A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome

Abstract

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.

Screening of highly informative and representative microsatellite markers for genotyping of major cultivated cotton varieties

“…In previous studies, accessions with significantly different phenotypes and genetic backgrounds were used for primer screening, and the obtained markers were applied for genetic diversity assessment, genetic map construction, quantitative trait loci mapping, etc. (Bertini et al, 2006;Chen and Du, 2006;Pang et al, 2006;Guo et al, 2007;Pan et al, 2008;Yu et al, 2012b). These markers may represent polymorphisms between different Gossypium species.…”

“…Chromosome 5(c05) showed the most abundant polymorphic SSR markers with 13. Based on the genetic map by Yu et al (2012b), c05 showed the longest genetic distance. Among the 12 leading cultivars, a total of 559 polymorphic genotypes were detected by 184 SSR markers, with an average of 3.04 genotypes per SSR marker, ranging from 2-6.…”

Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations

“…Three hundred microsatellite primer pairs based on even distribution across 13 chromosomes (Park et al 2005;Guo et al 2007;Ma et al 2008;Yu et al 2012) were taken for initial screening. Of these, 100 primers were selected on the basis of polymorphic and reproducible band pattern (Table S2 in ESM; the sequence information available at http://www.cottonmarker.org).…”

Molecular Markers in Cotton Improvement

“…Several methods have been pursued to develop SSR markers in cottons, including analysis of SSR-enriched small insert genomic DNA libraries (Kalia et al, 2011;Udall et al, 2006;Ince et al, 2010;Richard et al, 1995), SSR mining from ESTs (Shaheen et al, 2009), and large-insert BAC derivation by end sequence analysis (Reddy et al, 2002).Cotton researchers have explored simple sequence repeats (SSRs) for studies the phylogenetic and diversity analysis (He et al, 2007;Lacape et al, 2007)genetic mapping and QTL analysis for different traits Lacape et al,2009;Park et al,2005;Xiao et al,2009;Yu et al, 2012, Michael et al, 2014and Tang, et al, 2015, association mapping (Kantartzi and stewart, 2008).…”