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. 2015 May 24;16(1):108.
doi: 10.1186/s13059-015-0678-1.

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

Sen Wang  1 , Jiedan Chen  2 , Wenpan Zhang  3 , Yan Hu  4 , Lijing Chang  5 , Lei Fang  6 , Qiong Wang  7 , Fenni Lv  8 , Huaitong Wu  9 , Zhanfeng Si  10 , Shuqi Chen  11 , Caiping Cai  12 , Xiefei Zhu  13 , Baoliang Zhou  14 , Wangzhen Guo  15 , Tianzhen Zhang  16
Affiliations

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

Sen Wang et al. Genome Biol. .

Abstract

Background: SNPs are the most abundant polymorphism type, and have been explored in many crop genomic studies, including rice and maize. SNP discovery in allotetraploid cotton genomes has lagged behind that of other crops due to their complexity and polyploidy. In this study, genome-wide SNPs are detected systematically using next-generation sequencing and efficient SNP genotyping methods, and used to construct a linkage map and characterize the structural variations in polyploid cotton genomes.

Results: We construct an ultra-dense inter-specific genetic map comprising 4,999,048 SNP loci distributed unevenly in 26 allotetraploid cotton linkage groups and covering 4,042 cM. The map is used to order tetraploid cotton genome scaffolds for accurate assembly of G. hirsutum acc. TM-1. Recombination rates and hotspots are identified across the cotton genome by comparing the assembled draft sequence and the genetic map. Using this map, genome rearrangements and centromeric regions are identified in tetraploid cotton by combining information from the publicly-available G. raimondii genome with fluorescent in situ hybridization analysis.

Conclusions: We report the genotype-by-sequencing method used to identify millions of SNPs between G. hirsutum and G. barbadense. We construct and use an ultra-dense SNP map to correct sequence mis-assemblies, merge scaffolds into pseudomolecules corresponding to chromosomes, detect genome rearrangements, and identify centromeric regions in allotetraploid cottons. We find that the centromeric retro-element sequence of tetraploid cotton derived from the D subgenome progenitor might have invaded the A subgenome centromeres after allotetrapolyploid formation. This study serves as a valuable genomic resource for genetic research and breeding of cotton.

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Figures

Fig. 1
Fig. 1
Graphical representation of the high-quality linkage map of tetraploid cotton. Alignment of 4,049 bins along the 26 chromosomes reveals a pairwise BIT score (top-left diagonal) and REC score (low-right diagonal) in all pairs of marker bins, plotted here using CheckMatrix [82]. Red represents tight linkage; yellow represents weak linkage; and blue represents no linkage. The red along the diagonal and the lack of red off the diagonal indicate the high quality and strong statistical support of the map
Fig. 2
Fig. 2
Comparison of the genetic map of tetraploid cotton and the corresponding physical locations on the pseudo molecules of the D genome sequence of G. raimondii. TM-1 scaffolds in the 26 linkage groups (blue) were aligned to the D genome sequence of G. raimondii (yellow). Genome variations (green blocks) were identified
Fig. 3
Fig. 3
SNP distribution in the cotton genome. a Distribution of SNPs in the 26 chromosomes. The x-axis represents the physical distance along each chromosome, split into 50 kb windows. The green rectangles indicate SNP-poor regions. b Proportion of SNPs found in intergenic regions, introns, and exons
Fig. 4
Fig. 4
Recombination and bin map for 59 scored F2 individuals. a, c Frequency distribution of recombination nodes (RNs) per 2 Mb. The vertical scale indicates the number of recombination nodes (RNs); b, d Bin maps for the 59 scored F2 individual lines. Colored tracks represent the 59 individual lines of the THF2 population that were used for linkage map construction: red, alleles inherited from maternal parent (TM-1); blue, alleles inherited from paternal parent (Hai7124); yellow, alleles inherited from heterozygous genotype (TM-1 × Hai7124)F1. The horizontal scale indicates physical distance
Fig. 5
Fig. 5
The marker placements for the genetic map on the G. hirsutum acc. TM-1 chromosomes. The marker order on the y-axis is derived from the genetic maps and the marker order on the x-axis is derived from the physical maps. Both the relative genetic and physical distances of the chromosomes on the plots are represented by the cells of different sizes according to the ratio of the chromosome lengths. Cumulative genetic distance in cM and physical distance in bp are indicated on x-axis and y-axis, respectively. The red rectangles represent the recombination suppression regions (nearly flat shaded) which are predicted to be pericentromeric regions
Fig. 6
Fig. 6
Schematic diagrams of centromeric regions of G. hirsutum acc. TM-1. a Centromeric regions of the A subgenome were identified by GhCRs-5’LTR (green) and CRG1-5’LTR (orange). b Centromeric regions of the D subgenome were identified by GhCR1-5’LTR (red), GhCR3-5’LTR (blue), and CRG1-5’LTR (orange)
Fig. 7
Fig. 7
Neighbor-joining (NJ) phylogenetic tree based on RT amino acid sequences of GhCRs LTR from G. raimondii and G. hirsutum. Statistical support was evaluated by bootstrapping (1,000 replications); Green squares represent RTs from G. raimondii. Red and blue circles represent RTs from the A subgenome and D subgenome of TM-1, respectively. Hollow squares and circles represent RTs from scaffolds that were unanchored to chromosomes of G. raimondii and G. hirsutum, respectively
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