QTL analysis of root diameter in a wild diploid relative of sweetpotato (Ipomoea batatas (L.) Lam.) using a SNP-based genetic linkage map generated by genotyping-by-sequencing

Abstract

The complexity of sweetpotato genome, including hexaploidy and heterozygosity, has hindered genetic studies on agronomically important traits such as storage root formation and thickening. Ipomoea trifida (H. B. K.) G. Don. (2n = 2x = 30) is closely related to and cross-compatible with sweetpotato. The diploid I. trifida has been developed as a model plant for sweetpotato genetic research, due to its low ploidy and simple genetic background. In order to reveal the molecular mechanisms underlying storage root development in sweetpotato, F1 mapping population derived from diploid I. trifida was screened for root diameter by genotyping-by-sequencing method. A total of 11,555 raw polymorphic SNPs were identified, in which 8454 SNPs can be used in this F1 population. The SNP genotyping data was utilized to construct the genetic linkage map of I. trifida. The maternal and paternal linkage maps were produced, and 904 maternal and 2034 paternal markers resulted in 13 and 15 LGs respectively. The total length of the maternal maps covered 842.34 cM, while the paternal maps spanned 1540.98 cM. The integrated genetic map consisted of 2892 SNPs (average of 193 markers/linkage group) on 15 linkage groups (LGs) covering 1550.22 cM of the whole genome at an average inter marker distance of 0.55 cM. By using the phenotypic data obtained in this study, three significant QTL were detected for root diameter. These QTL were distributed among three LGs at three independent positions, and each QTL explained significant amount of phenotypic trait variation ranged from 6.1 to 12.0%. The qRD-2 QTL explained 12.0% of the phenotypic variation. This study results will assist in the map-based cloning of genes controlling storage root-related traits and further helps to reveal the genetic basis of root development in sweetpotato.