A simple and efficient cryopreservation of in vitro-grown shoot tips of `Troyer' citrange [Poncirus trifoliata (L.) Raf. × Citrus sinensis (L.) Osbeck.] by encapsulation-vitrification

Wheat of two strong high-protein and two weak low-protein cultivars from New Zealand and Australia were milled to commercial specifications. All millstreams were tested for α-amylase, β-amylase, falling number, protein, starch, damaged starch, amylose, amylopectin, pentosan and ash. The distribution of β-amylase in millstream flours was more variable among cultivars than α-amylase. Generally, both enzymes had lowest activity in sizing and early reduction flours. α-Amylase was very high in the bran, pollard and germ fractions, in which ash content was very high, whereas β-amylase was low in these fractions. These observations, together with the moderate correlation of α-amylase and poor correlation of β-amylase to ash content, suggest that most α-amylasein flour derives from contamination with bran, pollard and germ, whereas most β-amylase derives from the endosperm. Falling numbers varied between the cultivars, but variation amongst millstreams for each cultivar was low, except for cv. Frame, which had particularly high falling number values (834 and 1197) in second and third break flours. These two flours had some of the highest α-amylase levels and lowest starch levels. However, they also had very high protein content (22 and 26%) and very low starch damage (3.2 and 4.5%), which may contribute to the high falling numbers. When endogenous α-amylase in the flour with the highest falling number was supplemented with high levels of barleyα-amylase, the flour withstood the detrimental effects of α-amylasein baking (sticky crumb, poor crumb texture and loaf volume) better than flours of lower falling number, but did not withstand the effects ofα-amylase on falling number. This revised version was published online in August 2006 with corrections to the Cover Date.     

Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers

Fifty-eight accessions of sesame (Sesamum indicum L.), an important oil seed crop of the tropics and subtropics were analysed using random amplified polymorphic DNA (RAPD) technique. The material analysed comprised 36 collections from 18 different states of India and four adjoining countries of the Indian subcontinent, and 22 exotic accessions from 21 sesame growing countries around the world. The results from PCR amplifications with the selected 24 random 10-mer primers were statistically analysed. The value of Jaccard’s similarity coefficients ranged from 0.19 to 0.89. The results indicated the presence of high level of genetic diversity. However, the extent of genetic diversity was greater in the collections from Indian subcontinent as compared to the exotics. Among the Indian accessions, the collections from Rajasthan and North-eastern states were highly diverse. The phenetic analysis grouped 48 out of 58 accessions in six clusters and the remaining highly diverse accessions were placed outside these close-knit clusters. The Bootstrap estimates obtained by Wagner parsimony analysis were significant for seven out of 49 nodes in the majority-rule consensus tree (<95% occurrence). The results of both the analyses were, however, broadly comparable when the constitution of the individual clusters were considered. The principal components analysis indicated that the first two components accounted for only 21% of the total variations and in order to explain <75% of variations 18 components were required. The high level of genetic diversity prevalent among the Indian collections is probably indicative of the nativity of this crop species. Similarly, the relatively lower level of polymorphism in exotic germplasm could be ascribed to the comparatively recent introductions of limited germplasm of this crop into some of the non-traditional sesame growing countries. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular Marker based Genetic Diversity Analysis in Rice (Oryza sativa L.) using RAPD and SSR markers

The availability of an array of molecular marker systems allowed comparing the efficiency of two of these marker systems to estimate the relationships among various taxa. The objective of this study was to assess the genetic diversity among 40 cultivated varieties and five wild relatives of rice, Oryza sativa L. involving simple sequence repeat (SSR) randomly amplified polymorphic DNA (RAPD) markers. The accessions were evaluated for polymorphisms after amplification with 36 decamer primers and 38 SSR primer pairs. A total of 499 RAPD markers were produced among the 40 cultivated varieties and five wild relatives with a polymorphism percentage of 90.0. Out of 38 SSR primer pairs used, only one locus viz., RM115 was monomorphic. The average Polymorphism Information Content (PIC) value was 0.578 and it ranged from a low of zero (RM 115) to a high of 0.890 (RM 202). The Mantel matrix correspondence test was used to compare the similarity matrices and the correlation coefficient was 0. 582. The test indicated that clusters produced based on RAPD and SSR markers were not conserved since matrix correlation value was 0.582 as against the minimum required value of 0.800. The two marker systems contrasted most notably in pair-by-pair comparisons of relationships. SSR analysis resulted in a more definitive separation of clusters of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination of relationships between accessions that are too close to be accurately differentiated by RAPD markers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18^th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank. This revised version was published online in July 2006 with corrections to the Cover Date.     

Linkage of random amplified polymorphic DNA markers to downy mildew resistance in cucumber (Cucumis sativus L.)

Marker assisted selection (MAS) may improve the efficiency of breeding downy mildew resistant cucumber cultivars. A study was conducted to identify random amplified polymorphic DNA (RAPD) markers linked to the downy mildew resistance gene (dm) which would be suitable for MAS. A total of 145 F₃ families from two populations (55 from the WI 1983G × Straight 8 population and 90 from the Zudm1 × Straight 8 population) were evaluated over five locations in North America and Europe. Resistant and susceptible F₃ families were identified and mean family resistance ratings were used to type individual F₂ plants. No evidence for race differences in the pathogen (Psuedoperonospora cubensis (Berk. & Curt.) Rostow) between North America and Europe was found. Phenotypic correlations between locations ranged from 0.3 to 0.7. Of the 135 polymorphic RAPD markers identified from 960 primers, five were linked to dm - G14₈₀₀, X15₁₁₀₀, AS5₈₀₀, BC519₁₁₀₀, and BC526₁₀₀₀. In the WI 1983G × Straight 8 population, G14₈₀₀ was linked to dm at 16.5 cm, AS5₈₀₀ at 32.8 cm, BC519₁₁₀₀ at 9.9 cm, and BC526₁₀₀₀ at 19.2 cm. In the Zudm1 ×Straight 8 population, G14₈₀₀ was linked at 20.9 cm, X15₁₁₀₀at 14.8 cm, AS5₈₀₀ at 24.8 cm, and BC526_{_1000} at 32.9 cm. MarkersG14₈₀₀ and BC519₁₁₀₀ were linked in repulsion to the dm allele, and X15₁₁₀₀, AS5₈₀₀, and BC526₁₀₀₀ were linked in coupling phase. These genetic markers may be exploited to develop an efficient MAS strategy for breeding resistant cucumber cultivars. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparing RAPD and AFLPTM analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh.) cultivars

Forty-one apple (Malus × domestica Borkh.) cultivars were screened for RAPD (Random Amplified Polymorphic DNA) and AFLP(Amplified Fragment Length Polymorphism) markers. RAPD analysis was performed with 35 arbitrary 10-mer primers, selected from 60 primers tested (kits A, C and E, Operon Technologies, Inc.). Of a total of 362bands observed, 208 (57.5%) were polymorphic. Three-hundred-and-eighty-one AFLP fragments were obtained with 8primer combinations, of which 218 (57.2%) were polymorphic. Cultivars differentiated through mutation were included in this study and showed identical patterns when analysed with both RAPD and AFLP analysis. The estimated genetic relationships were correlated (r = 73.7%) between the analysis with the two different markers. UPGMA analysis was performed and dendrograms were constructed using either the data apart from each(RAPD and AFLP) method or combined in a single joint matrix. The relationships among the forty-one studied cultivars were basically consistent with the known lineage and geographic origins of the cultivars. The four Portuguese cultivars included in this study clustered together and diverged from the other cultivars. Apparently they constitute an independent genetic pool, which could be of interest for apple plant breeders. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of genetic variability in grapefruits (Citrus paradisi Macf.) and pummelos (C. maxima (Burm.) Merr.) using RAPD and SSR markers

The genetic variability of 38 grapefruit (Citrus paradisi Macf.) and three pummelos (C. maxima (Burm.) Merr..) accessions was evaluated using RAPD, and single sequence repeat (SSR) analyses. Approximately49% of the 198 RAPD were polymorphic, and 4.6 alleles per SSR loci were identified. PIC values changed from 0.093 to 0.450. A UPGMA phenetic tree was constructed and two main grapefruit groups were identified. The grapefruit accessions `do Cabo' and `Siamesa-Filipinas'clustered very close to the pummelos in Group A. The Group B consisted of three sub-groups, which comprised all of the other grapefruit accessions. The majority of grapefruit accessions showed a narrow genetic base suggesting that the observed morphological polymorphism within the group must be associated with somatic mutations, which were not detected by these molecular markers. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic analysis and identification of two soybean mosaic virus resistance genes in soybean [Glycine max (L.) Merr]

Soybean mosaic virus (SMV) commonly affects soybean production worldwide, and the SC18 strain has been widespread in China. This study aimed to characterize and map the SC18 resistance genes present in soybean cultivars ‘Kefeng No. 1’ and ‘Qihuang 22’. Inheritance analysis revealed that two independent single dominant genes in Kefeng No. 1 and Qihuang 22 confer resistance to SC18. Using simple sequence repeat (SSR) markers and bulked segregant analysis, the Kefeng No. 1 and Qihuang 22 resistance genes were located on soybean chromosomes 2 and 13, respectively. We further screened two populations of recombinant inbred lines with 32 SSR markers in the target region, where the resistance gene in Kefeng No. 1 was fine mapped to an 80‐kb region containing six putative genes. Sequence and expression analyses of these genes revealed that SMV resistance in Kefeng No. 1 was probably attributable to three of the candidate genes (i.e. Glyma.02G127800, Glyma.02G128200 and Glyma.02G128300). Collectively, the results of this study will greatly facilitate the cloning of SC18 resistance genes and marker‐assisted breeding of SMV‐resistant soybean cultivars.     

Plant Regeneration and Genetic Variability from Tissue Cultures of Sunflower (Helianthus annuus L.)

Adventitious buds were induced from in vitro culture of sunflower (Helianthus annuus L.) cotyledons. Four inbred lines (G1, G2, G3 and HA89), an open pollinated variety (‘Argentario’) and two hybrids with specific genetic markers were used. Cotyledons were cultured in vitro on MS medium (Murashlge and Skoog 1962) containing various concentrations of kinetin and indole 3-acetic acid (IAA). The quantitative interactions between auxin and cytokinin, the age of the cotyledons and the 2,3,5-triiodobenzoic acid (TIBA) treatments have been found to influence shoot regeneration. The plantlets, after rooting, were successfully established on soil. Qualitative variation was noted in self-pollinated progeny of plants regenerated from culture of two inbreds. Chimerism in regenerated plants was indicated by sectoring of the genetic markers. Some culture-induced variant phenotypes were similar to known spontaneous mutation in sunflower but others have been not yet described. Preliminary data indicate that most of them may have single-gene recessive inheritance.     

Molecular mapping of a new genic male-sterility gene causing chalky endosperm in rice ( Oryza sativa L.)

A genic male-sterility gene newly induced by chemical mutagenesis, tentatively designated as ms-h(t), was located on the molecular map of rice and tested for its effect on chalky endosperm. Bulked segregant analysis was used to determine the chromosomal location of the ms-h(t) locus by screening four to five RFLP markers per chromosome. After confirming that the gene was located on chromosome 9, twenty-four RFLP markers from chromosome 9 were surveyed for polymorphism in the parents of the mapping population. Of these, eleven markers were mapped around the ms- h(t) locus. RG451 and RZ404 flanked the ms-h(t) gene, at 2.5cM and 3.3cM, respectively. Heterozygous F2 to F4 progenies were tested for co- segregation of male-sterility and chalky endosperm and it was revealed that ms-h(t) might have a pleiotropic effect on chalky endosperm. This mutant would be a good biological material to characterize the biochemical mechanism of male sterility and related pleiotropic effects. Further studies should be needed to know the usefulness of this mutant for hybrid seed production. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic analysis of resistance in barley to barley yellow dwarf virus

The inheritance of resistance to barley yellow dwarf virus (BYDV) was studied in the selected 24 spring and winter barley cultivars that showed a high or intermediate resistance level in 1994‐97 field infection tests. The polymerase chain reaction diagnostic markers YLM and Ylp were used to identify the resistance gene Yd2. The presence of the Yd2 gene was detected with both markers in all the resistant spring barley cultivars and lines from the CIMMYT/ICARDA BYDV nurseries. The results of field tests and genetic analyses in winter barley corresponded with marker analyses only when the Ylp marker was used. Genes non‐allelic with Yd2 were detected by genetic analyses and the Ylp marker in moderately resistant spring barley cultivars ‘Malvaz’, ‘Atribut’ and ‘Madras’, and in the winter barley cultivars ‘Perry’ and ‘Sigra’. Significant levels of resistance to BYDV were obtained by combining the resistance gene Yd2 with genes detected in moderately resistant cultivars. The utilization of analysed resistance sources in barley breeding is discussed.     

Genetic analysis of Lolium. I. Identification of linkage groups and the establishment of a genetic map

A genetic map of Lolium has been produced using isozyme, restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers applied to a segregating family derived from an F₁ hybrid plant of L. perenne × L. multiflorum provenance, crossed on to a doubled haploid L. perenne. A total of 106 markers, out of a total of 160 polymorphic loci analysed, have been ascribed to seven linkage groups covering a map distance of 692cM, Two of these groups may be allocated to chromosomes 2 and 6 of the Lolium genome. The remaining unallocated markers, the majority of which showed severe segregation distortion, could be associated into small groups of two or three markers which showed no linkage with the main groups at a LOD of 2.8 or, if associated, could not be mapped in a satisfactory manner. This high incidence of disturbed segregations could be accounted for by the use of an interspecific hybrid between two species of differing genome size, with consequent cytological imbalance.     

河北省和中棉所育成陆地棉品种的遗传多样性分析

分别选取河北省历年育成的 1 9个陆地棉品种 ,中国农业科学院棉花研究所自 2 0世纪 70年代末到 90年代中期选育的品种中的 1 6个陆地棉品种 ,利用 RAPD分子标记研究各自育成品种的遗传多样性。 41个带型清晰、重复性好的多态性引物用于 RAPD分析 ,河北省育成的 1 9个品种得到 6 6个多态性位点 ,而中棉所育成的 1 6个品种扩增到 6 4个多态性位点。分析采用 Jaccard' s相似系数 ,使用 NTSYS- pc1 .80数据分析软件 ,非加权组平均法 (UPGMA)聚类。成对相似系数比较表明 ,中棉所在 2 0世纪 70年代末到 90年代中期育成的品种的遗传多样性水平高于河北省育成的品种。河北省育成的 1 9个品种的遗传基础很狭窄 ,斯字棉和岱字棉是河北省棉花两个最重要的基础种质 ,其中的 1 5个品种在聚类图上可以被分为两类 ,分别属于岱字棉和斯字棉系统。中棉所育成的 1 6个品种在聚类图上可被划分为三个类群。     

Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy

Genetic maps of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP) and inter simple sequence repeats (ISSR) markers in pineapple (2n = 2x = 50) are reported for the first time. On the basis of a segregating population of 46 F1 individuals from a cross Ananas comosus x A. bracteatus, genetic maps of these two species were constructed using the two‐way pseudo‐testcross approach. The A. bracteatus map consists of 335 markers (60 RAPDs, 264 AFLPs and 11 ISSRs) assembled into 50 linkage groups, 26 of them with at least four markers. The A. comosus map consists of 157 markers (33 RAPDs, 115 AFLPs, eight ISSRs and the ‘piping’ trait locus) organized into 30 linkage groups, 18 of them with at least four markers. These maps cover, respectively, 57.2% of the A. bracteatus genome estimated as 3693 cM long, and 31.6% of the A. comosus genome calculated as 4146 cM. A rough estimate of 120 and 127 kbp/ cM on average was found for the relationship between physical and genetic distance for A. bracteatus and A. comosus, respectively.     

Genetic mapping and inheritance of Russian wheat aphid resistance gene in accession IG 100695

The Russian wheat aphid (RWA), Diuraphis noxia (Kurdjumov), is an important pest of small‐grain cereals, particularly wheat, worldwide. The most efficient strategy against the RWA is to identify sources of resistance and to introduce them into susceptible wheat genotypes. This study was conducted to determine the mode of inheritance of the RWA resistance found in ICARDA accession IG 100695, to identify wheat microsatellite markers closely linked to the gene and to map the chromosomal location of the gene. Simple sequence repeat (SSR) marker scores were identified in a mapping population of 190 F₂ individuals and compared, while phenotypic screening for resistance was performed in F_2 : 3 families derived from a cross between ‘Basribey’ (susceptible) and IG 100695 (resistant). Phenotypic segregation of leaf chlorosis and rolling displayed the effect of a single dominant gene, temporarily denoted Dn100695, in IG 100695. Dn100695 was mapped on the short arm of chromosome 7D with four linked SSR markers, Xgwm44, Xcfd14, Xcfd46 and Xbarc126. Dn100695 and linked SSR markers may be useful for improving resistance for RWA in wheat breeding.     

Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers

Genetic variation among 43 date palm (Phoenix dactylifera L.) accessions, including 37 accessions from Morocco and 6 cultivars from Iraq and Tunisia, was studied using Random Amplified Polymorphic DNA (RAPD) markers. The pre-screening of 123 primers on four genotypes allowed selection of 19 primers which revealed polymorphism and gave reproducible results. All 43 analysed genotypes were distinguishable by their band patterns. RAPD technology therefore appears very effective for identifying accessions of date palm. RAPD-based genetic distance was used to determine the relationships between the accessions. The grouping-association identified by cluster analysis was rather weak. However, morphologically similar varieties clustered together. A relatively low polymorphism and a lack of evident organisation are observed among the date palm varieties grown in Morocco. This could be related to the mode of introduction and maintenance of the Moroccan date palm germplasm involving limited foundation germplasm, exchange of cultivars between plantations, and periodic development of new recombinant cultivars following sexual reproduction. This revised version was published online in August 2006 with corrections to the Cover Date.     

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F₈ recombinant inbred line population derived from Kiev Mutant/{"type":"entrez-protein","attrs":{"text":"P27174","term_id":"14195583","term_text":"P27174"}}P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.     

Genetic characterization of Malawian cowpea (Vigna unguiculata (L.) Walp) landraces: diversity and gene flow among accessions

Cowpea has been cultured from ancient timesin Africa and Asia and is now widespreadthroughout the tropics and subtropics.Cowpea accessions can be distinguishedphenotypically from one another by theirgrowth habit, time to maturity, yield, andseed size and colour. Data on geneticdiversity of farmer-developed accessionsare lacking. The main objective of thisstudy was to determine the pattern andextend of RAPD marker variation within andamong cowpea populations from differentagroecological zones and to determine thedegree of genetic relationships and geneflow among different landraces used bylocal farmers. Twenty of the 30 RAPDprimers tested allowed amplifications ofrandom polymorphic (RAPD) loci. Overall,80% of the scored loci were polymorphic. The degree of band sharing was used toevaluate genetic distance betweenaccessions and to construct a phylogenetictree. The genetic distance values amongaccessions varied between 0.09 to 0.57.Although some small clusters groupedaccessions of the same growth habits, ageneral lack of agreement betweenclustering and morphological features wasobserved. The analysis of molecularvariance revealed that within-region ortypes (among accessions) variationaccounted for 96% of the total molecularvariance. This high within-accessionvariability is being sustained by anuncontrolled gene flow among populations.     

Cloning, genetic and physical mapping of resistance gene analogs in barley (Hordeum vulgare L.)

The majority of verified plant disease resistance genes isolated to date belong to the NBS‐LRR class, encoding proteins with a predicted nucleotide binding site (NBS) and a leucine‐rich repeat (LRR) region. Using degenerate primers, designed from the conserved motifs of the NBS region in tobacco N and Arabidopsis RPS2 genes, we isolated 190 resistance gene analogs (RGA) clones from barley genomic DNA. A total of 13 single‐ and low‐copy RGAs were genetically mapped onto chromosomes 1H–7H (except 5H) using three barley double haploid (DH) mapping populations: Steptoe × Morex, Harrington × TR306 and LUGC × Bowman. Sequence analysis of the RGAs showed that they are members of a diverse group. As a result of BLAST searches, one RGA proved unique as it did not detect any significant hit. Another RGA is putatively functional, because it detected several barley expressed sequence tag (EST) matches. To physically map the RGAs, 13 sequences were used to screen a 6.3 × cv. ‘Morex’ bacterial artificial chromosome (BAC) library. After fingerprint analysis, eight contigs were constructed incorporating 62 BAC clones. These BAC contigs are of great value for positional cloning of disease resistance genes, because they span the regions where various barley R genes have been genetically mapped.