BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

Abstract

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.

Keywords: BAC-derived SNPs; SNP genotyping; cotton genomics; intraspecific; resequencing.

Figure 1

Distance between polymorphisms developed in (A) G. hirsutum, (B) G. barbadense, and (C) G. longicalyx relative to the G. hirsutum-derived BAC-end sequences.

Figure 2

Overlap of SNPs identified using G. hirsutum, G. barbadense, and G. longicalyx samples.

Figure 3

Linkage groups determined utilizing 118 interspecific (G. barbadense line 3-79 × G. hirsutum line TM-1) F₂ samples for BAC-end–derived SNPs in JoinMap.

Figure 4

Dendrogram produced by hierarchical clustering utilizing BAC-end sequence-associated SNPs for 12 G. hirsutum samples (TM-1, Sealand 542, PD-1, Paymaster HS-26, M-240 RNR, Fibermax 832, Coker 312, SureGrow 747, Stoneville 474, Tamcot Sphinx, Acala Maxxa, TX0231), G. barbadense (3-79), and G. longicalyx using the SNPRelate package in R.