Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

<p>Abstract</p> <p>Background</p> <p>Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS) and sequencing-by-synthesis (SBS). Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield), LaGrue (low milling yield), Ilpumbyeo (high eating quality), YR15965 (low eating quality), and Nipponbare (control).</p> <p>Results</p> <p>The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved <it>cis </it>regulatory elements were identified. Numerous specifically expressed transcription factor (TF) genes were identified in Cypress (282), LaGrue (312), Ilpumbyeo (363), YR15965 (260), and Nipponbare (357). Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation) that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase) and granule bound starch synthase I (GBSS I) in Cypress than that in LaGrue during early seed development.</p> <p>Conclusion</p> <p>This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved in the biosynthesis of starch, aspartate family amino acids, and storage proteins. Some of the differentially expressed genes could be useful for the development of molecular markers if they are located in a known QTL region for milling yield or eating quality in the rice genome. Therefore, our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars has provided a rich genomic resource for further elucidating the molecular basis of grain quality in rice.</p

Groundnut

Groundnut, a crop rich in nutrients, originated in South America and spread to the rest of the world. Cultivated groundnut contains a fraction of the genetic diversity present in their closely related wild relatives, which is not more than 13 %, due to domestication bottleneck. Closely related ones are placed in section Arachis , which have not been extensively utilized until now due to ploidy differences between the cultivated and wild relatives. In order to overcome Arachis species utilization bottleneck, a large number of tetraploid synthetics were developed at the Legume Cell Biology Unit of Grain Legumes Program, ICRISAT, India. Evaluation of synthetics for some of the constraints showed that these were good sources of multiple disease and pest resistances. Some of the synthetics were utilized by developing ABQTL mapping populations, which were screened for some biotic and abiotic constraints. Phenotyping experiments showed ABQTL progeny lines with traits of interest necessary for the improvement of groundnut

North American Wild Relatives of Grain Crops

The wild-growing relatives of the grain crops are useful for long-term worldwide crop improvement research. There are neglected examples that should be accessioned as living seeds in gene banks. Some of the grain crops, amaranth, barnyard millet, proso millet, quinoa, and foxtail millet, have understudied unique and potentially useful crop wild relatives in North America. Other grain crops, barley, buckwheat, and oats, have fewer relatives in North America that are mostly weeds from other continents with more diverse crop wild relatives. The expanding abilities of genomic science are a reason to accession the wild species since there are improved ways to study evolution within genera and make use of wide gene pools. Rare wild species, especially quinoa relatives in North American, should be acquired by gene banks in cooperation with biologists that already study and conserve at-risk plant populations. Many of the grain crop wild relatives are weeds that have evolved herbicide resistance that could be used in breeding new herbicide-resistant cultivars, so well-documented examples should be accessioned and also vouchered in gene banks

Chickpea

The narrow genetic base of cultivated chickpea warrants systematic collection, documentation and evaluation of chickpea germplasm and particularly wild Cicer species for effective and efficient use in chickpea breeding programmes. Limiting factors to crop production, possible solutions and ways to overcome them, importance of wild relatives and barriers to alien gene introgression and strategies to overcome them and traits for base broadening have been discussed. It has been clearly demonstrated that resistance to major biotic and abiotic stresses can be successfully introgressed from the primary gene pool comprising progenitor species. However, many desirable traits including high degree of resistance to multiple stresses that are present in the species belonging to secondary and tertiary gene pools can also be introgressed by using special techniques to overcome pre- and post-fertilization barriers. Besides resistance to various biotic and abiotic stresses, the yield QTLs have also been introgressed from wild Cicer species to cultivated varieties. Status and importance of molecular markers, genome mapping and genomic tools for chickpea improvement are elaborated. Because of major genes for various biotic and abiotic stresses, the transfer of agronomically important traits into elite cultivars has been made easy and practical through marker-assisted selection and marker-assisted backcross. The usefulness of molecular markers such as SSR and SNP for the construction of high-density genetic maps of chickpea and for the identification of genes/QTLs for stress resistance, quality and yield contributing traits has also been discussed

Radiofrequency Ablation of Adenoma Sebaceum

Adenoma sebaceum is one of the diagnostic features of tuberous sclerosis. Histologically, they are angiofibromas that occur over the central part of the face and hence, cause a major cosmetic disfigurement. Different forms of ablative treatments including laser ablation have been used for the treatment of this condition. Laser treatment is expensive and any form of treatment for adenoma sebaceum is not a one-time procedure but is a recurring process as the condition is genetic in aetiology. It is therefore appropriate to use a cheap and easily available modality, particularly in the Indian scenario. We hereby report a case of tuberous sclerosis in whom we ablated the lesions by radiofrequency technique with acceptable results

Long-term spatial and temporal trends in frost indices in Kansas, USA

Citation: Anandhi, A., Perumal, S., Gowda, P.H. et al. Climatic Change (2013) 120: 169. https://doi.org/10.1007/s10584-013-0794-4Frost indices such as number of frost days (nFDs), number of frost-free days (nFFDs), last spring freeze (LSF), first fall freeze (FFF), and growing-season length (GSL) were calculated using daily minimum air temperature (T[subscript min]) from 23 centennial weather stations across Kansas during four time periods (through 1919, 1920–1949, 1950–1979, and 1980–2009). A frost day is defined as a day with T[subscript min] < 0 °C. The long- and short-term trends in frost indices were analyzed at monthly, seasonal, and annual timescales. Probability of occurrence of the indices was analyzed at 5 %, 25 %, 50 %, 75 %, and 95 %. Results indicated a general increase in T[subscript min] from 1900 through 2009 causing a decrease in nFDs. LSF and FFF occurred earlier and later than normal in the year, respectively, thereby resulting in an increase in GSL. In general, northwest Kansas recorded the greatest nFD and lowest T[subscript min], whereas southeast Kansas had the lowest nFD and highest T[subscript min]; however, the magnitude of the trends in these indices varied with location, time period, and time scales. Based on the long-term records in most stations, LSF occurred earlier by 0.1–1.9 days/decade, FFF occurred later by 0.2–0.9 day/decade, and GSL was longer by 0.1–2.5 day/decade. At the 50 % probability level, Independence in the south-eastern part of Kansas had the earliest LSF (6 April), latest FFF (29 October) and longest GSL (207 days). Oberlin (north-western Kansas) recorded the shortest GSL (156 days) and earliest FFF (7 October) had the latest LSF (2 May) at the 50 % probability level. A positive correlation was observed for combinations of indices (LSF and GSL) and elevation, whereas a negative correlation was found between FFF and elevation