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

Abstract

BackgroundSNPs 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0678-1) contains supplementary material, which is available to authorized users.

Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors

“…The highly concentrated TEs in the middle of chromosomes may form heterochromatin areas in order to condense chromatin. Large regions of recombination suppression are present near centromeric or pericentromeric regions on each of the 26 chromosomes in G. hirsutum (Wang et al ). Perhaps Gypsy is involved in forming the large heterochromatin regions in the middle of chromosomes.…”

High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L

“…Wang et al constructed an ultra-dense genetic map consisting of 4,999,048 SNPs distributed across 4,042 cM, and these authors used their high-density genetic map for genome assembly of Gossypium hirsutum acc. TM-1 [21]. Wang et al applied the RAD-seq technique to upland cotton and identified 21,109 SNPs based on the genome sequence of G. hirsutum TM-1.…”

“…Because anonymous marker-based maps are becoming saturated, a genetic map based on conventional markers cannot achieve the resolution required for fine QTL mapping or positional cloning. Single nucleotide polymorphisms (SNPs) are highly abundant and suitable for high-density genetic mapping [20, 21]. Restriction-site associated DNA sequencing (RAD-seq) is a powerful and cost-effective method for detecting genetic variations [22, 23] and has become widely applied in plants [24–28].…”

Genome Mapping in Plant Comparative Genomics

“…The cotton system serves as an excellent model for identifying structural variations between species (Figure 1), more specifically, examining nonreciprocal homoeologous recombination, intergenomic spread of transposable elements, and alterations and biases in gene duplicate expression. Research has shown some evidence of chromosomal rearrangements between the homoeologous genomes in polyploids [65,67,69], but it is still not completely understood how genome variations compare across different cotton species and genomes. Genome mapping could be useful in pinpointing segmental losses and exchanges among homoeologous chromosomes, which are important aspects of polyploidy genome evolution [60].…”