Shahzad Naveed

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Dorian Q Fuller

University College London

Jayjit Majumdar

University of Kalyani

Prof. Nagwa Mohamed A . Aref

Ain Shams University

Prof. Dr. Moustafa Moharam

Sohag University

David Seamon

Kansas State University

Armando Marques-Guedes

UNL - New University of Lisbon

Jeffrey Townsend

Yale University

Fatma AYDINOĞLU

Gebze Technical University

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University of California, Santa Cruz

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Mansoura University

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Additional file 2: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

ANOVA results of the measured traits under Fe toxicity for 211 indica accessions. (DOCX 25Â kb)

Additional file 1: Figure S1. of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

PCA 3D plot of the first three principal components (PC) in 222 accessions (a) and 211 accessions... more

Detection of bacterial blight resistant gene xa5 using linked marker approaches

African Journal of Biotechnology, 2010

Rice is the primary source of food for 57% of the world’s population. Genetic resistance is impor... more Rice is the primary source of food for 57% of the world’s population. Genetic resistance is important to control many kinds of pathogenic diseases. Bacterial blight caused by Xanthomonas oryzae pv oryzae (Xoo) decreases rice production by 20 – 30% and up to about 90% loss of grain weight. xa5 is an important recessive bacterial blight resistant gene, which is effective and important in Asian rice breeding program. It was also used in combination by incorporation with various recessive and dominant BB resistant genes. The purpose of our study was to identify the bacterial blight resistant genes xa5 in Pakistani rice germplasm including Basmati varieties. The seeds were collected from different research institute and then sowed in the National Institute for Biotechnology and Genetic Engineering (NIBGE) in pots. DNAs were extracted and surveyed for polymorphism by using DNA marker linked to xa5 gene. During this polymorphic survey, out of 88 germplasm lines, 45 lines showed the presenc...

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Additional file 6: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Significant SNPs associated with measured traits in Zn experiment. (XLSX 40Â kb)

Additional file 5: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Significant SNPs associated with measured traits in Fe experiment. (XLSX 34Â kb)

Additional file 4: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Correlations between all measured traits under control (upper triangular) and stress (lower trian... more

Genetic dissection of heterosis of indica–japonica by introgression line, recombinant inbred line and their testcross populations

Scientific Reports

The successful implementation of heterosis in rice has significantly enhanced rice productivity, ... more The successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F1s (TCF1s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF1s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phen...

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Genome-wide association mapping of aluminum toxicity tolerance and fine mapping of a candidate gene for Nrat1 in rice

PloS one, 2018

Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Ri... more Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on...

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Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses

Scientific reports, Jan 25, 2018

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QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

BMC genomics, Jan 27, 2017

Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and ... more Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population. A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe or SZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a, qSdw3b, qSdw12 and qSFe5 / qSZn5) were detected in the same genomic regions under the two stress conditions and 22 candidate genes for 10 important QTL regions were also determin...

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Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses

Scientific Reports

To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core ac... more To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2-4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice. Enormous environmental changes have brought negative impact on food crops in the world. Among these environmental factors, salinity is known to be able to inhibit plant growth and ultimately cause various degrees of crop yield losses 1,2. As the most important staple food in Asia, a significant portion of rice crops are gworn along the coastal areas where rice paddy fields suffer various degrees of salinity. Salinity affects rice growth during all developmental stages from seed germination to reproduction 3. With the development and spread of direct-seeding technology in many Asian countries, which requires high levels of germination and seedling establishment to achieve good harvests, salt tolerance (ST) at the seed germination and seedling stages has become a major rice breeding goal of these countries. Most rice lines are sensitive to salt, particularly at the germination and seedling stage, but there is rich variability for ST among different rice accessions. It has been reported that some rice landraces such as Pokkali and Nona Bokra can withstand certain levels of salt stress 4. Rice ST is a complex phenomenon trait both genetically and physiologically 5-8. Thus, to efficiently exploit this genetic diversity of ST in breeding programs, it is important to identify quantitative trait loci (QTL)/quantitative trait nucleotides (QTN)/genes for ST at the seed germination and seedling stages so that marker-assisted breeding approach can be facilitated. Robin et al. 9 used backcross population of IR62266-426-2 × IR60080-46A for mapping of osmotic related QTL. They identified 14 QTL on 8 chromosomes. Hossain et al. 10 studied agronomic traits at the seedling and reproductive stages under saline condition and identified 16 QTL for salt tolerance, using an F 2 population of Cheriviruppu × Pusa Basmati 1. Ghomi et al. 11 identified 41 QTL affecting twelve physiological traits related to ST using 148 F 2 population derived from Gharib

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Effect of exogenously applied kinetin and glycinebetaine on metabolic and yield attributes of rice (Oryza sativa L.) under drought stress

Emirates Journal of Food and Agriculture, 2014

Drought is one of the major abiotic stress responsible for yield reduction of crops worldwide. Ki... more Drought is one of the major abiotic stress responsible for yield reduction of crops worldwide. Kinetin (KIN) and glycine betain (GB) have an essential role in regulating cell division during the early phase of grain setting; assimilate flow and osmotic adjustment under drought stress. Effects of exogenously applied kinetin and glycine betain on some metabolic and yield attributes of two rice (Oryza sativa L.) cultivars viz., Basmati-385 and KS-282 were evaluated under water stress. KIN and GB were applied by spraying the plants at flowering stage before drought stress treatment. Both treatments significantly increased proline concentration in leaves and panicles of both the rice cultivars as compared to their control. They also increased soluble sugar in the leaves and panicles under water stress. Starch concentration in leaves and panicles of both the rice cultivars were increased significantly (p<0.05) by KIN and GB spray. However, the magnitude of increase of the starch in panicles was more pronounced in cv. Basmatti-385 than cv. KS-282. Under the applied water stress both KIN and GB spray significantly increased paddy yield in both the rice cultivars. Both KIN and GB spray significantly increased the number of seeds per panicle in both the rice cultivars. The quantitative increase in paddy yield and seed number was greater in cv. Basmatti-385 as compared to cv. KS-282. Exogenous application of KIN at flowering stage could be used as an effective treatment to mimic the adverse effects of water stress in fine rice cultivars.

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