments to G. raimondii. (B) Interspecific linkage map (G. barbadense line 3-79 by G. hirsutum genetic standard line Texas Marker -1) displaying positions of 12,027 mapped SNP with alignments to G. raimondii.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478548&req=5

fig9: Dot plot of the syntenic positions of SNP markers in the allotetraploid linkage maps vs. the JGI G. raimondii reference genome. The 26 allotetraploid chromosomes are shown on the y-axis and the 13 chromosomes of G. raimondii are shown on the x-axis. Red arrows indicate translocation events relative to G. raimondii. (A) Intraspecific linkage map displaying positions of 4521 mapped SNP in G. hirsutum with alignments to G. raimondii. (B) Interspecific linkage map (G. barbadense line 3-79 by G. hirsutum genetic standard line Texas Marker -1) displaying positions of 12,027 mapped SNP with alignments to G. raimondii.
Mentions: All of the 70,000 putative SNP markers that were used for production of the CottonSNP63K array were aligned to the D5 reference genome using BWA in Galaxy; 59.7% of the markers produced alignments to the reference. Synteny was detected for a total of 4521 and 12,027 mapped SNPs for the intraspecific and interspecific maps, respectively. Dot plots of the linkage maps vs. the D5 reference genome show high collinearity across linkage groups and chromosomes as expected, except for four A-subgenome chromosomes, which are known to contain translocations relative to D-chromosomes. Translocations involving chromosomes 2, 3, 4, and 5 were identified in both maps and are indicated in Figure 9, A and B.

Bottom Line: Hutchinson and Lee.The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines.The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843.

No MeSH data available.