QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica)

Abstract

Background: Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C₄ photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal grasses because of its advantageous characters with the small genome size, self-fertilization, short growing cycle, small growth stature, efficient genetic transformation and abundant diverse germplasm resources. Therefore, excavating QTLs of yield component traits, which are closely related to aspects mentioned above, will further facilitate genetic research in foxtail millet and close cereal species.

Results: Here, 164 Recombinant inbreed lines from a cross between Longgu7 and Yugu1 were created and 1,047,978 SNPs were identified between both parents via resequencing. A total of 3413 bin markers developed from SNPs were used to construct a binary map, containing 3963 recombinant breakpoints and totaling 1222.26 cM with an average distance of 0.36 cM between adjacent markers. Forty-seven QTLs were identified for four traits of straw weight, panicle weight, grain weight per plant and 1000-grain weight. These QTLs explained 5.5-14.7% of phenotypic variance. Thirty-nine favorable QTL alleles were found to inherit from Yugu1. Three stable QTLs were detected in multi-environments, and nine QTL clusters were identified on Chromosome 3, 6, 7 and 9.

Conclusions: A high-density genetic map with 3413 bin markers was constructed and three stable QTLs and 9 QTL clusters for yield component traits were identified. The results laid a powerful foundation for fine mapping, identifying candidate genes, elaborating molecular mechanisms and application in foxtail millet breeding programs by marker-assisted selection.

Keywords: Bin map; Foxtail millet (Setaria italica); QTL; SNP; Yield component traits.

Fig. 1

Genes, SNP, InDel and specific SNP distribution on chromosomes by the two parents aligned with the reference genome. a: Gene positions (red = forward; blue = reverse); b: SNPs per 50Kb on Longgu7 (max = 1647); c: InDels per 50Kb on Longgu7 (max = 122); d: SNPs per 50Kb on Yugu1 (max = 1490); e: InDels per 50Kb on Yugu1 (max = 122); f: SNPs exclusive from Longgu7 per 50Kb (max = 1198); g: SNPs exclusive from Yugu1 per 50Kb (max =1172)

Fig. 2

Recombination bin map of 164 foxtail millet RILs. The whole map contains 3413 bin markers and 3963 breakpoints. Red: genotype of Longgu7; blue: genotype of Yugu1. Left number represent the number of recombinant inbred lines. Chromosomes are separated by vertical white lines. Chr: chromosome; RIL: recombinant inbred line

Fig. 3

QTL controlling yield component traits on nine chromosomes. The color intensity of the bar chart represents the marker density. The number on the left indicates the genetic distance in centimorgan (cM). On each chromosome, the name of each QTL is shown on the right. Parallel QTLs indicate the same location on the chromosome. The symbol’<, *, >’ in front of the QTL represent partial overlap with the QTL above, the both flanking QTL and the QTL below region, respectively. The symbol’#’ in front of the QTL represents the same QTL identified under two environments. QTL were identified for four yield traits and shown as straw weight per plant (SWP), panicle weight per plant (PWP), grain weight per plant (GWP), and 1000-grain weight (TGW)