Towards Effective Use of Gossypium A2 and D1 Genomes for Improvement of Upland Cotton.

Upland cotton (Gossypium hirsutum L.) contributes to over 90% of the globally produced cotton. Genetic improvement efforts must contend with relatively low levels of diversity due to reasons such as the self-fertilizing reproductive biology, low mutation rate and recent polyploidization; diversity among domesticated and modern elite types is even lower. With over 45 wild species within the Gossypium genus that have several agronomic traits of interest, cotton has abundant naturally occurring diversity that can be introgressed into the elite cultivars. However, introgression breeding into Upland cotton is time-consuming, labor intensive and complicated by reproductive physiology, differences in ploidy and meiotic affinity of genomes, chromosomal rearrangements, cytoplasmic male sterility, F1 sterility, hybrid lethality and other deleterious genetic interactions. We aim to study and facilitate diploid germplasm introgression breeding using a marker-assisted approach. Hybridization of G. arboreum (A2 genome, n=13) and G. thurberi (D1 genome, n=13), followed by chromosome doubling of the resulting F1 hybrid yielded a semi-fertile synthetic tetraploid, 2[A2D1]. More recently, we crossed the A2D1 synthetic to the inbred Upland line TM-1 and then backcrossed the F1 to TM-1 to develop a mapping population of 73 BC1F1 individuals. To develop SNP resources applicable to mapping and marker-assisted selection (MAS), we developed a diploid cluster file for the CottonSNP63K Array that includes Infinium II assays for over 63,000 potential SNPs. Using the Array and cluster file, we auto-genotyped 16,612 SNPs across all 73 BC1F1 hybrids. We then constructed a high-density genetic linkage map of SNP markers using the JoinMap 4.0 software. We grouped loci according to the maximum likelihood algorithm, and selected linkage groups (LGs) with LOD scores over 10, resulting in 26 linkage groups and a total of 5797 mapped loci. The LGs correspond to the 26 chromosomes and span 9143 cM. We analyzed map order by constructing and visually examining 2D Matrix Plots of the linkage groups constructed with CheckMatrix software. This information, along with comparisons to another recently published map of SNP markers based on the CottonSNP63K Array, was used to validate the map order. This linkage map provides us with positional information and a facile source of KASP markers for newly reported methods of cost-effective MAS of cotton seed or seedlings, e.g., for introgression and analysis of A2 and D1 germplasm via chromosome segment substitution line (CSSL) or “introgression line” (“IL”) development.