Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]

Abstract

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

Genetic diversity and origin of North American green foxtail [Setaria viridis (L.) Beauv.] accessions

“…In addition, a single S. verticillata accession was obtained from GRIN. The SSR markers, which were developed against S. viridis sequence data (Jia et al 2009) amplified equally well using S. viridis, S. italica, S. verticillata and S. faberi genomic DNA as a template. However, most primer sets failed to amplify or produced weak and/or complex patterns in S. pumila.…”

“…However, most primer sets failed to amplify or produced weak and/or complex patterns in S. pumila. This is in agreement with the results of phylogenetic analyses that place S. viridis, S. italica and one genome of the tetraploids S. faberi and S. verticillata into a single clade while S. pumila is more distantly related Layton and For each marker, the allele (in bp) that is present at a frequency of [50 % in one of the subpopulations and \5 % in both other subpopulations is indicated as specific alleles (Spe) a The chromosomal location was obtained by conducting a Blastn search of the primer sequences listed in Jia et al (2009) against the S. italica genome sequence (Bennetzen et al 2012) Kellogg 2014). Our analysis of 30 S. pumila accessions with 11 SSR markers yielded no evidence of gene flow between S. pumila and S. viridis growing in sympatry.…”

“…Each line was genotyped with 11 foxtail millet SSRs (p3, p16, p29, p88, p89, p95, b101, b102, b127, b163 and b166;Jia et al 2009). PCR reactions were carried out in 15 lL volumes comprising 50 ng of template DNA, 3 lL 59 buffer (Promega), 1.5 mM MgCl 2 , 200 lM dNTPs, 67 nM M13-tailed specific forward primer, 267 nM fluorescently labeled M13 primer, 267 nM specific reverse primer and 0.9 U GoTaq Ò Flexi DNA Polymerase (Promega).…”

Genetic Variation of Foxtail Millet [Setaria italica (L.) P. Beauv.] Among Accessions Collected From Korea Revealed by AFLP Markers

“…Source of material Village, town or city Country 물에서도 RFLP(restriction fragment length polymorphism), SSR(simple sequence repeats), AFLP(amplified fragment length polymorphism) 등 DNA 분석기술을 이용하여 재배 종 및 야생 근연종 계통들에 대하여 유전적 다양성 및 계통 유연관계 그리고 유전자지도 작성 등의 연구가 수행되고 있 다 (Fukunaga et al, 1997(Fukunaga et al, , 2002Jia et al, 2009;Le Thierry d'Ennequin et al, 2000;Li et al, 1998;Schontz & Rether, 1998, 1999. 특히 이들 분석기법들 중에서 AFLP 마커는 PCR(polymerase chain reaction)을 이용한 분석기법으로 재 현성이 뛰어나고, AFLP primer 조합당 많은 수의 대립유전 자를 증폭할 수 있기 때문에 유전적으로 가까운 작물의 품 종 또는 계통들의 유전적 특성을 분석하는데 효율적이다 (Cho et al, 1998;Garcia-Mas et al, 2000;Zhao et al, 2005).…”

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

“…Many different types of markers such as isozyme (Jusuf and Pernes, 1985), restriction fragment length polymorphism (RFLP) , RAPD (Schontz and Reather, 1999), AFLP (Kim et al, 2011), and simple sequence repeat (SSR) markers (Jia et al, 2009) have been used to study the genetic diversity of foxtail millet species. Similarly, Hirano et al (2011) employed transposons to determine the correlation between geographical area and genetic structure.…”