Introduction
Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice, specially in the tropical regions of the world. Developing rice varieties with host resistance ...against the disease is the most effective and economical solution for managing the disease.
Methods
Pyramiding resistance genes (Xa4, xa5, xa13,and Xa21) in popular rice varieties using marker-assisted backcross breeding (MABB) has been demonstrated as a cost-effective and sustainable approach for establishing durable BB resistance. Here, we report our successful efforts in introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) from IRBB60 to CARI Dhan 5, a popular salt-tolerant variety developed from a somaclonal variant of Pokkali rice, through functional MABB.
Results and discussion
Both BB and coastal salinity are among the major challenges for rice production in tropical island and coastal ecosystems. Plants with four, three, and two gene pyramids were generated, which displayed high levels of resistance to the BB pathogen at the BC3F2 stage. Under controlled salinity microplot environments, the line 131-2-175-1223 identified with the presence of three gene pyramid (Xa21+xa13+xa5) displayed notable resistance across locations and years as well as exhibited a salinity tolerance comparable to the recurrent parent, CARI Dhan 5. Among two BB gene combinations (Xa21+xa13), two lines, 17-1-69-334 and 46-3-95-659, demonstrated resistance across locations and years, as well as salt tolerance and grain production comparable to CARI Dhan 5. Besides salinity tolerance, five lines, 17-1-69-179, 46-3-95-655, 131-2-190-1197, 131-2-175-1209, and 131-2-175-1239, exhibited complete resistance to BB disease. Following multilocation testing, potential lines have been identified that can serve as a prospective candidate for producing varieties for the tropical Andaman and Nicobar Islands and other coastal locations, which are prone to BB and coastal salinity stresses.
The topology of the Internet at the autonomous system (AS) level is not yet fully discovered despite significant research activity. The community still does not know how many links are missing, where ...these links are and finally, whether the missing links will change our conceptual model of the Internet topology. An accurate and complete model of the topology would be important for protocol design, performance evaluation and analyses. The goal of our work is to develop methodologies and tools to identify and validate such missing links between ASes. In this work, we develop several methods and identify a significant number of missing links, particularly of the peer-to-peer type. Interestingly, most of the missing AS links that we find exist as peer-to-peer links at the Internet exchange points (IXPs). First, in more detail, we provide a large-scale comprehensive synthesis of the available sources of information. We cross-validate and compare BGP routing tables, Internet routing registries, and traceroute data, while we extract significant new information from the less-studied Internet exchange points (IXPs). We identify 40% more edges and approximately 300% more peer-to-peer edges compared to commonly used data sets. All of these edges have been verified by either BGP tables or traceroute. Second, we identify properties of the new edges and quantify their effects on important topological properties. Given the new peer-to-peer edges, we find that for some ASes more than 50% of their paths stop going through their ISPs assuming policy-aware routing. A surprising observation is that the degree of an AS may be a poor indicator of which ASes it will peer with.
In the present study, a total of 53 promising salt-tolerant genotypes were tested across 18 salt-affected diverse locations for three years. An attempt was made to identify ideal test locations and ...mega-environments using GGE biplot analysis. The CSSRI sodic environment was the most discriminating location in individual years as well as over the years and could be used to screen out unstable and salt-sensitive genotypes. Genotypes CSR36, CSR-2K-219, and CSR-2K-262 were found ideal across years. Overall, Genotypes CSR-2K-219, CSR-2K-262, and CSR-2K-242 were found superior and stable among all genotypes with higher mean yields. Different sets of genotypes emerged as winners in saline soils but not in sodic soils; however, Genotype CSR-2K-262 was the only genotype that was best under both saline and alkaline environments over the years. The lack of repeatable associations among locations and repeatable mega-environment groupings indicated the complexity of soil salinity. Hence, a multi-location and multi-year evaluation is indispensable for evaluating the test sites as well as identifying genotypes with consistently specific and wider adaptation to particular agro-climatic zones. The genotypes identified in the present study could be used for commercial cultivation across edaphically challenged areas for sustainable production.
Although well recognized in breast oncology literature, histologic subtypes have not been previously described in inflammatory breast cancer (IBC). The purpose of this study was to describe lobular ...subtype in IBC and assess the impact of histology on patient outcomes.
We performed a retrospective analysis of 659 IBC patients at MD Anderson Cancer Center between January 1984 and December 2009. Patients with Invasive Lobular, Mixed Invasive Ductal and Lobular, or Invasive Ducal Carcinomas (ILC, MIC, IDC, respectively) comprise the subject of this report. Patient characteristics and survival estimates were compared by using chi-square test and Kaplan-Meier method with log-rank statistic. Cox proportional hazards models were fit to determine association of histology with outcomes after adjustment for other characteristics.
A total of 30, 37, and 592 patients were seen to have invasive lobular, mixed, or ductal histology, respectively. Grade 3 tumors were more common in the ductal group (78%) than in the lobular (60%) or mixed (61%) group (P = 0.01). The 3-year overall survival rates were 68%, 64%, and 62% in the lobular, mixed, and ductal groups, respectively (P = 0.68). After adjustment, histology did not have a significant effect on death in the lobular group (HR = 0.70, 95% confidence interval CI: 0.26-1.94; P = 0.50) or mixed group (HR = 0.53, 95% CI: 0.25-1.13; P = 0.10) compared with the ductal group.
In this cohort of IBC patients, lobular histology was seen in 4.5% cases. Histology does not appear to have a significant effect on survival outcomes in IBC patients, unlike in patients with non-inflammatory breast cancer (n-IBC), indicating the distinct biological behavior of the IBC phenotype.
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in ...irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
We investigate the production of intense ү-rays following the interaction of ultraintense laser pulse with a hybrid combination of under-dense plasma associated with a thin foil of fully ionized Al ...or Cu or Au at the rear side. Relativistic electrons are accelerated following the interaction of high intensity laser pulses with an under-dense plasma. These electrons are then stopped by the thin foils attached to the rear side of the under-dense plasma. This results in the production of intense-ray bursts. So, the enhancement of photon generation is due to the under-dense plasma electrons interacting with different over-dense plasma. Using open-source PIC code EPOCH, we study the effect of different electron densities in the under-plasma on photon emission. Photon emission enhancement is observed by increasing the target Z in the hybrid structure. Hybrid structure can enhance photon emission; it can increase the photon energy and yield and improve photon beam divergence. Simulations were also performed to find the optimal under-dense plasma density for ү-ray production.
•The SALTOL QTL material in rice tested for tolerance to salinity and sodicity stresses under microplots conditions.•Stress tolerance index was found a better selection index than stress ...susceptibility index.•Sodic stress tolerance could be predictive of salinity stress tolerance or vice versa in QTL introgressed lines.•Yield potential was directly correlated with yield under stress and stress tolerance index.•Plant height, tillers number, biomass, grain yield and harvest index found important traits for indirect selection.
The present study was carried out by evaluation of twenty two rice genotypes including 18 SALTOL QTL introgressed rice genotypes under salt stress conditions during 2009 and 2010. It aimed to know the tolerance and productivity potential of marker assisted breeding (MAB) derived material under precisely controlled normal, sodicity (pH ∼9.5) and salinity (EC 10dS/m) micro-plots environments, judge the relative effectiveness of the stress tolerance indices and to understand the implications of eight plant traits in influencing yield potential and stress tolerance. Mean squares due to genotypes were highly significant for all nine characters studied. Across genotypes, the seedling stage tolerance was associated with grain yield performance and adult stage salinity tolerance. The SALTOL lines IR 84645-305-6-1-B, IR84649-275-3-2-B and IR84649-292-3-1-B performed significantly better in terms of seedling stage tolerance, grain yield and STI (stress tolerance index) as compared to sensitive check under sodic as well as salinity stress environments. STI was found to be a better selection criterion than stress susceptibility index (SSI). Yield potential was directly correlated with yield under stress and STI under both stresses. Interestingly, STI values for sodicity stress were positively correlated with those of salinity stress, thus sodicity stress tolerance could be predictive of salinity stress tolerance or vice versa. The STI values under moderate sodic and high saline conditions were positively correlated with plant height, total and productive tillers, biomass, grain yield and harvest index in normal and both stress environments thus revealing importance of these traits for indirect selection in the MAB derived material.
The aim of this study was to identify stable rice genotypes tolerant to a salt stress environment and to identify ideal mega-environments using AMMI (additive main effects and multiplicative ...interaction) stability model analysis. A total of 13 rice genotypes and three salt tolerance checks were evaluated across 13 salt stress locations (alkaline and saline) for the two kharif seasons of 2014 and 2015. Genotype CSR 36 (CHK3) was found to be the most ideal of those tested. Genotypes CHK2 (CST 27) and IR 87952-1-1-1-2-3-B (G05) were found to be the most stable, with above average yields. The check CSR 36 (CHK3) genotype was the best performer in the majority of the environments studied, followed by CSR 27 (CHK2) and IR 87952-1-1-1-2-3-B (G05) which were the best genotypes in the mega-environment consisting of 21 environments evaluated across stress locations and year combinations. Overall, the most promising genotype (IR 87952-1-1-1-2-3-B) had high mean yield and stability and could be used for commercial cultivation or used as donor for breeding programs across salt-affected soils. The genotypes GN13 (IR 87938-1-1-2-1-3-B) and GN11 (IR 87938-1-2-2-1-3-B) showed 60–80% yield advantage at specific salt stress locations, showing that these genotypes could be used for specific environments of salt-affected soils in India.
Salinity stress is the most prominent stress impacting rice productivity worldwide. In the past, several quantitative trait loci (QTLs) for salinity tolerance had been identified in rice, however ...their utilization in rice breeding programs is largely confounded due to the unwanted linkage drag associated with the QTL region. Thus, it is strongly desirable to delimit the QTL region to a least possible chromosomal interval minimising any unwanted association. Addressing this, we have evaluated 68 recombinant inbred lines (RILs) derived from a cross between a salinity tolerant parent ‘Kolajoha’ and a salinity sensitive parent ‘Ranjit’ for identification of QTL(s) involved in imparting salinity tolerance at seedling stage. Genotyping by sequencing approach (GBS) was followed for SNP identification at genome wide scale. Around 3649 SNPs were identified by GBS method initially at 20% minor allele frequency. After filtering of SNPs with polymorphism with less than 10–15% of missing data, a total of 1248 SNPs were mapped to 1247 recombination points and the genetic map was constructed with a total map length of 1201.21 cM and resolution of 0.95 cM between markers. For 10 traits, a total of 23 additive QTLs were identified of which only 1 was a major QTL and 22 were minor QTLs. The average QTL interval size is about 2945 kb. Epistatic QTL mapping had identified one pair of QTLs that contribute significantly in the phenotypic variation of traits among the RILs. Total 1895 genes were identified in the QTL intervals, majority of them are located in Chr1 of rice genome between 22.09 and 38.29 Mb region. Although, this region is not very narrow, some of the genes falling in this region can be utilized for validation of QTLs in future. One differentially methylated region was found to be colocalized within the QTL intervals determined in Chr2 which indicates their potential role in epigenetic modifications in improving stress tolerance in rice.
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