Abstract
BackgroundFoxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.ResultA total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.ConclusionsA large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.
Highlights
Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop
The large number of new Simple sequence repeat (SSR) markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, Quantitative trait locus (QTL) exploration and molecular breeding in foxtail millet and its closely related species
Its small diploid genome (~515 Mb) and inbreeding nature has led to foxtail millet becoming a model for grass functional genomics, especially in investigating plant architecture, drought tolerance, crop domestication, C4 photosynthesis and the physiology of bioenergy crops [7,8,9]
Summary
Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Foxtail millet (Setaria italica) is an ancient crop that is grown worldwide in arid regions, especially in East and South Asia, Africa and Europe [1,2,3]. Its small diploid genome (~515 Mb) and inbreeding nature has led to foxtail millet becoming a model for grass functional genomics, especially in investigating plant architecture, drought tolerance, crop domestication, C4 photosynthesis and the physiology of bioenergy crops [7,8,9]. The release of the genome sequence [10,11] and a haplotype map [12] have made the use of foxtail millet as a model species more attractive
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