Genetic evaluation for understanding combining ability effects and Heterotic grouping in Maize (Zea mays L.)

Combining ability of the genotypes/lines is a major factor in planning the breeding programme and for development of Heterotic hybrids. In the present study, twenty maize inbred lines were crossed to three diverse testers CM-111, GPM-549 and GPM-581 and the resultant F1 hybrids were evaluated in an alpha lattice design. General combining ability of lines which is representation of additive gene action was found to be significant for all the quantitative traits. Specific combining ability which is indication of non-additive gene action was found to be significant for the traits number of kernel rows per cob, number of kernels per row, cob girth, cob length, test weight and grain yield. Lines VL-058725, VL-1018527 and VL-108723 produced heterotic hybrids in cross combination with any of the tester due to their high GCA effects. Whereas, the lines VL-0536, SNL-1574 and VL-109086 interacted positively with their testers thus producing heterotic hybrids with high positive SCA. GGE biplot analysis was helpful in visualizing the combining ability effects and identify heterotic pattern among theinbred lines. Heterotic grouping based on SCA and mean grain yield was able to classify thirteen of the twenty inbred lines into two distinct heterotic groups i.e., Heterotic group A and B consisting of six and seven lines respectively. Heterotic group A consisted of lines with high GCA whereas, heterotic group B with low GCA lines. SCA effect showed significant positive correlation with all the quantitative traits and played a prominent role in determining the performance of hybrids, thus indicating the importance of non-additive gene action in developingheterotic hybrids

Broadband Passive Sonar Signal Simulation in Shallow Ocean

The broadband plane wave model is valid only in the far-field of a point source under free-field propagating conditions. However the acoustics in ocean is characterized by multi-modal acoustic propagation due to its top-bottom limited boundary conditions. The effect of multi-modal field is to alter the source spectrum while the effect of dispersion is to modify the pulse shape. Moreover the use of a plane wave beamformer in a multi-modal field leads to a bias in the bearing estimates. These effects are highly dependant on the environment parameters and have important ramifications for target localization and classification in an ocean waveguide. We propose a more realistic simulator which essentially models these effects and therefore serves to provide test signals for first hand verification of signal processing algorithms to be developed for such scenarios. This model is to be understood as a better model than the naïve plane wave model which is entirely oblivious of even the gross features such as wave propagation in an oceanic waveguide. The channel parameter so estimated from the present simulation can be convolved with the radiated noise spectra of the source to generate the passive sonar signal.Defence Science Journal, 2011, 61(4), pp.370-376, DOI:http://dx.doi.org/10.14429/dsj.61.8

A prospective comparative study of efficacy of lenalidomide plus dexamethasone combination therapy versus VAD (vincristine, doxorubicin and dexamethasone) regimen in the treatment of multiple myeloma

Background: Lenalidomide plus Dexamethasone (Len-Dex) and VAD (Vincristine, Doxorubicin and Dexamethasone) regimen are the two common drug therapies employed in the treatment of Multiple myeloma.Objectives: To compare the efficacy of Len-Dex versus VAD regimen based on complete remission achieved with treatment in newly diagnosed cases of multiple myeloma in a tertiary care hospital in Kerala.Methods: Eighty patients (forty in each group) of newly diagnosed cases of multiple myeloma, who were willing to give the informed consent, were included in the study. Patients were allocated by the treating physician to two groups; one group was given Len-Dex (lenalidomide + dexamethasone) regimen and the other VAD (Vincristine, Adriamycin, Dexamethasone) regimen. A total of six cycles were given for both groups. Their baseline investigations and follow up investigations were collected at regular intervals, based on these values, the outcome was classified as partial remission and complete remission and the results were compared and analyzed.Results: Among the forty patients in each group, 17 (38%) on VAD regimen and 28 (62%) on Len-Dex regimen achieved complete remission. The statistical analysis was done using chi square test (χ2= 6.13, df= 1, p= 0.01) which showed statistically significant difference.Conclusions: The study showed that the efficacy of Lenalidomide-Dexamethasone (Len-Dex) combination therapy is clearly higher than that of VAD regimen among the study population. The overall efficacy of Len-Dex combination is 70% and that of VAD regimen is only 42.5%

Identification of nephropathy candidate genes by comparing sclerosis-prone and sclerosis-resistant mouse strain kidney transcriptomes

Abstract Background The genetic architecture responsible for chronic kidney disease (CKD) remains incompletely described. The Oligosyndactyly (Os) mouse models focal and segmental glomerulosclerosis (FSGS), which is associated with reduced nephron number caused by the Os mutation. The Os mutation leads to FSGS in multiple strains including the ROP-Os/+. However, on the C57Bl/6J background the mutation does not cause FSGS, although nephron number in these mice are equivalent to those in ROP-Os/+ mice. We exploited this phenotypic variation to identify genes that potentially contribute to glomerulosclerosis. Methods To identify such novel genes, which regulate susceptibility or resistance to renal disease progression, we generated and compared the renal transcriptomes using serial analysis of gene expression (SAGE) from the sclerosis-prone ROP-Os/+ and sclerosis resistant C57-Os/+ mouse kidneys. We confirmed the validity of the differential gene expression using multiple approaches. We also used an Ingenuity Pathway Analysis engine to assemble differentially regulated molecular networks. Cell culture techniques were employed to confirm functional relevance of selected genes. Results A comparative analysis of the kidney transcriptomes revealed multiple genes, with expression levels that were statistically different. These novel, candidate, renal disease susceptibility/resistance genes included neuropilin2 (Nrp2), glutathione-S-transferase theta (Gstt1) and itchy (Itch). Of 34 genes with the most robust statistical difference in expression levels between ROP-Os/+ and C57-Os/+ mice, 13 and 3 transcripts localized to glomerular and tubulointerstitial compartments, respectively, from micro-dissected human FSGS biopsies. Network analysis of all significantly differentially expressed genes identified 13 connectivity networks. The most highly scored network highlighted the roles for oxidative stress and mitochondrial dysfunction pathways. Functional analyses of these networks provided evidence for activation of transforming growth factor beta (TGFβ) signaling in ROP-Os/+ kidneys despite similar expression of the TGFβ ligand between the tested strains. Conclusions These data demonstrate the complex dysregulation of normal cellular functions in this animal model of FSGS and suggest that therapies directed at multiple levels will be needed to effectively treat human kidney diseases.http://deepblue.lib.umich.edu/bitstream/2027.42/112491/1/12882_2011_Article_362.pd

Marker-Assisted Breeding of Improved Maternal Haploid Inducers in Maize for the Tropical/Subtropical Regions

For efficient production of doubled haploid (DH) lines in maize, maternal haploid inducer lines with high haploid induction rate (HIR) and good adaptation to the target environments is an important requirement. In this study, we present second-generation Tropically Adapted Inducer Lines (2GTAILs), developed using marker assisted selection (MAS) for qhir1, a QTL with a significant positive effect on HIR from the crosses between elite tropical maize inbreds and first generation Tropically Adapted Inducers Lines (TAILs). Evaluation of 2GTAILs for HIR and agronomic performance in the tropical and subtropical environments indicated superior performance of 2GTAILs over the TAILs for both HIR and agronomic performance, including plant vigor, delayed flowering, grain yield, and resistance to ear rots. One of the new inducers 2GTAIL006 showed an average HIR of 13.1% which is 48.9% higher than the average HIR of the TAILs. Several other 2GTAILs also showed higher HIR compared to the TAILs. While employing MAS for qhir1 QTL, we observed significant influence of the non-inducer parent on the positive effect of qhir1 QTL on HIR. The non-inducer parents that resulted in highest mean HIR in the early generation qhir1+ families also gave rise to highest numbers of candidate inducers, some of which showed transgressive segregation for HIR. The mean HIR of early generation qhir1+ families involving different non-inducer parents can potentially indicate recipient non-inducer parents that can result in progenies with high HIR. Our study also indicated that the HIR associated traits (endosperm abortion rate, embryo abortion rate, and proportion of haploid plants among the inducer plants) can be used to differentiate inducers vs. non-inducers but are not suitable for differentiating inducers with varying levels of haploid induction rates. We propose here an efficient methodology for developing haploid inducer lines combining MAS for qhir1 with HIR associated traits

Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05–3.06), 5 (bin5.03), 8 (bin8.05–8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines

Heat-tolerant maize for rainfed hot, dry environments in the lowland tropics: from breeding to improved seed delivery

Climate change-induced heat stress combines two challenges: high day- and nighttime temperatures, and physiological water deficit due to demand-side drought caused by increase in vapor-pressure deficit. It is one of the major factors in low productivity of maize in rainfed stress-prone environments in South Asia, affecting a large population of smallholder farmers who depend on maize for their sustenance and livelihoods. The International Maize and Wheat Improvement Center (CIMMYT) maize program in Asia, in partnership with public-sector maize research institutes and private-sector seed companies in South Asian countries, is implementing an intensive initiative for developing and deploying heat-tolerant maize that combines high yield potential with resilience to heat and drought stresses. With the integration of novel breeding tools and methods, including genomics-assisted breeding, doubled haploidy, field-based precision phenotyping, and trait-based selection, new maize germplasm with increased tolerance to heat stress is being developed for the South Asian tropics. Over a decade of concerted effort has resulted in the successful development and release of 20 high-yielding heat-tolerant maize hybrids in CIMMYT genetic backgrounds. Via public–private partnerships, eight hybrids are presently being deployed on over 50,000 ha in South Asian countries, including Bangladesh, Bhutan, India, Nepal, and Pakistan

Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally

GBS-based SNP map pinpoints the QTL associated with sorghum downy mildew resistance in maize (Zea mays L.)

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts