Phylogenetic analysis of the rDNA intergenic spacer subrepeats and its implication for the domestication history of foxtail millet, Setaria italica

Abstract

We sequenced ribosomal DNA intergenic spacer subrepeats and their flanking regions of foxtail millet landraces from various regions in Europe and Asia and its wild ancestor to elucidate phylogenetic differentiation within each of types I-III found in our previous work and to elucidate relationships among these three types. Type I was classified into seven subtypes designated as Ia-Ig based on subrepeat sequences; C repeats downstream of those subrepeats are also polymorphic. Of these, subtypes Ia-Id and Ig were found in foxtail millet landraces. Subtypes Ia and Ib were distributed broadly throughout Asia and Europe. Subtype Ic was distributed in China, Korea and Japan. Subtype Id has a 20-bp deletion in subrepeat 3 and has a unique C repeat sequence. This subtype was found in a morphologically primitive landrace group from Afghanistan and northwestern Pakistan and differed greatly from other type I subtypes, implying that these landraces were domesticated independently. Subtypes Ig was found in a landrace from Pakistan and Ia and Ie-Ig were in six wild ancestor accessions. Type II was also highly polymorphic and four subtypes were found and designated as subtypes IIa-IId, but sequence analyses indicated type III as monomorphic. The present work indicates that type III should be classified as a subtype of type II (subtype IIe). Sequence polymorphism of subrepeats of types I-III indicated that subrepeats of subtype IIa are greatly divergent from others. Relationships among types I-III are much more complicated than anticipated based on previous RFLP work.

Foxtail Millet: A Sequence-Driven Grass Model System

“…This has been interpreted as supporting multiple domestications of foxtail millet Sakamoto, 1984, 1987;Jusuf and Pernes, 1985;Fukunaga et al, 1997Fukunaga et al, , 2002Fukunaga et al, , 2005Fukunaga et al, , 2006Li et al, 1998;Nakayama et al, 1998;Le Thierry d'Ennequin et al, 2000;Benabdelmouna et al, 2001;Kawase et al, 2005), followed by episodes of genetic introgression from green millet (Darmency et al, 1987;Wang et al, 1995;Jarvis and Hodgkin, 1999). Green millet is a serious weed, not only of foxtail millet, but of wheat and other temperate cropping systems worldwide (Defelice, 2002;Dekker, 2003).…”

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

“…From studies on wild green foxtail and cultivated foxtail millet, monotopic (Fukunaga et al ., 2006; Hirano et al ., 2011; Li et al ., 2012) and polytopic (Jusuf and Pernes, 1985) origins of foxtail millet have been inferred, and most reports agree that China was the first site of foxtail millet domestication, if not the only one (Vavilov, 1926; Austin, 2006; Li et al ., 2012). This is supported not only by the earliest archeological evidence of foxtail millet identified in Northern China, which existed >10 500 years ago (Lu et al ., 2009; Barton et al ., 2009; Yang et al ., 2012), but also by the high level of genetic diversity of Chinese foxtail millet landraces (Le Thierry d’Ennequin et al ., 2000; Fukunaga et al ., 2006; Hirano et al ., 2011). The analysis of genetic diversity and population structure based on a large sample size of 250 Chinese foxtail millet landraces, which represent 1% of the foxtail millet germplasm kept in the Chinese National Gene Bank, revealed a high genetic diversity of 20.9 alleles per locus, and classified the accessions into four subpopulations, in accordance with its eco-geographical distribution in China (Wang et al ., 2012).…”

Earliest domestication of common millet ( Panicum miliaceum ) in East Asia extended to 10,000 years ago

“…S2), but without any spodogram evidence for the grain crop remains in the Cishan site (7)(8)(9)(10). These have been reported as the world's oldest foxtail millet in the literature (6,9,10,14). However, the millet identification has been questionable (4,11,12,15), because the macro (ash) remains were too friable to be observed under the microscope.…”

“…Only 2 14 C dates of charcoal from previously excavated H145 and H48 storage pits yielded uncalibrated ages of 7355 Ϯ 100 yr BP and 7235 Ϯ 105 yr BP, respectively (8). These remains represent the earliest evidence for the significant use of dry-farming crop plants in the human diet in East Asia.…”