Genetic variability of foxtail millet (Setaria italica P. Beauv.)

Summary The genetic diversity of a world collection of foxtail millet strains (Setaria italica) and some samples of wild populations (Setaria viridis) was studied by means of electrophoresis on five enzymes (10 loci) Est, Acph, Got, Mdh, Pgd. In spite of an overall limited polymorphism, the diversity appeared to be clearly regionalized. The wild populations collected in France and China introduced new genetic variability to the cultivated forms. However, the interregional diversity within both species was greater than the between species (S. viridis/S. italica) diversity.     

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

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 F₂ 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. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Induced mutations in foxtail millet (Setaria italica Beauv.)

Summary Viable mutations for ear characters in two cultures of foxtail millet (Setaria italica Beauv.) were induced by individual and combined treatments of gamma rays, EMS (ethyl methanesulphonate), and dES (diethylsulphate). Four doses of gamma rays (10Kr to 40Kr), and four durations (6hrs to 24hrs) each of EMS (0.1 %) and dES (0.1 %) were used. In the combined treatments, only two durations (6hrs, 12hrs) of the chemical mutagens were used following each of the four doses of gamma rays.The mutation frequencies were recorded as mutants per 100 M₂ plants and these were found to be higher in MU-1 than in MU-2 in all the treatments except dES. The frequencies also increased with increase in dose or duration of treatments and were found to be much higher in the combined treatments than in the individual treatments. In several combined treatments, a synergistic effect was observed in culture MU-1, the degree of synergism ranging from 1.01 to 1.62. Thus there was a differential response by the two cultures to the mutagenic treatments. The mutation spectrum was also found to be wider in culture MU-1, where 11 different kinds of mutants were recorded compared with only eight kinds of mutants recorded in MU-2.     

Induced mutations in foxtail millet (Setaria italica Beauv.)

Summary Chlorophyll mutations induced by gamma rays, EMS and DES were studied in foxtail millet (Setaria italica), using two cultures, MU-1 (bristled) and MU-2 (non-bristled). No major differences in the mutagenic response of the two cultures were observed. The treatments included four doses of gamma rays (10Kr, 20Kr, 30Kr, 40Kr) and four durations (6 hrs, 12 hrs, 18 hrs, 24 hrs) each of EMS (0.1%) and DES (0.1%). The combined treatments of gamma rays + EMS and gamma rays + DES were also given.Frequencies of chlorophyll mutations were recorded by three different methods, viz. (a) mutations per cent M₁ plants, (b) mutations per cent M₁ spikes and (c) mutants per cent M₂ plants. No significant differences in the results obtained by these three methods were observed. The frequencies and spectrum of mutations are discussed.Chlorina type were most frequent andviridoalbina least frequent.Striata and virescens were also quite common.Albinos, reported frequently in other crops, were found to be less frequent in foxtail millet during the present study. Number of sectors per spike were also determined from segregation ratios and only one sector per spike was found at all doses. Efficiency and effectiveness of mutagens were also determined and discussed. The results are also discussed with respect to mutagen specificity.     

Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv.

 An RFLP-based map consisting of 160 loci was constructed in an intervarietal cross of foxtail millet [Setaria italica (L.) P. Beauv.], Longgu 25×Pagoda Flower Green. The map comprises nine linkage groups, which were aligned with the nine foxtail millet chromosomes using trisomic lines, and spans 964 cM. The intraspecific map was compared to an interspecific map, constructed in a S. italica×S. viridis cross. Both the order of the markers and the genetic distances between the loci were highly conserved. Deviations from the expected 1 : 2 : 1 Mendelian segregation ratios were observed in both the intra- and inter-specific populations. The segregation data indicate that chromosome VIII in the Longgu 25×Pagoda Flower Green cross carries a gene that strongly affects gamete fertility. Received: 18 December 1996 / Accepted: 4 August 1997     

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

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.     

Geographical distribution and genetic analysis of phenol color reaction in foxtail millet,Setaria italica (L.) P. Beauv.

Summary Phenol color reaction was examined in a total of 376 strains of foxtail millet, Setaria italica (L.) P. Beauv., collected from different areas throughout Eurasia. Positive and negative phenotypes, and no intermediate type could be recognized by the phenol color reaction. Of 376 strains examined, 50 were positive, 319 were negative, five were mixtures of both phenotypes, and the coloration in two strains with blackish lemmata and paleae could not be distinguished. The strains that showed the positive phenotype of phenol color reaction were found in rather limited regions, while those with the negative phenotype occurred in almost all the regions. The positive phenotype occurred more frequently in the lower latitudinal regions of Asia. Genetic analysis of the F₁ and F₂ generations between the two phenotypes showed that the phenol color reaction is controlled by a single gene, and that the positive phenotype is dominant.Contribution No. 28 from the Plant Germ-plasm Institute, Faculty of Agriculture, Kyoto University, Kyoto (Japan)     

Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces

We determined the sequence of ribosomal DNA (rDNA) intergenic spacer (IGS) of foxtail millet isolated in our previous study, and identified subrepeats in the polymorphic region. We also developed a PCR-based method for identifying rDNA types based on sequence information and assessed 153 accessions of foxtail millet. Results were congruent with our previous works. This study provides new findings regarding the geographical distribution of rDNA variants. This new method facilitates analyses of numerous foxtail millet accessions. It is helpful for typing of foxtail millet germplasms and elucidating the evolution of this millet.     

Variation,geographical distribution and genetical analysis of esterase isozymes in foxtail millet,Setaria italica (L.) P. Beauv.

Summary The esterase isozymes of 432 strains of foxtail millet, Setaria italica (L.) P. Beauv., collected from different areas throughout Eurasia, were investigated by gel isoelectric focusing. Five phenotypes were recognized, based on the combination of five major activity bands. Cross experiments among different phenotypes revealed these isozymes to be controlled by two codominant alleles and a null allele on the locus, Est-1, and three codominant alleles on another independent locus, Est-2. On locus Est-1, 388 strains had Est-1 ^a, 41 had Est-1 ^b and three had Est-1 ^null alleles. Est-1 ^a was widely distributed throughout Eurasia, while the distribution of Est-1 ^b and Est-1 ^null was distinctly restricted. On locus Est-2, 417 strains had Est-2 ^a, nine had Est-2 ^b and six had Est-2 ^c alleles. Est-2 ^a was widely distributed throughout Asia to Czechoslovakia, but was not detected in the western part of Europe. Est-2 ^b was found in all of the strains from the western part of Europe and in one of the Indian strains. Est-2 ^c was rarely found in Japan and China. The distribution of Est-2 ^a and -2 ^b might indicate some degree of phylogenetic differentiation between the Asian and the European strains. Polymorphism in both loci was observed only in Chinese strains.Contribution No. 30 from the Plant Germ-plasm Institute, Faculty of Agriculture, Kyoto University, Kyoto, Japan     

Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms

The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r ² in the sequenced region (exon 1–intron 1–exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K _s values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P. Beauv., and a survey of variation from Europe and Asia

 Restriction fragment length polymorphism (RFLP) and the structure of ribosomal RNA genes (rDNA) were investigated in 117 landraces of foxtail millet, Setaria italica (L.) P. Beauv. Five RFLP phenotypes were found when the genomic DNA was digested with BamHI; these were named types I–V. Of these types I, II and III were the most frequent. Type I was mainly distributed in the temperature zone, type II in the Taiwan-Philippines Islands and type III in South Asia. Restriction mapping of the cloned rDNA and comparison with RFLP phenotypes showed that the different types originated from a polymorphism in the length within the intergenic spacer (IGS) and BamHI site changes within the IGS. Received: 28 August 1996 / Accepted: 28 February 1997     

Genes controlling prolamin biosynthesis, Pro1 and Pro2, in foxtail millet, Setaria italica (L.) Beauv

Variation and genetic control of seed protein in foxtail millet (Setaria italica) were studied using SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Variation in the electrophoregram of the total seed protein were detected in the range between 20 and 30 kDa which is derived from the polymorphism of five prolamin bands. The segregation for each of the bands in F2 seeds showed that these bands are governed by seven alleles at two loci, Pro1 and Pro2, which are not linked to one another. Among 271 local cultivars examined, eight out of ten possible genotypes were observed. With its level of diversity comparable to that of isozymes, the alleles conferring prolamin polymorphism are useful genetic markers.     

Study of genetic diversity and relationships among accessions of foxtail millet [Setaria italica (L.) P. Beauv.] in Korea, China, and Pakistan using SSR markers

In this study, 28 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, population structure, and genetic relationships among 37 accessions of foxtail millet from Korea, China and Pakistan. A total of 298 alleles were detected with an average allele number of 10.6 per locus among 37 foxtail millet accessions. The number of alleles per locus ranged from 2 (b226) to 20 (b236). Of the 298 alleles, 138 alleles (46.3%) were rare (frequency < 0.05), 152 alleles (51.0%) were detected at an intermediate frequency (range, 0.05?C0.50), and eight alleles (2.7%) were abundant (frequency > 0.50), respectively. The average gene diversity values were 0.652, 0.692, and 0.491 and polymorphic information content values were 0.621, 0.653, and 0.438, for accessions from Korea, China, and Pakistan, respectively. The accessions from China showed higher SSR diversity than those from Korea and Pakistan. A phylogenetic tree constructed using the un-weighted pair group methods with arithmetic mean algorithm revealed three major groups of accessions that were not congruent with geographical distribution patterns with a few exceptions. The lack of correlation between the accession clusters and their geographic location indicates that the diffusion of foxtail millet from China to Korea might have occurred through multiple routes. Our results provide support for the origin and diffusion route of foxtail millet in East Asia. This SSR-based assessment of genetic diversity, genetic relationships, and population structure among genetic resources of foxtail millet landraces will be valuable to foxtail millet breeding and genetic conservation programs in Korea.     

Inheritance of some marker genes in Setaria italica (L.) P. Beauv.

Summary A study on a series of genetic markers was run on five hybrids of foxtail millet, Setaria italica, and on one interspecific hybrid S. viridisxS. italica (S. viridis is the wild relative of S. italica). Seven enzymatic systems were investigated using starch gel electrophoresis (esterase, alcohol dehydrogenase, glutamate oxaloacetate transaminase, acid phosphatase, malate dehydrogenase, 6-phosphogluconate dehydrogenase, cathodic peroxidase). This genetic analysis of the 6 F2 has allowed us to define 12 polymorphic loci: Est-1, -2 and -3, Adh-1, Got-1 and -2, Acph-1, Mdh-1 and -2, Pgd-1 and -2, and Pox-1. All of them behaved like dimers, except Est-1 and Est-2 which showed monomeric structures. Two other markers were examined: waxy endosperm, which appeared to be controlled by one locus, and anthocyanic pigmentation of the collar, for which at least two loci are responsible. Studies of linkage carried out on three F2 showed two linkage groups: Mdh-1, Pox-1, Wx, Est-3, and a locus for collar colour, and Est-2, and one or two other loci of colouring.     

Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.)

Italian millet is a commercially important grain crop. Nineteen polymorphic simple sequence repeat (SSR) markers, developed through construction of an SSR-enriched library from genomic DNA of Italian millet (Setaria italica L., P. Beauv.), were used for assessment of molecular genetic diversity against 40 accessions of S. italica. In total, 85 alleles were detected, with an average of 4.5 alleles per locus. The average gene diversity and polymorphism information content (PIC) values were 0.412 and 0.376, ranging from 0.02 to 0.88 and from 0.02 to 0.87, respectively. Values for observed (H _O) and expected (H _E) heterozygosities ranged from 0 to 0.73 and from 0.03 to 0.89, respectively. Nine loci deviated from Hardy-Weinberg equilibrium. The mean similarity coefficient among accessions was 0.6593. Based on the UPGMA algorithm, six different groups were successfully identified. In this clustering analysis, all Korean accessions grouped in one cluster, indicating that Korean accessions are genetically quite distinct from other introduced accessions. These newly developed microsatellite markers should be very useful tools for several genetic studies, including an assessment of diversity and population structure in Italian millet.     

不同谷子（Setaria italica(L.)Beauv）品种对除草剂的耐药性

试验对34个谷子品种进行盆栽试验,研究两种土壤处理除草剂扑草净、速收对谷子安全性的影响.测定相关的生理和生化指标,通过聚类分析比较不同谷子品种之间的耐药性的差异.试验结果表明:这两种除草剂对大部分谷子的株高、叶面积有一定的抑制作用.不同除草剂对同一种谷子的生理指标影响是有差异的.大部分谷子品种对扑草净(0.07g/m2)有一定的耐药性,扑草净药剂处理后,大部分谷子品种的POD酶活性有所提高,可溶性糖含量提高,蒸腾强度、气孔导度也有一定程度的提高.大多数谷子品种施用速收(0.015g/m2)后其SOD酶活性下降,其蒸腾强度、气孔导度有所提高.同一种除草剂对不同谷子品种的生理指标影响也是不同的,对其进行聚类分析后,聚类结果各为四大类,表明不同谷子品种之间存在耐药性差异.     

Analysis of molecular genetic diversity in a representative collection of foxtail millet [Setaria italica (L.) P. Beauv.] from different agro-ecological regions of India

Foxtail millet [Setaria italica (L.) P. Beauv.], an important crop of East Asia is known for its drought tolerance and was once an indispensible crop of vast rainfed areas in semi-arid regions in India. In India it is cultivated in Andhra Pradesh, Karnataka, Maharashtra, Tamil Nadu, Rajasthan, Madhya Pradesh, Uttar Pradesh and north eastern states. The grain finds use in several local recipes such as roti (bread), jaula, singal, sirol. Foxtail millet grain contains 12.3 % protein, 4.7 % fat, 60.6 % carbohydrates, and 3.2 % ash. The present study was conducted to analyse the genetic diversity among foxtail accessions from different states of India and a few exotic accessions using RAPD and ISSR techniques and identify diverse accessions for use in variety improvement programmes. A set of 125 foxtail millet accessions selected from 11 different agro-ecological regions of India were analyzed using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker techniques. A total of 146 (115 RAPD and 31 ISSR) scoreable markers were generated with 16 RAPD and four ISSR primers. The dendrogram generated using Nei’s genetic distances and principal component analyses revealed presence of two clusters and two subclusters in group I. The accessions from Andhra Pradesh, Karnataka, Maharashtra and Uttarakhand were more diverse since they were distributed in both the clusters. There was no clear geographical differentiation observable. The bootstrap support for the major groups identified was strong (above 80 %) indicating good statistical support. The average value of Nei and Li’s genetic distance was lowest (0.081) for accessions from West Bengal while the collections from Karnataka showed highest dissimilarity (average genetic distance = 0.239). The average genetic distance for all 125 accessions together was 0.177 indicating presence of only moderate genetic diversity in the collections. The analysis of molecular variance indicated that only 2.76 % variation was explained by variations among the groups and 11.55 % among populations within groups. However the percentage of variation observed within populations was high (85.68). The value of Fst was observed to be very low (0.028) indicating low differentiation of the accessions analysed. The population genetic analysis carried out indicates that highest number of alleles per locus (1.745 ± 0.438) was observed for Andhra Pradesh with 35 accessions. When four eco-geographic regions were considered, the southern region comprising AP, Karnataka and TN showed the highest number of alleles per locus (1.787 ± 0.411). The value of Gst was lowest for south (0.123) and highest for central west (0.455). This indicated that all the landraces from south share common alleles. The gene flow between the accessions from different regions was also observed to be high with the highest migration (3.557) recorded for south.