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Bai H.,Hebei Academy of Agriculture and Forestry Science | Bai H.,National Foxtail Millet Improvement Center | Bai H.,CAS Institute of Genetics and Developmental Biology | Bai H.,Minor Cereal Crops Laboratory of Hebei Province | And 19 more authors.
PLoS ONE | Year: 2013

Foxtail millet (Setaria italica) is a drought-resistant, barren-tolerant grain crop and forage. Currently, it has become a new model plant for cereal crops and biofuel grasses. Although two reference genome sequences were released recently, comparative genomics research on foxtail millet is still in its infancy. Using the Solexa sequencing technology, we performed genome re-sequencing on one important foxtail millet Landrace, Shi-Li-Xiang (SLX). Compared with the two reference genome sequences, the following genetic variation patterns were identified: 762,082 SNPs, 26,802 insertion/deletion polymorphisms of 1 to 5 bp in length (indels), and 10,109 structural variations (SVs) between SLX and Yugu1 genomes; 915,434 SNPs, 28,546 indels and 12,968 SVs between SLX and Zhang gu genomes. Furthermore, based on the Yugu1 genome annotation, we found out that ~ 40% SNPs resided in genes containing NB-ARC domain, protein kinase or leucine-rich repeats, which had higher non-synonymous to synonymous SNPs ratios than average, suggesting that the diversification of plant disease resistance proteins might be caused by pathogen pressure. In addition, out of the polymorphisms identified between SLX and Yugu1, 465 SNPs and 146 SVs were validated with more than 90% accuracy, which could be used as DNA markers for whole-genome genotyping and marker-assisted breeding. Here, we also represented an example of fine mapping and identifying a waxy locus in SLX using these newly developed DNA markers. This work provided important information that will allow a deeper understanding of the foxtail millet genome and will be helpful for dissecting the genetic basis of important traits in foxtail millet. © 2013 Bai et al. Source


Zhang A.,Hebei Academy of Agriculture and Forestry Science | Zhang A.,National Foxtail Millet Improvement Center | Zhang A.,Minor Cereal Crops Laboratory of Hebei Province | Liu X.,Hebei Academy of Agriculture and Forestry Science | And 11 more authors.
Cereal Chemistry | Year: 2015

Crude fat and fatty acid profile of 35 foxtail millets including seven varieties planted in five different regions of China were studied. The fat content ranged from 3.38 to 6.49% (averaging 4.51%). The major fatty acid in foxtail millets was linoleic acid (averaging 66.68%), followed by oleic acid (averaging 16.11%), palmitic acid (averaging 7.42%), stearic acid (averaging 6.84%), and linolenic acid (averaging 2.48%). Two-way ANOVA showed that fat content was significantly affected by millet variety and cultivation area (P < 0.05). Fatty acids including linoleic acid, palmitic acid, stearic acid, and linolenic acid varied significantly in different foxtail millet varieties (P < 0.05), except oleic acid (P > 0.05). Fatty acids including linoleic acid, oleic acid, palmitic acid, and stearic acid did not change significantly in foxtail millets from different regions (P > 0.05), except linolenic acid (P < 0.05). Correlation analysis indicated that oleic acid was negatively correlated with palmitic acid and linoleic acid (P < 0.05), and linolenic acid was positively correlated with palmitic acid and linoleic acid but negatively correlated with stearic acid (P < 0.05). The research showed that millets with good fat composition can be obtained through breeding techniques or cultivation management. © 2015 AACC International, Inc. Source

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