Abstract
A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.
Highlights
Four cotton (Gossypium) species (i.e., two diploid species, G. arboreum L. and G. herbaceum L. (n = x = 13) of the A genome, and two allotetraploid species, G. barbadense L. and G. hirsutum L. (n = 2x = 26) of the AD genome) contribute to the production of natural fiber around the world [1]
Reinisch et al [16] reported the first detailed RFLP genetic map in cotton using 57 F2 plants derived from a cross
The map consisted of 1,097 loci including sequence-related amplified polymorphism (SRAP), target-region amplified polymorphism (TRAP), AFLP, and SSR markers
Summary
Majority of the loci were represented by the RFLP markers This map provided one of the first insights into the genome structure and evolution of the allotetraploid cotton. Lacape et al [9] reported a consensus genetic map integrating 1,745 marker loci (AFLP, RFLP and SSR) from combined data from 2 populations (BC1 and RIL, totalling 215 individuals) involving Gh Guazuncho 2 and Gb VH8-4602. Though less comprehensive in genome coverage, other maps have been constructed using Gh intraspecific populations [19,20,21,22], a cross between G. hirsutum and G. tomentosum [23], and lastly, different crosses involving different diploid Gossypium species [18,24,25]
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