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.     

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     

Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa)

 A foxtail millet-rice comparative genetic map was constructed using mapped rice RFLP markers and wheat genomic and cDNA clones with known map position in rice. About 74% and 37% of the cDNA and genomic clones, respectively, were transferable to foxtail millet, confirming that conservation at the DNA level is greatest in genic regions. A high degree of conserved colinearity was observed between the two genomes. Five entire foxtail millet chromosomes appear to be colinear with five entire rice chromosomes. The remaining four foxtail millet linkage groups each show colinearity with segments of two rice chromosomes. The rearrangements of rice chromosomes 3 and 10 to form foxtail millet chromosome IX, and 7 and 9 to form chromosome II are very similar to those required to form maize chromosomes 1 and 7 and sorghum linkage groups C and B, indicating Setaria’s clear taxonomic position within the subfamily of the Panicoideae. Received: 18 December 1996 / Accepted: 4 August 1997     

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.     

The occurrence and identification of <Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv. (foxtail millet) grains from the Chengtoushan site (ca. 5800 cal B.P.) in central China,with reference to the domestication centre in Asia

Archaeobotanical remains of Setaria grains and chaff were found at the Chengtoushan site in south-central China (ca. 5800 cal b.p.). Grain shape was determined, using length to breadth ratios, and morphological variation in the upper lemma of modern domesticated and wild Setaria species were examined using scanning electron microscopy as a basis for identifying archaeobotanical remains. Grains of S. viridis, S. yunnanensis, and S.×pycnocoma are slender, whereas S. italica, S. italica var. germinica, S. lutescenes, S. faberi, S. glauca, S. pallidefusca and S. intermedia are round in shape. The papillae distributed on the upper lemma of S. italica are small (8–15 μm) with a non-ridged base, while other Setaria species have large papillae (15–20 μm) with a widely ridged base. The remains of the Setaria from the Neolithic layers at Chengtoushan included S. italica, based on these identification characters. These new finds of foxtail millet are the earliest discoveries from the Yangtze River basin of southern China and are also the earliest evidence for co-cultivation of foxtail millet with rice. The implications of these findings for understanding foxtail millet domestication centres are discussed.     

谷子主要育成品种在新疆的遗传多样性研究

以274份谷子种质资源为材料,利用聚类分析和主成分分析方法,对参试资源16个农艺性状的遗传多样性进行综合评价。结果表明,参试材料的11个数量性状的遗传多样性指数均大于2.000,在新疆表现出广泛的遗传多样性。基于种质资源间形态标记的遗传差异,将274份谷子种质资源聚类并划分为6大类群。第Ⅰ类群(105份材料)生育期较短,属早熟类型,但其他性状表现一般;第Ⅱ类群(19份材料)出苗-抽穗日数最小,全生育期最短,早熟性明显,穗下节间长度相对其他类群较长;第Ⅲ类群(10份材料)生育期较短,主穗长相对较长,其余性状表现均处于较低水平;第Ⅳ类群(58份材料)主穗长、单穗重在各类群中处于较高水平,生育期相对较短;第Ⅴ类群(26份材料)生育期最长,属晚熟类型,除主穗长度最小外其余性状均表现突出;第Ⅵ类群(56份材料)生育期相对较长,属中晚熟类型,株高较低,生物产量处于中等水平。9个数量性状的主成分分析结果表明,前3个主成分因子(单株秆重、株高、主穗直径)累计贡献率达70.41%,各主成分因子性状载荷值反映了育种中各性状的选择方向及潜力。综合评价谷子种质资源农艺性状,为新疆谷子资源收集、评价和利用提供一定的科学依据。     

夏谷群体呼吸特性及其与群体光合的关系

中秆大穗型和矮秆紧凑型2种不同类型的夏谷群体呼吸速率在整个生育时期的变化呈单峰曲线,且随密度的增大而提高,抽穗开花期达最大值,紧凑型品种后期呼吸速率高于中秆大穗型品种,后期呼吸消耗大是低产的重要原因,群体呼吸日变化为一随温度而变化的单峰曲线,群体呼吸速率在冠层中的分布,依此是上3叶＞茎鞘＞中3叶＞穗＞下部叶,群体呼吸／光合的比值,两品种相近,在47％左右。     

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)     

谷子MYB类转录因子SiMYB42提高转基因拟南芥低氮胁迫耐性

Myeloblastosis (MYB)类转录因子是高等植物中最大的转录因子家族之一,在植物发育及防御反应过程中发挥重要作用,还参与植物对干旱等非生物胁迫的响应。谷子(Setaria italica L.)起源于中国,具有抗旱、耐瘠薄的特性,是研究单子叶作物非生物胁迫抗性的理想材料。本研究对耐低氮胁迫谷子品种郑204经低氮处理后进行转录组分析,鉴定出一个在低氮胁迫条件下明显上调的MYB类转录因子SiMYB42。系统发育树结果表明,SiMYB42属于R2R3-MYB亚族,具有2个MYB保守域;表达模式分析显示,SiMYB42在低氮、高盐、干旱和ABA胁迫条件下表达量显著上调;亚细胞定位、quantitative real-time PCR及转录激活活性分析结果表明,SiMYB42蛋白定位于植物的细胞核和细胞膜中,主要在谷子的叶部或根部表达,具有转录激活活性;基因功能分析结果表明,在正常条件下,转SiMYB42基因拟南芥与野生型Columbia-0拟南芥(WT)无明显差异,但在低氮条件下,转SiMYB42基因拟南芥的主根长、根系表面积及鲜重均显著高于WT,结果证明SiMYB42基因可以提高转基因植物对低氮胁迫的耐性;下游基因表达分析结果显示,在转SiMYB42基因拟南芥中,参与植物氮素转运的硝酸盐转运基因NRT2.1、NRT2.4和NRT2.5的表达水平均高于WT,启动子分析结果显示NRT2.1、NRT2.4和NRT2.5基因启动子序列中均具有MYB结合位点。以上结果证明,SiMYB42可以通过调控下游硝酸盐转运体基因的表达提高植物在低氮条件下的耐性。本研究揭示了SiMYB42基因在低氮胁迫反应途径中的作用,为进一步了解谷子低氮胁迫响应的调控网络奠定了基础。     

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.     

中国谷子主产区谷子近缘种狗尾草的遗传多样性

用同工酶淀粉凝胶电泳技术分析了在中国北方谷子主产区采集与收集的谷子、谷子近缘野生种青狗尾草(包括谷莠子)和金狗尾草的代表群体。分析了12种等位酶(AAT、ADH、AMP、DIA、GDH、IDH、MDH、ME、PGD、GPI、PGM、SKD)的21个等位酶位点的数据。结果表明：青狗尾草同其它以自花授粉为主的一年生植物相比表现更高的遗传变异性。AAT—3、PGD、PGM在所有供试材料中均表现单态,而在金狗尾草中缺失(沉默)IDH-l。不同地理来源的青狗尾草同谷子的亲缘关系存在一定的差异,而且青狗尾草间的遗传差异同地理区域相关。本研究结果支持把谷子和青狗尾草划为一个种的观点。     

增强UV-B辐射与不同水平氮素对谷子（Setaria italica (L.) Beauv.） 叶片保护物质及保护酶的影响

研究了生长在1.875 mmol·L-1和15 mmol·L-1硝态氮素水平条件下的谷子(Setaria italica(L.)Beauv.)开花期间在进行强度为7.12 kJ·m-2.d-1增强UV.B辐射处理时叶片类黄酮含量、苯丙氨酸解氨酶(PAL)和保护酶活性变化差异.主要结果表明在开花期无论是否进行增强UV-B辐射处理,较低水平氮素均比较高水平氮素更有利于提高谷子叶片PAL活性;叶片类黄酮含量除在进行增强UV-B处理时较低氮素条件下生长的谷子在开花末期显著高于较高氮素条件下生长的谷子外,受氮素水平影响不甚明显.而在开花期不进行与进行增强UV-B辐射处理,氮素水平对叶片保护酶的影响有所差异:不进行增强UV-B辐射处理,整个开花期氮素水平对谷子叶片SOD活性有显著影响而对ASP活性无显著影响,对CAT和POD活性则在开花期部分阶段有显著影响.进行增强UV-B辐射处理,整个开花期氮素水平对谷子叶片SOD与CAT活性有显著影响而对ASP、POD活性影响不显著.     

影响谷子原生质体看护培养的一些因素

研究了谷子原生质体看护培养中的一些问题。结果表明：不同种植物愈伤组织做看护细胞对谷子原生质体培养植板率有不同的影响。用光头种草愈伤组织对谷子胚性、非胚性或中间型意伤组织的原生质体进行看护培养,以对胚性意伤组织原生质体的效果最好。看护培养主要是作用于原生质体形成完整细胞后的生长发育。试验没有观察到明显的看护细胞数量效应。     

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.     

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.     

Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.)

Introns are noncoding sequences in a gene that are transcribed to precursor mRNA but spliced out during mRNA maturation and are abundant in eukaryotic genomes. The availability of codominant molecular markers and saturated genetic linkage maps have been limited in foxtail millet (Setaria italica (L.) P. Beauv.). Here, we describe the development of 98 novel intron length polymorphic (ILP) markers in foxtail millet using sequence information of the model plant rice. A total of 575 nonredundant expressed sequence tag (EST) sequences were obtained, of which 327 and 248 unique sequences were from dehydration- and salinity-stressed suppression subtractive hybridization libraries, respectively. The BLAST analysis of 98 EST sequences suggests a nearly defined function for about 64% of them, and they were grouped into 11 different functional categories. All 98 ILP primer pairs showed a high level of cross-species amplification in two millets and two nonmillets species ranging from 90% to 100%, with a mean of ～97%. The mean observed heterozygosity and Nei's average gene diversity 0.016 and 0.171, respectively, established the efficiency of the ILP markers for distinguishing the foxtail millet accessions. Based on 26 ILP markers, a reasonable dendrogram of 45 foxtail millet accessions was constructed, demonstrating the utility of ILP markers in germplasm characterizations and genomic relationships in millets and nonmillets species.     

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.     

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.     

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.