Intraspecific Polymorphic SNP and Indel Marker Discovery Based on Whole Genome Sequencing of a MAGIC Population in Upland Cotton

Development of a large number of intraspecific single nucleotide polymorphisms (SNPs) has been a challenge for allotetraploid Upland cotton due to the presence of two closely related sub-genomes in addition to the narrow genetic base of the cultivated varieties. The objective of this research was to develop a large number of robust intraspecific polymorphic SNP and insertion-deletion (indel) markers with broad utility in Upland cotton genetic studies and breeding. We developed a multi-parent advanced generation inter-cross (MAGIC) population derived from 11 diverse cotton cultivars through random-mating. We deep-sequenced (20× coverage) the genomes of 11 parents, and skim-sequenced (2.5× coverage) the genomes of 290 MAGIC recombinant inbred lines (RIL). We identified 1,520,684 SNPs and 327,509 indels among the 11 parents. Of them, 849,070 SNPs and 83,810 indels segregated in the MAGIC RIL population. By comparing the minor allele frequencies of the segregating SNPs and indels between the parents and RILs, 498,939 SNPs and 48,074 indels passed a Chi-square test. More polymorphisms were observed in the peri-telomeric regions of chromosomes than the peri-centromeric regions. We tested 26 non-synonymous SNPs and 26 indels in 96 Upland cotton cultivars. All SNPs and indels tested were successfully converted to functional PCR-based genetic markers, indicating the robustness of these markers.