Geographical variation of foxtail millet, Setaria italica (L.) P. Beauv. based on rDNA PCR–RFLP

The rDNA PCR–RFLP of foxtail millet (Setaria italica) germ-plasm collected throughout Eurasia and from a part of Africa was investigated with five restriction enzymes according to our previous study. Foxtail millet germ-plasms were classified by length of the rDNA IGS and RFLP; clear geographical differentiation was observed between East Asia, the Nansei Islands of Japan-Taiwan-the Philippines area, South Asia and Afghanistan-Pakistan. We also found evidence of migration of foxtail millet landraces between the areas. We calculated diversity index (D) for each region and found that center of diversity of this millet is East Asia such as China, Korea and Japan.     

Development of EST-SSR in foxtail millet (<Emphasis Type="Italic">Setaria italica</Emphasis>)

The development of EST-SSR in foxtail millet (Setaria italica) for polymorphism and transferability study was reported here. From 1213 EST sequences, 30 SSRs were obtained and primers were designed for 26 SSRs. Among them, four pairs of SSR primers amplified polymorphic products in 12 foxtail millet cultivars and one accession of Setaria viridis, a wild relative of foxtail millet, with 10 alleles detected for the four loci and 2.5 alleles per locus. In addition, ten SSR markers could be transferred to other nine Gramineae species. The putative functions of 11 ESTs containing polymorphic and transferable SSRs were also identified.     

Geographic distribution of Waxy gene SNPs and indels in foxtail millet, Setaria italica (L.) P. Beauv.

To elucidate diversity and evolution of the Waxy gene in foxtail millet, Setaria italica, we analyzed sequence polymorphism of Waxy gene in 83 foxtail millet landraces collected from various regions covering the entire geographical distribution of this millet in Europe and Asia. We found a unique geographic distribution pattern at the sequence level of gene haplotypes and also found a large diversity in East Asian landraces. We also found a higher degree of genetic polymorphism in a non-waxy phenotype than in other low amylose types, supporting the hypothesis that low amylose types recently originated from non-waxy type.     

外源放线菌对谷子生长和成熟期根际可培养微生物的影响

为研究外源放线菌对谷子生长及成熟期根际可培养微生物的影响，本研究通过盆栽和田间试验分析施加放线菌微白黄链霉菌（Streptomyces albidoflavus，T4）和密旋链霉菌（Streptomyces pactum，Act12）后成熟期谷子生物量、产量形成指标及根际可培养微生物结构组成的差异，并对谷子生长与根际微生物之间相互关系进行分析。结果表明，①T4促进了盆栽和田间试验中谷子生物量的增加，而T4和Act12也使田间试验中单株谷子籽粒干重和产量增加了13.7%～22.6%。②对于根际微生物，T4处理使培养箱盆栽试验中谷子根际可培养细菌（B）、真菌（F）、放线菌（A）及微生物总数量增加了29.5%～56.9%。T4和Act12使室外盆栽试验中根际真菌数量分别提高了73.3%和222.0%，A/F和B/F降低了34.7%～72.4%。③相关分析表明，成熟期谷子茎叶干重、单株谷子籽粒干重与根际B、F、A和总微生物数量显著正相关（r = 0.748～0.971，P < 0.01），而与A/F和B/F显著负相关（r = -0.764 ～ -0.906，P < 0.01）。综上，供试放线菌通过调整根际可培养微生物群落结构促进了谷子生长，增加了谷子产量。因此，通过外源施加放线菌优化根际可培养微生物群落结构是谷子促生增产的可行途径之一。     

Genetic Variation of Blast Resistance in Foxtail Millet (<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.) and its Geographic Distribution

To clarify the geographic variation and isolate specificity in blast resistance, 20 cultivars of foxtail millet (Setaria italica (L.) P. Beauv.) originating from Eurasia were examined for their resistance using 11 Japanese Setaria isolates of blast fungus. Cultivars from the countries east of Pakistan generally showed resistance to most of the 11 fungus isolates, whereas those from the countries west of Afghanistan indicated higher susceptibility. The origin of this geographical regularity was discussed in relation to the deficiency or specificity of relevant resistance gene(s). No identical reaction pattern was observed among cultivars, indicating their highly distinctive isolate specificity. The virulence of isolates was also diverse, since only 2 out of 10 virulent isolates were identical for their reaction patterns. Preliminary genetic analysis of blast resistance to four fungus isolates suggests that they are governed by more than two dominant genes.     

不同生态区骨干谷子品种表型鉴定与遗传分析

骨干谷子品种对谷子产业发展发挥了重要的作用,为了解其优异性状遗传基础及利用价值,选用来源于不同生态区的12个骨干谷子品种,进行表型鉴定和遗传差异分析。结果表明,12个来源于不同生态区的骨干品种在株高、穗长、穗粗、穗下节间长、单穗重、生育期以及黄色素含量等方面差异较大。79对SSR多态性标记共检测到258个多态性变异位点,平均3.265 8个;SSR标记多态性(PIC)的变幅为0.141 1~0.711 6,平均为0.510 1;其中PIC>0.5的SSR标记有50对,占多态性标记的63.3%。12份材料的遗传距离变幅为0.140 2~0.801 1,平均为0.473 7;来自华北夏谷区的豫谷1号和沧谷4号遗传距离最近,而沧谷4号和来自内蒙高原的地方品种金香玉距离最远;总体而言,华北夏谷区品种和西北早熟春谷区品种遗传距离相对较大。相似性系数为0.594时,12个品种可聚为两类,华北夏谷区的豫谷1号、矮88、冀谷19号、沧谷4号和济谷12聚为一类,来自西北春谷早熟区、晚熟区和东北春谷区的7个品种聚为一类,聚类分析结果和品种的生态类型具有较高的一致性。群体结构分析和聚类分析的结果相似,华北夏谷区品种和春谷区品种之间存在基因交流。总之,不同生态区来源品种间遗传差异较大,同一生态区来源品种遗传差异较小;华北夏谷区骨干品种之间遗传差异较春谷区品种遗传差异相对较小;华北夏谷区品种和西北早熟春谷区品种间遗传差异较大,丰富华北夏谷区遗传变异,应加强与西北早熟春谷区品种之间的交流。本研究结果为优异谷子品种培育及种质资源利用提供了一定依据。     

Nuclear DNA content estimations in wild olive ( Olea europaea L. ssp. europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry

Olive tree (Olea europaea L.) is an economically important woody fruit crop widely distributed in the Mediterranean regions. In this work the genome size of six Portuguese cultivars of olive (O. europaea ssp. europaea var. europaea) and wild olive (O. europaea spp. europaea var. sylvestris) was estimated for the first time. The nuclear DNA content of O. europaea cultivars ranged between 2.90 ± 0.020 pg/2C and 3.07 ± 0.018 pg/2C and the genome size of wild olive was estimated as 3.19 ± 0.047 pg/2C DNA. These results suggest a low intraspecific variation at least among the studied cultivars and between them and wild olive. This is not in accordance with previous results in some Italian cultivars where high genome size heterogeneity was found. The methodology presented here seems appropriate for genome size estimations within this genus and opens good perspectives for a large screening of estimation of nuclear DNA content among O. europaea cultivars and Olea species that could clarify this issue.     

Phenotypic diversity in wild barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L. ssp. <Emphasis Type="Italic">spontaneum</Emphasis> (C. Koch) Thell.) accessions collected in Jordan

Wild barley, Hordeum vulgare L. ssp. spontaneum (C. Koch) Thell., is the progenitor of cultivated barley. Almost unanimously the center of diversity is considered to be in the Fertile Crescent of the Near East, where wild barley grows under a wide range of environmental and climatic conditions. Jordanian wild barley is expected to harbor genes useful for the improvement of cultivated barley, particularly those associated with tolerance to drought. This study evaluated 103 wild barley accessions collected from different areas of Jordan along with 29 cultivated barley genotypes for several morphological and agronomical traits. The Hordeum vulgare ssp. spontaneum C. Koch accessions were grouped into six populations according to the longitude, latitude, altitude, and rainfall zone of the collection site, and the cultivated barley in one population. The evaluation was conducted during the 2004–2005 growing season under field conditions in three locations in Jordan; namely, Khanasri, Ramtha, and Maru with 123.0, 222.9, and 429.2 mm annual rainfall, respectively. We used an unreplicated design with two systematic checks (the cultivars Rum and Mu’ta) each repeated 15 times. The results showed the existence of high variability among the Hordeum vulgare ssp. spontaneum C. Koch accessions for most of the traits, especially for plant height, tiller number, days to heading, days to anthesis, peduncle length, and peduncle extrusion. Plant height, earliness, peduncle length, and peduncle extrusion were found to be adaptive traits under drought conditions and several superior genotypes for each trait were identified. Genetic variation within population was much higher than between populations. Clustering of populations was according to their ecological geographical pattern.     

大气CO2浓度升高对谷子生长发育及玉米螟发生的影响

人类活动导致全球大气CO_2浓度持续升高,研究大气CO_2浓度升高对C4作物谷子(Setaria italica)生长发育及虫害发生的影响,可以为谷子等C4作物制订应对气候变化栽培措施提供理论依据。本研究利用OTC(Open Top Chamber)系统,设两个CO_2浓度梯度(正常大气CO_2浓度、正常CO_2浓度+200μmol·mol-1)模拟CO_2浓度升高对谷子生长发育的影响。结果表明:大气CO_2浓度升高后,谷子净光合速率(Pn)、气孔导度(gs)、叶片蒸腾速率(Tr)和水分利用率(WUE)分别增加38.73%、27.53%、6.93%和40.56%;谷子叶片光系统Ⅱ最大光化学量子产量(Fv/Fm)和非光化学淬灭系数(NPQ)显著下降,光系统Ⅱ实际光化学量子产量(ΦPSII)和表观电子传递效率(ETR)显著增加,而对光化学淬灭系数(q P)无显著影响;此外,谷子株高、茎粗和小穗数分别增加3.41%、13.28%和13.11%;而叶重、茎重、千粒重、单株粒数和产量无显著变化,穗重和地上部分生物量分别显著下降12.8%和7.44%;大气CO_2浓度升高后,谷子灌浆期和收获期玉米螟(Ostrinia furnacalis)发生数量显著增加。大气CO_2浓度升高将有利于谷子的生长发育,但会增加玉米螟危害。     

Intraspecific and interspecific variation in Setaria revealed by RAPD analysis

Random amplified polymorphic DNA (RAPD) analysis was applied to foxtail millet (Setaria italica) and other Setaria species in order to assess the degree of polymorphism among and within the species and to investigate their genetic relationships. Twenty accessions of foxtail millet, five of green foxtail (S. viridis), five of yellow foxtail (S. glauca), one each of S. germanica, S. verticilliformis, S. pallidifusca, S. macrostachya, S. sphacelata and S. faberi, and one unidentified, were evaluated for variability using a set of 19 random 10-mer primers. A total of 148 markers were scored for all the accessions. Wide variations in banding profiles among species were observed with nearly every primer used. The results showed that foxtail millet and S. glauca had a considerable degree of variation. The geographic differentiation of RAPD patterns in foxtail millet accessions examined seemed to exist. The present study confirmed that foxtail millet is more closely related to green foxtail than to other species in Setaria, providing support for the origin of foxtail millet from S. viridis and the conspecificity of these two species. The results confirmed that S. germanica and S. italica are conspecific and the former can be replaced by the latter. Setaria glauca and S. sphacelata are distinct from foxtail millet, implying that elite traits found in these two species are relatively difficult to be used in foxtail millet improvement. This study demonstrates that RAPD analysis can be used in assessing intraspecific and interspecific variation in foxtail millet and its wild relatives.     

Close Genetic Proximity Between Cultivated and Wild Bactris gasipaes Kunth Revealed by Microsatellite Markers in Western Ecuador

Bactris gasipaes Kunth (peach palm or Pejibaye) is the only domesticated palm of the Neotropics. The genetic relationships between the crop and its wild relatives are still unclear. We undertook field and laboratory work in order to describe differentiation and relationships between the wild and cultivated populations of the species in Western Ecuador, and their possible interactions. A volumetric study was undertaken on the fruits of both populations, as well as a population genetic analysis in order to clarify these relationships. Fruits from cultivated plants collected in the region of sympatry of wild and cultivated plants in North-West Ecuador showed intermediate volumes between those of reference samples for the wild and cultivated plants in allopatry. Using 8 microsatellite loci, we assessed 83 wild and cultivated individuals from Western Ecuador and cultivated plants from Amazonia and Central America as a reference for the cultivated form. We detected high polymorphism in the wild and cultivated samples and low, but significant level of genetic differentiation between wild and cultivated populations. The cultivated population in North-Western Ecuador showed close genetic proximity with the sympatric wild population, consistent with the volumetric study. These results have implications for hypotheses on evolution of this crop and for strategies of genetic conservation of the wild forms.     

AFLP Fingerprinting in Pigeonpea (Cajanus cajan (L.) Millsp.) and its Wild Relatives

Detection of DNA polymorphism in cultivated pigeonpea (Cajanus cajan) and two of its wild relatives Cajanus volubilis and Rhynchosia bracteata is reported here for the first time using amplified fragment length polymorphism (AFLP) fingerprinting. For this purpose, two EcoRI (three selective nucleotides) and 14 MseI (three selective nucleotides) primers were used. The two wild species shared only 7.15% bands with the pigeonpea cultivars, whereas 86.71% common bands were seen among cultivars. Similarly, 62.08% bands were polymorphic between C. volubilis and pigeonpea cultivars in comparison to 63.33% polymorphic bands between R. bracteata and pigeonpea cultivars, and 13.28% polymorphic bands among pigeonpea cultivars. The cluster analysis revealed low polymorphism among pigeonpea cultivars and very high polymorphism between cultivated pigeonpea and its wild relatives. The AFLP analysis also indicated that only one primer combination (EcoRI + ACT and MseI + CTG), at the most any four primer pair combinations, are sufficient for obtaining reliable estimation of genetic diversity in closely related cultivars like pigeonpea material analyzed herein. AFLP analysis may prove to be a useful tool for molecular characterization of pigeonpea cultivars and its wild relatives and for possible use in genome mapping.     

Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (<Emphasis Type="Italic">Siraitia grosvenorii</Emphasis> [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China,using RAPD and AFLP markers

Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic diversity of Luohanguo was observed at the species level. The percentage of polymorphic loci (P) was 89.4%, Nei’s gene diversity (H _e) was 0.239, and Shannon’s information index (H _o) was 0.373 based on the combined AFLP and RAPD data. There was a high degree of genetic differentiation, with 45.1% of the genetic variation attributed to differences between the populations. The genetic diversity of the Luohanguo cultivars is much lower than that of wild populations (P = 41.8%, H _e = 0.141, H _o = 0.211), and a distinct genetic differentiation is observed between the cultivars and wild accessions. The pool of genetic variation in the wild populations provides an excellent gene resource for Luohanguo breeding.     

Oleaster (var. sylvestris) and subsp. cuspidata are suitable genetic resources for improvement of the olive (Olea europaea subsp. europaea var. europaea)

The olive belongs to Olea, a complex genus and to a species with six subspecies. Subsp. europaea includes both the cultivated olive and the oleaster, the wild ancestor of the olive. Little is known on the phenotype of fruits from subsp. cuspidata. We aimed to compare europaea and cuspidata trees for oil content and composition and to verify whether natural hybrids may exist between the two subspecies. Specimens were from Kenya and putative natural hybrids between cuspidata and europaea were from Stellenbosch (South Africa). Cultivar and oleaster trees were sampled in France (continental and Corsica), Italy (Continental and Sardinia) and Tunisia. We have examined the fruit (drupe) structure between subsp. cuspidata and europaea and extracted oil from the pulp, seed and total drupe. Comparison for oil content was made between the cultivated olive and the oleaster and some cuspidata trees from Kenya. A few of cuspidata individuals from Botanical gardens do not enable phenotyping for oil content and composition. Oil composition analyses were performed for the main fatty acids to compare the three taxa. We used microsatellite markers at 11 loci to compute genetic distances between cuspidata, oleaster and cultivar trees and to reveal eventual hybrids. The SSR polymorphisms were huge between the two subspecies and they revealed that putative hybrids were true hybrids sampled around olive orchards. The whole comparison of oil content shows that olive cultivars display higher oil content than the subsp. cuspidata and that the oleaster trees are intermediate, whereas for oil composition of the drupe, cuspidata from Kenya shows less oleic acid than europaea. However, the cuspidata trees show seed oil composition similarities with the other two taxa. The discussion deals with possible reasons to explain the differences and of the possible uses of these taxa for breeding both the olive and brown olive. H. Hannachi and H. Sommerlatte have equal contribution in the article.     

Amplified fragment length polymorphism-based genetic diversity among cultivated and weedy rye (Secale cereale L.) accessions

Amplified fragment length polymorphism markers were evaluated to determine the genetic diversity and relationships among cultivated and weedy ryes (Secale cereale L.) using a large global set of accessions. On the basis of 395 polymorphic bands resulted from nine PstI-MseI primer combinations, cultivated rye exhibited higher average genetic diversity (H_t?=?0.34) than that of the weedy rye (H_t?=?0.27), however, it had lower genetic differentiation (F_st?=?0.16). The average genetic diversity of cultivated rye varied from region to region ranging from 0.21 to 0.31. As expected, all cultivated accessions clustered together both in dendrogram and principal coordinate diagram indicating common breeding program selection criteria based on similar value-added agronomic characteristics. A clustering of cultivated rye accessions into groups based strictly on geographical origin was not found. The relationships among cultivated, weedy and wild ryes were discussed.     

Combined use of gliadins and SSRs to analyse the genetic variability of the Spanish collection of cultivated diploid wheat (Triticum monococcum L. ssp. monococcum)

This work studied the combined use of gliadins and SSRs to analyse inter- and intra-accession variability of the Spanish collection of cultivated einkorn (Triticum monococcum L. ssp. monococcum) maintained at the CRF-INIA. In general, gliadin loci presented higher discrimination power than SSRs, reflecting the high variability of the gliadins. The loci on chromosome 6A were the most polymorphic with similar PIC values for both marker systems, showing that these markers are very useful for genetic variability studies in wheat. The gliadin results indicated that the Spanish einkorn collection possessed high genetic diversity, being the differentiation large between varieties and small within them. Some associations between gliadin alleles and geographical and agro-morphological data were found. Agro-morphological relations were also observed in the clusters of the SSRs dendrogram. A high concordance was found between gliadins and SSRs for genotype identification. In addition, both systems provide complementary information to resolve the different cases of intra-accession variability not detected at the agro-morphological level, and to identify separately all the genotypes analysed. The combined use of both genetic markers is an excellent tool for genetic resource evaluation in addition to agro-morphological evaluation.     

Comparison of the genetic structure of populations of wild emmer wheat, <Emphasis Type="Italic">Triticum turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides</Emphasis>, from Israel and Turkey revealed by AFLP analysis

The aim of the present study was to assess the genetic variation in several Israeli and Turkish populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, the progenitor of most domesticated wheat. Single spikes were collected in 2002 from 60 plants that grew in six different habitats in Ammiad, northeastern Israel (8–12 plants from each habitat), and in 1998 from 56 plants that grew in seven different habitats in Diyarbakir, southeastern Turkey (8 plants from each habitat). Seeds were planted in a nursery and DNA was extracted from every plant and analyzed by the fluorescent-based amplified fragment length polymorphism (AFLP) method. Seven primer combinations produced 788 discernible loci of which 48.6% were polymorphic in Israel and 40.5% in Turkey. The genetic diversity estimates P (frequency of polymorphic loci) and He (gene diversity) were higher in Ammiad than in Diyarbakir (means of P = 0.34 and He = 0.13 in Ammiad vs. P = 0.20 and He = 0.08 in Diyarbakir). Ammiad populations contained more unique alleles than Diyarbakir populations. The relative genetic diversity estimates (θ) values were 0.188 in Ammiad and 0.407 in Diyarbakir, suggesting better differentiation of the populations in Turkey. Genetic distance was larger between Israeli and Turkish populations than between populations of each country. The data indicate that the Israeli and Turkish populations are considerably diverged and that the Israeli populations are more polymorphic than the Turkish ones, having a larger within-populations genetic variation than among-populations one. The significance of the results in relation to the differentiation pattern of wild emmer in the Near East is discussed.     

Rediscovery of Indian dwarf wheat (Triticum aestivum L. ssp. sphaerococcum (Perc.) MK.) an ancient crop of the Indian subcontinent

Indian dwarf wheat (Triticum aestivum L. ssp. sphaerococcum (Perc.) Mac Key, synonym: T. sphaerococcum Perc.) is endemic to southern Pakistan and northwestern India. It was one of the main winter crops grown by ancient Indian cultures. However, it disappeared from the record during the early twentieth century, especially after the Green Revolution brought modern wheat varieties into India and Pakistan. Whether or not Indian dwarf wheat is presently cultivated has been unclear. Here we report on the rediscovery of the cultivation of this wheat in northern Karnataka and southern Maharashtra in India. Molecular genetic analysis of the chloroplast DNA of the two specimens collected at location 3 revealed that both samples have a unique haplotype that is specific to Indian dwarf wheat. We found this wheat at three locations in 2010, but at only one of the three locations in 2011. Therefore, the future survival of this subspecies is uncertain. Further ethnobotanical research is urgently needed to conserve this unique genetic resource for the future.     

Maintenance of Squash (<Emphasis Type="Italic">Cucurbita</Emphasis> spp.) Landrace Diversity by Farmers' Activities in Mexico

Squash (Cucurbita spp.) is a common component in traditional cropping systems in Mexico, mainly in the agroecosystem known as the “milpa”, in which squash is cultivated in association with maize (Zea mays), the main crop. Using a questionnaire, 80 farmers were interviewed about crop production and selection practices in order to understand how these factors affect genetic diversity of local squash populations. We found that the most of the farmers who cultivate squash were elderly 59.8 ± 14.5 (mean ± SD; n = 78) years old. Squash varieties in the area were exclusively locally adapted landraces, and had not been replaced by modern squash cultivars. Two cultivated squash species, C. argyrosperma ssp. argyrosperma and C. moschata, had been grown intercropped with maize by 97.5% of the interviewed farmers, but only 50.0% were still producing squash at the time of the study. Farmers recognize typical characteristics of particular varieties within each of the local cultivated squash species, and selection is directed to maintain their identity. Nearly two thirds of the farmers (62.0%) had exchanged seeds of squash for planting, a practice that serves to increase genetic variability in the populations. All of the interviewed farmers were conscious of the possible hybridization between the wild gourd (C. argyrosperma ssp. sororia) and their cultivated squash. Despite various natural and human managed factors identified as contributing to enhancement of genetic diversity in these populations, results of the study show that genetic erosion of Cucurbita is likely in the region in the near future.