Xianmin Diao

Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.

The majority of well-documented cases of horizontal transfer between higher eukaryotes involve the movement of transposable elements between animals. Surprisingly, although plant genomes often contain vast numbers of these mobile genetic elements, no evidence of horizontal transfer of a nuclear-encoded transposon between plant species has been detected to date. The most mutagenic known plant transposable element system is the Mutator system in maize. Mu-like elements (MULEs) are widespread among plants, and previous analysis has suggested that the distribution of various subgroups of MULEs is patchy, consistent with horizontal transfer. We have sequenced portions of MULE transposons from a number of species of the genus Setaria and compared them to each other and to publicly available databases. A subset of these elements is remarkably similar to a small family of MULEs in rice. A comparison of noncoding and synonymous sequences revealed that the observed similarity is not due to selection at the amino acid level. Given the amount of time separating Setaria and rice, the degree of similarity between these elements excludes the possibility of simple vertical transmission of this class of MULEs. This is the first well-documented example of horizontal transfer of any nuclear-encoded genes between higher plants.

Abstract Background Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works. Results In this paper, we describe an R package ‘geneHapR’ developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. ‘geneHapR’ also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution. Conclusions The R package ‘geneHapR’ provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.

Foxtail millet, as a leading variety in arid and semi-arid areas of Asia and Africa, can provide broad potential benefits to human health. However, its digestion properties have not been reported. So in this study, the in vitro starch digestibilities and in vivo glycemic indices (GI) of foxtail millet and pure millet products were investigated. The results showed that starch digestibility of the foxtail millet flour is obviously lower than that of wheat flour. However, deproteinization and heating significantly increased its rapidly digestible starch and decreased its slowly digestible starch and resistant starch. The GIs of pure millet products were in the following order: millet porridge (93.6 ± 11.3) > millet steamed bread (89.6 ± 8.8) > No. 1 millet pancake (75.0% millet flour and 25.0% extrusion flour, 83.0 ± 9.6) > No. 2 millet pancake (without extrusion flour, 76.2 ± 10.7) > cooked millet (64.4 ± 8.5). They were significantly positively correlated with the rapidly digestible starch (r = 0.959), degree of gelatinization (r = 0.967) and estimated glycemic index (r = 0.988). Both in vitro and in vivo tests suggested that boiling, steaming and extrusion enhanced the formation of digestible starch and subsequently increased the GI values. Additionally, the No. 1 millet pancake and cooked millet had a relatively gentle stimulation on β-cell. Therefore, foxtail millet, especially the cooked millet, may serve as a potential source of nutraceutical and functional food that could delay the development of type 2 diabetes.