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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #328388
Title: Insights into upland cotton (Gossypium hirsutum l.) genetic recombination based on 3 high-density single-nucleotide polymorphism and a consensus map developed independently with common parents

Author
item Ulloa, Mauricio
item HULSE-KEMP, AMANDA - Texas A&M University
item STELLY, DAVID - Texas A&M University
item Burke, John

Submitted to: Genomics Insights
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2017
Publication Date: 10/12/2017
Citation: Ulloa, M., Hulse-Kemp, A.M., Stelly, D.M., Burke, J.J. 2017. Insights into upland cotton (Gossypium hirsutum l.) genetic recombination based on 3 high-density single-nucleotide polymorphism and a consensus map developed independently with common parents. Genomics Insights. 10:1-5.

Interpretive Summary: Cotton is the most important renewable natural textile fiber worldwide. In the last decade, considerable progress has been made towards the development of new cotton tools and genomic resources. However, genomic resources in cotton are still behind compared with other crops such as maize, sorghum, rice, soybeans, etc. With the availability of a new technology to sequence DNA or blueprints/genes called next generation sequencing, additional resources and platforms are being developed, and larger number of molecular markers such as single nucleotide polymorphism (SNP) are being identified in the cotton crop for assisting breeding. In this study, three high-density genetic linkage SNP maps and a consensus map or joinmap using the CottonSNP63K array were developed from three independently developed intra-specific Upland cotton populations. Molecular linkage maps based upon DNA markers serve as the backbone for genetic analyses and are widely recognized as an essential tool for genetic research in many crops. In addition, maps provide an excellent framework for discovering loci and/or genes responsible for traits of interest. This is the first intraspecific SNP genetic linkage joinmap assembled in Upland cotton with a core of reproducible SNP markers assayed on different populations, and it provides further knowledge on the order and arrangement of genes, chromosome arrangements, and relationships of progeny vs parents. Together, the joinmap and cotton populations provide a synergistically useful platform for expedited localization and identification of genes and agronomically important genes for improvement of the cotton crop.

Technical Abstract: High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement; high-density linkage maps are especially important in paleopolyploids with exceptionally complex genomes such as Upland cotton (Gossypium hirsutum L., 2n=52). Three independently developed intra-specific (G. hirsutum) mapping populations were used to develop three high-density genetic linkage single nucleotide polymorphism (SNP) maps, plus a consensus map or joinmap; the populations consisted of a previously reported F2, a recombinant inbred line (RIL), and reciprocal RIL from the cultivars ‘Phytogen 72’ (PHY72) and ‘Stoneville 474’ (STV474). The CottonSNP63K array and cluster file provided 7,417 genotyped SNP markers. The F2 population averaged 49.4 % heterozygote loci, whereas the RIL and reciprocal populations averaged 1.51 % and 1.92 % heterozygote loci, respectively. Overall, more than 7,000 SNPs were mapped in all three populations, each resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid Upland cotton (AD)1. The two RIL-based maps were about 7% and 10% longer than the F2-based map. The high-density genetic joinmap included 7,244 SNP markers that spanned 3,538 cM, and comprised 3,824 SNP bins, of which 1,783 and 2,041 were in the At and Dt subgenomes with 1,825 and 1,713 cM map lengths, respectively. Bins of the joinmap averaged 1.89 SNPs and 0.92 cM length, while marker spacing averaged 0.49 cM. The At-and Dt-subgenome chromosomes that were most and least recombinant were the homeologous pairs c06/c25, and the segmentally homeologous pairs c05/c19, respectively. Comparative alignment analyses identified historical ancestral At-subgenomic translocations of c02 and c03, as well as to c04 and c05. The joinmap SNP sequences aligned with high congruency to the NBI assembly of G. hirsutum, and genomic comparisons revealed that some joinmap At-subgenome linkage group-SNP sequences were absent from the NBI At-subgenome sequence assembly, and these absent sequences were sometime included in NBI Dt-subgenome sequence assembly. This finding may merely reflect analytical bias resulting from differences in coverage of the At- and Dt-subgenome assemblies and that the sequence genome assembly needs improvement; additionally, it could indicate directionality of “crosstalk” between At and Dt subgenomes following polyploidization. The alignments also indicated that 364 SNP-associated unintegrated scaffolds could be placed onto pseudochromosomes of the NBI G. hirsutum assembly, prospectively increasing coverage by 47.7 Mbp. This is the first intraspecific SNP genetic linkage joinmap assembled in G. hirsutum with a core of reproducible Mendelian-SNP markers assayed on different populations, and it provides further knowledge on the order and arrangement of genic and non-genic SNPs, chromosome arrangements and parental relationships. Together, the joinmap and RIL populations provide a synergistically useful platform for expedited localization and identification of genes and agronomically important loci for improvement of the cotton crop.