Genetic structure of landraces in foxtail millet (Setaria italica(L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Abstract

Origin and domestication process of foxtail millet [Setaria italica (L.) P. Beauv.] have been studied by several groups but still in discussion with ambiguity. It is cardinal to elucidate the issue by studying large number of accessions with enough number of markers covering the whole genomic regions. Genetic structures were analyzed by transposon display (TD) using 425 landraces of foxtail millet and 12 accessions of the wild ancestor, green foxtail. We applied three recently-active transposons as genome-wide markers and succeeded in demonstrating geographical structures of foxtail millet. A neighbor-joining dendrogram based on TD grouped the set of foxtail millet accessions into eight major clusters each of which consisted of accessions collected from geographically adjacent areas. Eleven out of twelve green foxtails were 2 grouped separately from the clusters of foxtail millet. These results pointed that the strong regional differentiations and long history of the cultivation in each region.Relationship between foxtail millet and green foxtail regarding intraspecific hybridization and suggested monophyletic origin of foxtail millet domestication were also discussed.

EST-SSR Based Genetic Diversity and Population Structure among Korean Landraces of Foxtail Millet (Setaria italica L.)

“…Similarly, Hirano et al (2011) employed transposons to determine the correlation between geographical area and genetic structure. However, these genetic markers represent limited information regarding genomic polymorphism (Wright and Gaut, 2005).…”

Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis

“…(1995) investigated the genetic diversity and structure of green foxtail accessions collected from North America and Eurasia using allozyme markers, and suggested that there were similar isozymatic forms between foxtail millet and green foxtail collected from the same regions. Chinese accessions were identified as having a high level of genetic diversity using amplified fragment length polymorphism (AFLP) markers (Le Thierry d’Ennequin et al ., 2000), transposon display (Hirano et al ., 2011), and intersimple sequence repeat (ISSR) markers (Li et al ., 2012), and the well known A10 accession which was used as a model for C 4 photosynthesis study was also from China (Brutnell et al ., 2010; Li and Brutnell, 2011; Bennetzen et al ., 2012; Caemmerer et al ., 2012). However, all these studies were carried out with a small sample size of no more than 40 accessions.…”

Development of Simple Sequence Repeats (SSR) Markers in Setaria italica (Poaceae) and Cross-Amplification in Related Species

“…It is able to endure droughts and grows quickly; therefore, the indigenous people cultivate foxtail millet instead of rice. Though several researches have used a few millet strains from Taiwan, little is known about the genetic diversity in hundreds of local landraces scattered throughout Taiwan [1,2]. …”