Genetic diversity of Pakistan wheat germplasm as revealed by RAPD markers

Wheat breeding in Pakistan started in 1930s before partition in the United India and so far has released more than 68 cultivars, but no systematic analyses of the genetic diversity of Pakistan wheat have been made. Twenty Pakistan wheat cultivars released from 1933 to 2002 were examined for genetic diversity and relationships using random amplified polymorphic DNA (RAPD) markers. Forty-two RAPD primers were applied and 184 polymorphic bands were generated for each cultivar. Most of the cultivars were genetically interrelated, although six of them displayed some genetic distinctness. The RAPD variation observed among these cultivars was low. Only 40.7% of the total scorable bands were polymorphic, and 26.1% of the polymorphic bands were observed most frequently (f = 0.95) among the 20 cultivars. The proportions of polymorphic bands for each cultivar ranged from 0.67 in ‘Yecora’ to 0.84 in ‘C-250’ with an average of 0.76. About 1.4% of the RAPD variation might have been fixed over the 69 years of wheat breeding, but such fixation was not statistically significant. These results are significant for future improvement and conservation of Pakistan wheat.     

Genetic diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.     

Diversity analysis of provitamin A maize inbred lines using single nucleotide polymorphism markers

ABSTRACT

The success of a breeding programme can be determined by the level of genetic diversity that exists among breeding materials. This study was carried out to (i) determine the level of genetic diversity that exist among the collection of tropical provitamin A maize inbred lines and (ii) evaluate the genetic structure and divergence of provitamin A maize inbred lines. Forty-six advanced provitamin A inbred lines obtained from the International Maize and Wheat Improvement Centre (CIMMYT) and International Institute of Tropical Agriculture (IITA) were genotyped using 3047 single nucleotide polymorphism (SNP) markers. Genotyping was done following an Illumina Infinium HD Assay Ultra protocol. Eight six percent of the SNPs were polymorphic with the mean polymorphic information content of 0.36. Cluster analysis displayed two distinct clusters. The average pairwise genetic distance among the inbred lines was 0.60. The average gene diversity was 0.359. Variation was partitioned into among individuals (78%), among populations (12%) and within individuals (10%). Overall results suggest the inbred lines are genetically diverse. The key implication of this study is that selection should be done from genetically diverse inbred lines in order to exploit heterosis when developing hybrids.     

Genetic diversity studies and screening for rice stem borer (Chilo Agamemnon) resistance in six Egyptian rice cultivars (Oryza sativa L.) using DNA based-markers

Genetic Resources and Crop Evolution - In order to assess the genetic diversity among six Egyptian rice cultivars and developing cultivars resistant to different rice stem borers, random amplified...     

Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers

ABSTRACT

The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identi?ed four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly signi?cant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identi?cation and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.     

High-resolution DNA fingerprinting of Indian rice (Oryza sativa L) varieties by amplified fragment length polymorphism

To assess diversification of indica rice, fingerprinting of 42 Indian rice varieties (Oryza sativa L) and one accession of O. brachyantha Chev. et Roehr. was taken up using amplified fragment length polymorphism (AFLP). Six primer combinations of PstI and MseI were used for this purpose. On denaturing polyacrylamide sequencing gel, on average 41 scorable AFLP bands were obtained of which 81% were polymorphic. Each variety revealed a distinct fingerprint. Data were scored on the basis of presence and absence of bands and cluster analysis was performed using Dice similarity coefficients. The resultant dendrogram showed four major clusters and traits. Some varieties especially landraces revealed more polymorphism and unique loci. Such study will be a valuable tool for proper choice of parents in mapping populations or breeding programs to produce heterotic several inexplicable minor clusters. Some varieties were grouped according to parentages of the cross while some were grouped according to physiological combinations apart from providing a characteristic fingerprint.     

Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers

Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the center of domestication is essential for sustainable production of fine-flavored cacao beans and contributes to in situ/on-farm conservation of farmer varieties. Based on 70 single nucleotide polymorphism markers, we analyzed 84 fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. The study also included 31 clones from the international cacao collections to serve as references. The SNP based multilocus matching identified six synonymous groups, including 14 Criollo and two Amelonado varieties. A moderately high level of genetic diversity was observed in these farmer varieties, indicating the possibility to further explore intra-population variation and breed for fine-flavored cocoa. Multivariate analysis showed clustering of the 84 farmer accessions in five genetic groups: ancient Criollo, Amelonado, Trinitario (including Nicaragua Trinitario and Honduras Trinitario) and Upper Amazon Forastero (only one accession). The Honduras Trinitario differed from the Nicaragua Trinitario group. The clustering results largely supported the perceived classification of cacao by local farmers and researchers, which was mainly based on morphological traits. However, the well known traditional variety “Indio” in this region was identified as synonymous with Amelonado. Parentage analysis showed that the variety “Indio” (or Amelonado) contributed more to the Trinitario type farmer varieties, whereas ancient Criollo had less influence. The present study demonstrates the efficacy of using a small set of SNP makers for cacao germplasm characterization, and further depicts the diverse origins and parentage in farmer varieties from Mesoamerica. This information thus will be highly useful for conservation and utilization of cacao germplasm from this region.     

Genetic diversity of the African wild rice (Oryza longistaminata Chev. et Roehr) from Ethiopia as revealed by SSR markers

Data from microsatellite markers have been extensively used for both in situ and ex situ conservation strategies by determining the level of genetic diversity of natural populations that can widen the gene pool of cultivated plants. Such conservation practices are based on understanding of the between and within population genetic variations and partitioning populations on the basis of geographic origin. Therefore, the objective of this study was to assess the genetic diversity of Oryza longistaminata Chev. et Roehr and how this variation is partitioned within and between the eight O. longistaminata populations found in the different geographic regions of Ethiopia using simple sequence repeat markers. Five microsatellite markers in 320 samples generated 64 alleles that revealed the presence of large amount of genetic variability (Ho = 0.225; He = 0.768; Na = 7.375; Ne = 6.565 and P = 0.744). The F-statistics detected by the microsatellite loci showed Fst = 0.064 and Fis = 0.743 and there was no population in Hardy–Weinberg equilibrium. The genetic diversity results obtained from this data indicated that there are high levels of genetic diversity in the populations of O. longistaminata studied and it is higher within than between populations. Among the eight populations sampled, five populations were identified as priorities for conservation strategies. Thus, national collection and conservation strategies need to consider these populations.     

Silicon‐induced cadmium resistance in rice (Oryza sativa)

Silicon (Si)‐induced cadmium (Cd) tolerance in rice (Oryza sativa L.) was investigated by analyzing Cd uptake, growth, and physiological parameters. Silicon treatments (0.0, 0.2, or 0.6 mM) were added to 6 d–old seedlings, and Cd treatments (0.0 or 5.0 μM) were added to 20 d–old seedlings. Parameters determined included: maximum net CO₂ assimilation (A_max), stomatal conductance (g_smax), and transpiration (E_max) rates at varying intercellular CO₂ concentrations (C_i). Also measured were chlorophyll fluorescence, growth, and Cd‐uptake parameters. Results showed a Si‐induced inhibition of Cd uptake. However, 0.2 mM or 0.6 mM Si treatment concentrations did not differentially inhibit Cd uptake or differentially alleviate Cd‐induced growth inhibition, despite a significant increase in tissue Si concentration due to 0.6 mM Si treatment compared to 0.2 mM Si treatment. Additionally, photosynthesis and chlorophyll‐fluorescence analysis showed that treatment with Cd significantly inhibited photosynthetic efficiency. Interestingly, the addition of 0.2 mM Si, more so than the addition of 0.6 mM Si, significantly alleviated the inhibitory effects of Cd toxicity on photosynthesis and chlorophyll‐fluorescence parameters. Our results suggest that 0.2 mM Si could be close to an optimum Si‐dose requirement for the alleviation of toxicity symptoms mediated by moderate (5 μM) Cd exposure.     

Heat shocks increase the chilling tolerance of rice (Oryza sativa) seedling radicles

The growth of rice (Oryza sativa L., cv. M202) seedling radicles, initially 10 +/- 1 mm long, was linear for the 96 h it took them to grow to 150 mm at 25 degrees C. Exposure to 5 degrees C for 24 h reduced the rate of growth by about 50%, and longer exposures caused a progressive reduction in growth. Initial radicle length significantly affected chilling sensitivity: with 2 days at 5 degrees C inhibiting growth at 25 degrees C by 23% for 1-mm radicles, 63% for 10-mm radicles, and 87% for 40-mm radicles. Heat shocks of 35 degrees C for 4 min, 40 degrees C for 3 min, 45 degrees C for 2 min, or 50 degrees C for 1 min, prior to chilling, reduced the 75% inhibition of radicle growth caused by 2 days at 5 degrees C to 34%, 25%, 14%, and 13%, respectively. The length of exposure that conferred chilling tolerance increased from less than 2 min for 50 degrees C to over 8 min for 35 degrees C. This increase in effective treatment duration was accompanied by a reduction in the maximum induced chilling tolerance. Practical application of heat-shock treatments to increase the chilling tolerance of rice seedlings may sacrifice a small reduction in maximum chilling tolerance at the lower inductive temperatures for a larger margin of safety in their application.     

Arsenic mobilization in rice (Oryza sativa) and its accumulation in the grains

Flooded rice (Oryza sativa L.) may contain high arsenic (As) concentrations compared to other grain crops. For the development of measures to reduce the As concentration of rice grains, knowledge about the mobility of As within the rice plant is required. Therefore, to investigate the mobilization of As within the plant, rice was grown in nutrient solution and exposed to As either before flowering, after flowering, or continuously until maturity. Furthermore, rice was grown in four soils under greenhouse and field conditions and the time course of As accumulation in grains during the grain‐filling period was investigated. When grown in nutrient solution, As removal at flowering did not reduce As concentrations in polished rice compared to plants supplied with As continuously or after flowering. Plants that received As only after flowering had the same As concentrations in shoot and bran as plants receiving As only before flowering. However, continuous As supply resulted in doubling of As concentrations in both plant parts. In contrast to grain and shoot, the As concentration in the root decreased after As removal compared to the treatments receiving As only after flowering or continuously. The observations indicate that As was mobilized from root or shoot to the grain and that it was accumulated in the grain, although it was not available in nutrient solution during the grain‐filling period. In soil experiments, the 1000‐grain weight increased up to 2 weeks before harvest in the field as well as in the greenhouse. The As concentration in rice grain was constant during the whole grain‐filling period. It was at a similar level under field and greenhouse conditions, and its variation among soils was in the same order indicating that soil was the decisive factor for As concentration in grains. Our results suggest that temporary cultural measures during the cultivation period, for example drainage, might be ineffective because of the mobilization capacity within the rice plant. Moreover, harvest before final maturity of grains would not reduce the As concentration since it remained constant during the grain‐filling period.     

A retrotransposon-based probe for fingerprinting and evolutionary studies in rice (Oryza sativa)

A genomic DNA fragment (pAA7-2) amplified by a random amplified polymorphic DNA primer from the rice cultivar IR68 was used to assess the genetic variation and genetic relationships among the species of genus Oryza. A Southern hybridization experiment of diverse upland rice accessions using a single restriction enzyme HindIII generated unique DNA fingerprint for each accession. The differential hybridization pattern reflecting the copy number variation of pAA7-2 in a collection of wild species and cultivated species of rice provided insight about the genetic relationships among them. All AA genome species exhibited clear banding pattern suggesting presence of fewer copies of this sequence. Strongest hybridization signal was obtained in species belonging to BB, CC, GG, BBCC, CCDD genomes, whereas weakest hybridization signal was visible in EE, FF, and HHJJ genome species. Oryza brachyantha was the most divergent species. Clear difference in banding pattern was evident between Oryza schlechteri and Oryza coarctata belonging to HHKK genome. Although pAA7-2 had no repetitive sequences often associated with hypervariable loci, homology to a putative unclassified expressed retrotransposon distributed over several rice chromosomes was responsible for the complex banding patterns. There were more sites homologous to pAA7-2 sequence in corn and sorghum genome compared with the rice genome. The study demonstrates the potential of pAA7-2 as a powerful molecular tool for DNA fingerprinting, genetic diversity, phylogenetic, and evolutionary studies in Oryza sativa and its wild relatives and other grasses.     

荧光定量PCR检测淹涝胁迫下水稻Adh2基因的表达量变化

采用荧光定量PCR方法,应用特异性引物,对淹涝胁迫下水稻叶片中低丰度表达的乙醇脱氢酶基因Adh2（Alcohol dehydrogene2）进行转录水平上的定量分析。实验得到一组基线平整、斜率大、指数区明显的S形荧光曲线。结果显示,在淹涝胁迫前期,Adh2基因表达持续增加,在水淹后8h表达量最大,随后下降。淹涝胁迫能诱导叶片中Adh2基因大量表达,且呈低一高一低的变化趋势。     

Use of sequence-related amplified polymorphism (SRAP) markers for comparing levels of genetic diversity in centipedegrass (Eremochloa ophiuroides (Munro) Hack.) germplasm

Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) has great potential as a low-input turf within the U.S. because of its lower management requirements and its tolerance to an array of environmental stresses. Only a handful of centipedegrass cultivars have been released to date, however. This is mainly due to limited morphological variation present in U.S. centipedegrass germplasm. With the objective of broadening the genetic base of this species, a germplasm collection trip was conducted in seven Chinese provinces in 1999. Although the resulting accessions exhibited morphological variation for a number of traits, little is known about levels of molecular variability in these accessions or how those levels compare to diversity in materials previously present in the U.S. Sequence-related amplified polymorphism (SRAP) markers were used in the current study to investigate these issues. Eleven primer combinations yielded 279 scored fragments. Genetic diversity, in terms of number of alleles and Dice similarity values, was highest in the Henan and U.S. groups. AMOVA indicated that while both the among and within components of variance were significant (P < 0.0001), most of the variation (94%) could be explained by differences within groups. The PCO plot showed large differences in levels of diversity in all groups evaluated. Overall, our results indicate that while the U.S. collection had high levels of diversity compared to other groups, there are alleles in the Chinese groups not represented in the U.S. collection. These materials could represent additional sources of variation to be used in centipedegrass cultivar development programs.     

Potential use of rock-phosphate-solubilizing bacteria associated with wild rice as inoculants for improved rice (Oryza sativa)

A study was conducted to isolate P-solubilizing bacteria from the rhizosphere of three wild rice species and to test their ability to mobilize P from rock phosphate (RP). Inoculated seeds or seedlings of eight different strains were grown in soils supplemented with a P fertilizer mixture (PFM) consisting triple super phosphate (TSP) and RP, each providing equal amounts of P₂O₅. Crop growth, NaHCO₃-extractable P, crop P uptake and yield were compared with two uninoculated controls, with either TSP or PFM added. In the pot experiment, P availability varied from 20 to 48 mg P kg^?1 soil. Yields ranged between 4.8 and 6.6 g per pot and were not significantly different between treatments. In the field experiment, shoot P accumulation in inoculated and TSP-control treatments at the heading stage ranged between 79–129 mg and 219 mg per pot, respectively. Dual inoculants comprising Staphylococcus scirui, Bacillus pumilus, Bacillus subtilus and Bacillus cereus increased yield by about 29% over PFM-controls (324 g m^?2) but those yields were 21% lower than TSP-controls (510 g m^?2). Therefore, application of inoculants combined with PFM is not a viable alternative for TSP under the tested conditions because yield was limited by the P availability.