Waseem Hussain

Waseem Hussain

Scientist-I, Rice Breeder

Posts by Collection

RforPlantBreeding

portfolio

publications

Engineering cold stress tolerance in crop plants.

Published in Current Genomics, 2011

In this paper we review the various mechanisms and genes involved in cold acclimatization and the possibilities where transgenic technology has been explored for breeding cold tolerance in crop plants.

Recommended citation: Sanghera, G. S., Wani, S. H., Hussain, W., and Singh, N. . 2011. Engineering cold stress tolerance in crop plants. Curr. Genomics,12, 30–43.

The magic of heterosis: new tools and complexities.

Published in Nature and Science, 2011

In this paper we review the moder concept of heterosis, and genetic and molecular basis of heterosis.

Recommended citation: Sanghera, G. S., Wani, S. H., Hussain, W., Shafi, W., and Haribhushan, A. 2011. The magic of heterosis: New tools and complexities. Nature and Science. 9(11).

Heterosis and combining ability estimates using line x tester analysis to develop rice hybrids for temperate conditions.

Published in Notulae Scientia Biologicae, 2012

Here, we studied the heterosis and combining ability by crossing 18 lines (Males) with two cytoplasmic newly developed male sterile (CMS) lines (Females).

Recommended citation: Sanghera, G. S., and Hussain, W. 2012. Heterosis and combining ability estimates using Line x Tester analysis to develop rice hybrids for temperate conditions. Notulae Scientia Biologicae. 4:131–142.

Interactive genotypic influence of triticale and wheat on their crossability and haploid induction under varied agroclimatic regimes.

Published in Cereal Research Communications, 2014

Here, we studied the response of diverse genotypes of triticale and wheat and environment on their crossability as well as to evaluate the efficiency of Imperata cylindrica-mediated chromosome elimination approach for haploid induction in triticale × wheat (Triticum aestivum) hybrids.

Recommended citation: Badiyal, A., Chaudhary, H. k., Jamwal, N. s., Hussain, W., Mahato, A., and Bhatt, A. k. 2014. Interactive genotypic influence of triticale and wheat on their crossability and haploid induction under varied agroclimatic regimes. Cereal Research Communications. 42:700–709.

Genetic diversity of genus Avena from North Western-Himalayas Using molecular markers.

Published in Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 2016

Here, we assess the diversity of wild relatives and cultivars of geneus Avena using RAPD and SSR markers.

Recommended citation: Sood, V. K., Rana, I., Hussain, W., and Chaudhary, H. K. 2016. Genetic Diversity of Genus Avena from North Western-Himalayas Using Molecular Markers. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 86:151–158.

Factors influencing crossability among triticale and wheat and its subsequent effect along with hybrid necrosis on haploid induction.

Published in Acta Agriculturae Scandinavica, Section B—Soil & Plant Science, 2016

The manuscript investigates the influence of genotypic and environmental factors on the crossability of elite triticale and wheat genotypes, screen the effect of necrotic genes in the F1 hybrids and the relative performance of hybrids towards haploid induction.

Recommended citation: Jamwal, N. S., Chaudhary, H. K., Badiyal, A., and Hussain, W. 2016. Factors influencing crossability among triticale and wheat and its subsequent effect along with hybrid necrosis on haploid induction. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science. 66:282–289.

Comparative assessment of different auxin analogues on haploid induction in triticale x wheat derived backcross generations.

Published in Agriculture Research Journal, 2016

The manuscript studies the effect of different possible auxin analogues like 2,4-D, NAA, IAA and IBA for their influence on haploid induction in triticale x wheat backcross generations.

Recommended citation: Badiyal, A., Chaudhary, H. K., Jamwal, N. S., Bhatt, A. K., and Hussain, W. 2016. Comparative assessment of different auxin analogues on haploid induction in triticale x wheat derived backcross Generations. Agricultural Research Journal. 53:157.

A multi-sensor system for high throughput field phenotyping in soybean and wheat breeding.

Published in Computers and Electronics in Agriculture, 2016

The manuscript reports the development of a new multi-sensor system for high throughput phenotyping in plant breeding.

Recommended citation: Bai, G., Ge, Y., Hussain, W., Baenziger, P. S., and Graef, G. 2016. A multi-sensor system for high throughput field phenotyping in soybean and wheat breeding. Computers and Electronics in Agriculture. 128:181–192.

Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat

Published in Scientific Reports, 2017

In this manuscript we describes the development of high-density linkage map in Harry x Wesley derived RIL population, confirm the accuracy, reliability and validity of the map, and also its application in mapping QTLs for flag leaf traits.

Recommended citation: Hussain, W., Baenziger, P. S., Belamkar, V., Guttieri, M. J., Venegas, J. P., Easterly, A., et al. 2017. Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Scientific Reports. 7:16394.

Success in inducing effective rooting in triticale x wheat and wheat x wheat derived haploid plantlets in cocopeat mixture.

Published in International Journal of Current Microbiology and Applied Sciences, 2018

The manuscript reveals the success of the Cocopeat mixture in inducing rooting in Triticale derived wheat haploid plants.

Recommended citation: S. Jamwal, N., K. Chaudhary, H., Badiyal, A., Hussain, W., Katoch, P., and Kumar, N. 2018. Success in inducing effective rooting in triticale x wheat and wheat x wheat derived haploid plantlets in cocopeat mixture. International Journal of Current Microbiology and Applied Sciences. 7:15–23.

Genomic selection in preliminary yield trials in a winter wheat breeding program.

Published in G3: Genes|Genomes|Genetics, 2018

The manuscript provides insights and assesses the the integration of genomic selection for grain yield in Nebraska wheat breeding programe.

Recommended citation: Belamkar, V., Guttieri, M. J., Hussain, W., Jarquín, D., El-basyoni, I., Poland, J., et al. 2018. Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program. G3: Genes|Genomes|Genetics. 8:2735–2747.

Registration of a bread Wheat recombinant inbred line mapping population derived from a cross between ‘Harry’ and ‘Wesley’.

Published in Journal of Plant Registrations, 2018

he manuscript describes the development and registration of Harry x Wesley derived recombinant inbred line mapping population. The mapping population is an important germplasm resource to breed for drought tolerance and wider adaptation in the US Great Plains.

Recommended citation: Hussain, W., Guttieri, M. J., Belamkar, V., Poland, J., Sallam, A., and Baenziger, P. S. 2018. Registration of a bread wheat recombinant inbred line mapping population derived from a cross between ‘Harry’ and ‘Wesley.’ Journal of Plant Registrations. 12:411–414.

Genetic variation in drought tolerance at seedling stage and grain yield in low rainfall environments in wheat ( Triticum aestivum L.).

Published in Euphytica, 2018

The manuscript describes the newly developed protocol to identify the drought genotypes in winter wheat at seedling stage in the green house and compare it across the field trials.

Recommended citation: Sallam, A., Mourad, A. M. I., Hussain, W., and Stephen Baenziger, P. 2018. Genetic variation in drought tolerance at seedling stage and grain yield in low rainfall environments in wheat. Euphytica. 214:169.

ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies.

Published in Plant Direct, 2018

ShinyAIM is a nice tool to visualize the Manhattan plots in interactive and easy way. The application has unique features to interpret and view dynamically GWAS outputs particularly from temporal GWAS studies.

Recommended citation: Hussain, W., Campbell, M., Walia, H., and Morota, G. 2018. ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies. Plant Direct. 2:e00091.

Identification of quantitative trait loci conferring resistance to tan spot in a bi-parental population derived from two Nebraskan hard red winter wheat cultivars.

Published in Molecular Breeding, 2018

This paper characterizes the Tan spot resistance in Harry and Wesley cultivars and reveals high resistance to tan spot in Wesley cultivar is largely due to lack of two Ptr ToxA-Tsn1 and Ptr ToxC-Tsc1 tan spot sensitivity genes.

Recommended citation: Kariyawasam, G. K., Hussain, W., Easterly, A., Guttieri, M., Belamkar, V., Poland, J., et al. 2018. Identification of quantitative trait loci conferring resistance to tan spot in a biparental population derived from two Nebraska hard red winter wheat cultivars. Mol Breeding. 38.

Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

Published in BioRxiv, 2020

In this work we reported unique vQTLs and mvQTLs for grain cadmium in wheat. Also showed that epistasis is important component of genetic variance in regulation of grain cadmium in wheat

Recommended citation: Hussain, et al .2018. Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions. The Plant Genome.

resources

talks

Genotyping-by-sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

Published:

In this talk I discuss about the development of linkage map in Harry x Wesley derived RIL population. I also discussed about our newly developed pipeline using R/qtl and ASMap how to correct for genotyping errors in genotyping-by-sequencing derived SNPs. Also, talked about the validity, accuracy and comparison of the developed linkage map with newly developed genome assembly of wheat. Lastly, discuss the application of linkage map in identifying QTLs for plant height. The talk is on webpage. The detailed instruction about the R codes used to correct can be found in supplementary materials published in Scientific reports journal at https://www.nature.com/articles/s41598-017-16006-z

Shiny Based Imaging GWAS Server

Published:

In this talk I discuss about Shiny, its applications and how Shiny and R-software can be used to develop the applications in plant genentics.

teaching

Teaching experience 1

Guest lecture, University of Nebraska, Lincoln, Department of Animal Sciences, 2018

This lecture was one of the lecture in course ASCI 944/STAT 844 Quantitative Methods for Genomics of Complex Traits taught by Dr. Gota Morota. In this lecture I talk about basic concepts in GWAS, how to correct for population stratification, and statistical models to run GWAS and also showed practical demonstration how to perform GWAS in R-software.

Teaching experience 2

Lecture, University of Nebraska Licoln, Department of Agronomy and Horticulture, 2018

This lecture was delivered in Rclub hosted by students in the Agronomy and Horticulture department, University of Nebraska, Lincoln. In this lecture I discussed about data visualizations in ggplot, interactive visualizations using plotly, multiple plots in same panel, correlations and correlation heat maps.

Teaching experience 3

Guest lecture, University of Nebraska, Lincoln, Department of Agronomy and Horticulture, 2019

This is two lecture series in the course STAT 892-007- Integrative Data Science for Plant Phenomics taught by multiple instructors. I deliver two lectures, in first lecture I discussed about basic concepts in GWAS, how to correct for population stratification, and statistical models to run GWAS and also showed practical demonstration how to perform GWAS in R-software. In the Second lecture, I discussed the Basics of Genomic Predictions and Statistical Models