Abstract
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.
Highlights
A limited number of markers were applied to construct genetic linkage maps and identify quantitative trait loci (QTL) for agronomic and yield traits, except for 79 simple sequence repeat (SSR) detected by Sato et al [19] and 0.8 million SNP detected by Jia et al [12]
We have developed 10598 SSR markers based on the reference genome sequence
A total of 29 QTL were identified for 11 agronomic and yield traits, and the new genetic markers along with genomic-SSRs linked to the QTL may help breeders to construct desirable allelic combinations and accelerate breeding programs for the development of foxtail millet cultivars with improved agronomic performance through MAS
Summary
Foxtail millet (Setaria italica L.) has a long history of cultivation in China. Because grains of foxtail millet are enriched for various amino acids and nutritive minerals and the crop possesses some advantageous traits, e.g. high photosynthetic efficiency and drought tolerance, foxtail millet is still a very important crop in arid and semiarid regions of northern China [2]. Seeds of foxtail millet are generally not dormant and can be cultivated at density of up to 100 plants/m2 in the glasshouse or in the field in temperate or tropical regions [3]. Because of its small genome (∼515 Mb) with a small number of chromosomes (2n = 2x = 18) and inbreeding nature, foxtail millet is a valuable model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops [3,4,5,6]. Development of high yielding, high quality, and stress resistant foxtail millet cultivars is an important goal for foxtail millet scientists
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