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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 #326480

Title: Comparative hi-density intraspecific linkage mapping using three elite populations from common parents

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

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 5/6/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: High-density linkage maps are fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, e.g., Upland cotton (Gossypium hirsutum L., 2n=52). Using 3 full-sib intra-specific mapping populations from the cultivars Phytogen 72 (PHY72) and Stoneville 474 (STV474), including 93 F2s and reciprocal RILs (132 and 104), we developed 3 independent single nucleotide polymorphism (SNP) maps, plus a 4th consensus map or joinmap. The CottonSNP63K array and cluster file provided 7,417 genotyped SNP markers. The F2 population averaged 49.4% heterozygous loci, whereas the recombinant inbred line (RIL) populations averaged 1.51% and 1.92% heterozygous loci. The linkage groups LG12 and LG26 corresponding to homeologous chromosomes 12 and 26 had the highest percentages of heterozygous loci in F2 (0.525 and 0.542) and RIL populations (0.030-0.037 and 0.024-0.021). Using similar cut-offs/thresholds for grouping and linkage between two SNP markers, 7,030 SNPs were mapped in the F2 PHY72 x STV474 (93 individuals) population; 7,059 SNPs were mapped in the RIL PHY72 x STV474 (132 lines) population; and 6,320 SNPs were mapped in the RIL STV474 x PHY72 (104 lines) population. In all populations, these SNPs were assimilated into 26 linkage groups corresponding to the 26 cotton chromosomes. The percentage of similar or common SNPs among the populations ranged from 96 % to 99 %. The high-density genetic joinmap of the Upland allotetraploid comprised 3,824 SNP bins (7,244 SNP markers) and covered 3,537 centiMorgans (cM) (At- subgenome 1,783 bins and Dt-subgenome 2,041 bins) with an average SNP interval between two linked markers of 1.0 cM. Recombination frequencies were similar in the two subgenomes. Lengths of LGs ranged from 87.6 (LG04 F2 population) to 239.3 (LG05 RIL population) cM. The new maps were highly collinear with the previous published F2 maps. Additional analyses are ongoing with available Gossypium genome assemblies to provide further knowledge of chromosome arrangement, recombination frequencies, parental relationships, and gene order. This is the first high-density SNP genetic linkage joinmap developed for G. hirsutum with a core of reproducible Mendelian SNP markers assayed on different intraspecific populations from crosses involving the same parents.