BackgroundFoxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement.ResultA total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar ‘Yugu1’. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1.ConclusionsNew SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2628-z) contains supplementary material, which is available to authorized users.
Background: Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C 4 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. Thirtynine 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 markerassisted selection.
Drought has become a serious problem that threatens global food security. Foxtail millet (Setaria italica) can be used as a model crop for drought-resistant research because of its excellent performance in drought tolerance. In this study, the typical drought-tolerant foxtail millet landrace ‘Huangjinmiao’ was grown in a field under control and drought stress conditions to investigate its response to drought stress. The proteins in the harvested grains were analysed through two-dimensional electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization-tandem time-of-flight (MALDI-TOF/TOF) analysis to characterize the response of foxtail millet under drought stress at a proteomic level. A total of 104 differentially abundant protein spots (DAPs) were identified; among them, 57 were up-regulated and 47 were down-regulated under drought treatment. The identified proteins were involved in an extensive range of biological processes, including storage proteins, protein folding, starch and sucrose metabolism, glycolysis/gluconeogenesis, biosynthesis of amino acids, detoxification and defense, protein degradation, tricarboxylic acid (TCA) cycle, protein synthesis, energy metabolism, transporter, pentose phosphate pathway, and signal transduction. Post-translational protein modifications might also occur. Moreover, the albumin content greatly decreased under drought stress, whereas the gliadin content considerably increased (p<0.01). In conclusion, this study provides new information on the proteomic changes in foxtail millet under drought stress and a framework for further studies on the function of these identified proteins.
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