QTL mapping of sheath blight resistance in a deep-water rice cultivar

Sheath blight, caused by the pathogen Rhizoctonia solani Kühn, is one of the most serious diseases of rice and leads to severe yield loss worldwide. A recombinant inbred line (RIL) population consisting of 121 lines was constructed from a cross between HH1B and RSB03, the latter of which is a deep-water rice variety. Five traits were used to evaluate sheath blight resistance, namely disease rating (DR), lesion length (LL), lesion height (LH), relative lesion length [RLL, the ratio of LL to plant height (PH)], and relative LH (RLH, the ratio of LH to PH). Using the RIL population and 123 molecular markers, we identified 28 quantitative trait loci (QTLs) for the five traits in two environments. These QTLs are located on nine chromosomes and most of them are environment specific. A major QTL for DR (qSBR1) on chromosome 1 was identified with contributions of 12.7% at Shanghai and 42.6% at Hainan, and it collocated with a QTL for PH. The allele at this locus from RSB03 enhances sheath blight resistance and increases PH. Another QTL for DR on chromosome 7 was adjacent to QTLs for heading date (HD) and four other disease traits. RSB03 also carries the resistant allele at this locus and shortens HD. The susceptible parent, HH1B, provides the resistance allele at the locus qSBR8, where QTLs for four other disease traits were identified. QTL mapping results showed that most QTLs for LL, LH, RLL, and RLH are collocated with QTLs for DR. Three QTLs for DR are independent from HD, PH, and four other disease traits, while four QTLs are closely related to HD and PH. Four QTLs for LL, LH, RLL, and RLH are independent from DR, HD, and PH, while there is only one region harboring QTLs for these four traits and HD. Correlation analysis and QTL mapping results indicated that LL, LH, RLL, and RLH might be important indices, like DR, for evaluating the level of resistance to rice sheath blight.     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Flow cytometric analysis of nuclear DNA content,mitotic chromosome number and protein separation by SDS-PAGE in three accessions of African locust bean (<Emphasis Type="Italic">Parkia biglobosa</Emphasis> Benth.)

Nuclear DNA of three accessions of Parkia biglobosa collected from three locations in northern Cross River State was investigated using a Patec PA II flow cytometer equipped with an argon ion laser (488 nm), and pictures of mitotic chromosomes were taken using a digital micro-camera (Canon) placed on the eye piece of a binocular microscope at 100X oil immersion. Metaphase chromosome counts of 2n = 22 for accessions A and C and 2n = 24 for accession B, were obtained and through flow cytometry, the three accessions were confirmed to be diploids. The nuclear DNA content and genome size for the accessions were 1.5085, 1.489, and 1.5266 pg (737.7054, 728.121, and 746.5074 Mbp) for accessions A, B, and C, respectively. In another experiment, leaf samples from greenhouse-germinated seeds were analyzed for variation in the banding pattern of the protein by SDS-PAGE in the three accessions. Protein was resolved into three banding groups according to their electrophoretic mobility: slow, medium, and fast, clustering between 100–200, 40–70, and 10–25 kDa, respectively. There was 76% similarity in the banding pattern between the accessions.     

Varietal difference in physicochemical properties of pigmented rice varieties

The physicochemical properties of pigmented (Midorimochi, Jeokjinjubyeo, and Heukmichalbyeo) and non-pigmented (Hwayoungbyeo) rice varieties were investigated. Starch from non-pigmented rice consisted mainly of large polyhedral granules that were more loosely packed than those of the non-pigmented sample. Pigmented rice showed higher linoleic acid content (36–40%) and hydrolysis rate (63–79%) but lower oleic acid content (35–39%), blue value (0.05–0.17), and viscosity values than the non-pigmented one. Significantly higher mineral content, blue value, and pasting and viscosity values were observed in the Jeokjinjubyeo sample compared to those of the other pigmented rice samples. The Midorimochi variety, on the other hand, exhibited the highest total amino acid (816.82 ng mg⁻¹) and sugar (0.15–3.35 μg g⁻¹) contents and the lowest pasting and viscosity values. No substantial difference in the X-ray diffraction pattern was observed among the samples. Results of this study could serve as baseline information for the quality evaluation of three pigmented rice cultivars and provide a better understanding of their potential uses and food industry applications.     

Characterisation of aromatic rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) germplasm and correlation between their agronomic and quality traits

Eighty-eight aromatic cultivars collected from Maharashtra state were assessed for determinants of kernel quality (kernel size-shape, test weight and aroma) and grain morphology such as awning, lemma and palea characters, pubescence, colour of sterile lemma and apiculus colour. We, report seven cultivars—‘Girga’, ‘Kothmirsal’, ‘Kala bhat’, ‘Chimansal’, ‘Jiri’, ‘Kalsal’ ‘Velchi’ and ‘Kali kumud’ as indigenous to southern India. Of the 69 cultivars characterized for agronomic traits 36 cultivars were exquisite genotypes and possessed one or more superior traits such as early flowering, dwarf stature, higher number of productive tiller per plant; long panicles; higher number of filled grains per panicle and strong aroma. Variability in aromatic cultivars was assessed on the basis of nine traits placed aromatic rice cultivars in five clusters. Number of cultivars in each cluster ranged from 1 to 33. 27 significant correlations were obtained in the physical, agronomic and grain morphology traits. Aroma was found to be negatively associated with days to 50% flowering as well as with filled grains per panicle. However, correlation between panicle length and effective tillers with aroma was not observed. Therefore, to increase the yield, improvement in length of panicle and increasing number of productive tillers in medium or mild scented cultivars would be the best strategy.     

Increase in growth,productivity and nutritional status of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L. cv. Basmati) and enrichment in soil fertility applied with an organic matrix entrapped urea

Field experiments were conducted to evaluate the effects of eco-friendly organic matrix entrapped urea (OMEU) on growth, productivity, and yield of rice (Oryza sativa L. cv. Basmati) and soil enrichment in the paddy field at Rohtak (Haryana) located near Delhi. The OMEU prepared in granular form contained cow dung, rice bran (grain cover of Oryza sativa), powder of neem leaves (Azadirachta indica), and clay soil (diameter of particles < 0.02 mm) in 1:1:1:1 ratios and saresh (plant gum of Acacia sp.) as binder along with half of the recommended dose of commercially available soluble urea (free urea; FU). Single basal application of OMEU showed an increase in plant growth in terms of fresh and dry weights, root length, root, leaf and tiller numbers, soluble protein, total N and ammonium in leaves, productivity in terms of grain and straw yield, and nutritional and microbial activities of field soil over free form of urea and no fertilizer application. Nutritional status of rice grains was also improved over the free urea and no fertilizer controls. Our data indicate that OMEU, which is low cost and based on bio-degradable, non-toxic, and locally available agro-waste, can be attempted to replace the conventional use of soluble urea in rice.     

Inheritance of anthocyanin content in the ripe berries of a tetraploid × diploid grape cross population

Variation patterns and inheritance of anthocyanin content in the ripe berries of a tetraploid × diploid table grape cross population were investigated in two successive years. The population segregated for three different ploid levels: dipolids, triploids, and tetraploids. A total of 28 different anthocyanins were detected and quantified in the progeny population. Transgressive segregation for the total anthocyanin content was observed in all the three ploid progeny populations. The total anthocyanin content increased as the ploid level increased. The broad sense heritabilities (H²) of the total anthocyanin content were all relatively high, ranging from 0.53 to 0.98, 0.57 to 0.97 and 0.43 to 0.94 in the diploid, triploid and tetraploid population, respectively. Our results suggested that the total anthocyanin content followed an additive inheritance model in this polyploid segregation population. We also observed that the relative contribution of individual anthocyanins to the total anthocyanin content varied significantly among different ploid populations, suggesting that genetic background has important impact on the accumulation of the individual anthocyanin compounds. These results will help develop better breeding strategies in a polyploid table grape breeding program for improving the content of anthocyanins, an important class of polyphenolics possessing antioxidant activities and many other health-related benefits.     

Improved <Emphasis Type="Italic">S</Emphasis>-genotyping and new incompatibility groups in Japanese plum

The selection of cross-compatible cultivars is essential to ensure fruit set in self-incompatible species like Japanese plum and thus the S-genotype must be determined in order to establish incompatibility groups. In this study an improved Japanese plum S-genotyping method, based in polymerase chain reaction and capillary electrophoresis detection of intron polymorphisms of S-locus genes, S-RNase and SFB, has been assayed and validated in a wide sample of cultivars. This method allows a more precise determination of amplified fragment sizes and therefore a better differentiation of self-incompatibility alleles. The assayed methodology was proven effective in the detection of 13 different S-alleles of S-RNases and SFBs and was used to S-genotype 105 Japanese plum cultivars, 32 of which are described by first time in this work. Analysed cultivars were assigned into 11 incompatibility groups and two new incompatibility groups (XX and XXI) were identified, increasing to 21 the number of incompatibility groups described in this crop.     

Genetic analysis and genotype × environment (G × E) for grey leaf spot disease resistance in elite African maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) germplasm

Maize grey leaf spot (GLS) disease remains an important foliar disease in sub-Saharan Africa accounting for more than 25% yield losses in maize. Information on inheritance of GLS resistance of germplasm adapted to African environments is required in new sources being identified. Therefore, hybrids generated from a 10 × 10 half-diallel mating of tropical advanced maize inbred lines were evaluated in six environments to determine combining ability, genotype × environment interaction (G × E) and the impact of GLS disease on grain yield. General combining ability effects were highly significant and accounted for 72 and 68% of the variation for GLS resistance and grain yield, respectively. Significant specific combining ability effects associated with reduced disease levels were observed in some hybrids when one parent was resistant, and these may be exploited in developing single cross maize hybrids. Regression analysis showed a 260–320 kg ha^?1 decrease in maize grain yield per each increase in GLS disease severity score, and significant associations (r = ?0.31 to ?0.60) were observed between grain yield and GLS severity scores. This showed the potential of GLS disease to reduce yield in susceptible varieties grown under favourable disease conditions, without control measures. Genotype and genotype × environment biplots and correlation analysis indicated that the significant G × E observed was not due to changes in hybrid ranking, implying absence of a significant crossover interaction. Therefore, predominance of additive gene effects imply that breeding progress for GLS disease resistance would be made through selection and this could be achieved at a few hot-spot sites, such as Baynesfield and Cedara locations in South Africa, and still deploy the resistant germplasm to other environments in which they are adapted.     

Mineral bioavailability in grains of Pakistani bread wheat declines from old to current cultivars

Estimating variation in grain mineral concentration and bioavailability in relation to grain yield and the year of cultivar release is important for breeding wheat with increased content of bioavailable minerals. The grain yield and yield components, grain phytate concentration, and concentration and bioavailability of minerals (zinc Zn, iron Fe and calcium Ca) in wheat grains were estimated in 40 wheat cultivars released in Punjab (Pakistan) during the last five decades. Mean grain Zn and Ca concentrations in current-cultivars were significantly lower (≥14%) than in obsolete cultivars released during the Green Revolution (1965–1976). Much of this variation was related to increased grain weight in current-cultivars. There was a positive correlation among minerals (r = 0.39 or higher, n = 40) and minerals with phytate in wheat grains (r = 0.38 or higher, n = 40). The tested cultivars varied widely in grain yield and grain phytate-to-mineral molar ratios (phytate:mineral). Compared to obsolete cultivars, the current-cultivars had a higher phytate:mineral ratio in grains, indicating poor bioavailability of minerals to humans. The study revealed a non-significant relationship between grain yield and phytate:mineral ratios in grains. Therefore, breeding for lower phytate:mineral ratios in wheat grains can ensure increased mineral bioavailability without significant reduction in the yield potential. Future breeding should be focused on developing new genotypes suitable for mineral biofortification and with increased mineral bioavailability in grains.