Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet

Abstract

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.

Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis

“…The task of whole-genome re-sequencing was performed on an Illumina HiSeq2000™ by Biomarker Technologies (Beijing, China). The procedure was performed in accordance with the standard Illumina protocol as described previously36. The detection of SNPs and Indels were mainly performed by GATK software tools (https://www.broadinstitute.org/gatk/guide/best-practices.php).…”

Construction of a high-density genetic map using specific-locus amplified fragments in sorghum

“…SLAF (specific-locus amplified fragments) markers, which has been used for genetic investigation, have the properties of being present in large amount, being evenly distributed and avoiding repeated sequences [21]. These markers have been used for crop genetic analysis such as sesame, millet, rice and soybean [22–26], especially in the applications of high-density genetic map construction and functional genes verification. Exploiting this approach to scan the whole sorghum genome has great importance for high density marker development and gene mining for sorghum breeding.…”

Biofortification in Millets: A Sustainable Approach for Nutritional Security

“…Novel markers obtained by re-sequencing helped in genome mapping of starch synthase encoding GBSS 1 peptide. Sequencing of GBSS 1 gene found the insertion of transposable elements confirming its waxy nature (Bai et al, 2013). …”