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Sallam A, Alqudah AM, Dawood MFA, Baenziger PS, Börner A. Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research. Int J Mol Sci 2019; 20:E3137. [PMID: 31252573 PMCID: PMC6651786 DOI: 10.3390/ijms20133137] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.
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Affiliation(s)
- Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt.
| | - Ahmad M Alqudah
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany.
| | - Mona F A Dawood
- Department of Botany & Microbiology, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - P Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Andreas Börner
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
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Sheoran S, Jaiswal S, Kumar D, Raghav N, Sharma R, Pawar S, Paul S, Iquebal MA, Jaiswar A, Sharma P, Singh R, Singh CP, Gupta A, Kumar N, Angadi UB, Rai A, Singh GP, Kumar D, Tiwari R. Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS. FRONTIERS IN PLANT SCIENCE 2019; 10:527. [PMID: 31134105 PMCID: PMC6511880 DOI: 10.3389/fpls.2019.00527] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 05/13/2023]
Abstract
Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders' 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.
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Affiliation(s)
- Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Deepender Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Nishu Raghav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ruchika Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sushma Pawar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Surinder Paul
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - M. A. Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Akanksha Jaiswar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Arun Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeraj Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - U. B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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103
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Marker-trait association for grain weight of spring barley in well-watered and drought environments. Mol Biol Rep 2019; 46:2907-2918. [PMID: 30904979 DOI: 10.1007/s11033-019-04750-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/07/2019] [Indexed: 01/08/2023]
Abstract
Climate change will increase the effect of drought stress which is one of major constrains for barley production and productivity in Egypt. Identification and development new cultivars having a high drought tolerance combined with a high yield are urgently needed. In this study, a set of 60 highly homozygous and diverse barley genotypes was evaluated in well-watered (N) and dry (D) environments for two successive seasons. Five yield traits were scored; plant height, spike length, days to flowering, grain yield per spike (GYPS), and thousand kernel weight (TKW). High genetic variation was found among genotypes in all studied traits under N and D. High heritability for all traits was observed in both seasons. The drought susceptibility index (DSI) for GYPS and TKW was estimated to determine the tolerant and susceptible genotypes in both seasons. As a result, four spring barley genotypes were considered drought tolerant for TKW and GYPS in both seasons. A set of ten single sequence repeats primers, developed from wheat genome, were tested in the 60 genotypes. All SSR primers had a high polymorphism among the genotypes producing 82 marker alleles. Single marker analysis was performed for DSI, TKW, and GYPS in both seasons. Twenty QTLs were found to be associated with low DSI and high GYPS and TKW in N and D. The marker alleles associated with the 20 QTL were screened in the four tolerant genotypes. PNBYT15 included only one marker allele associated with one QTL, while, SCYT-28 included six marker alleles controlling nine QTL. The high genetic variation and heritability for the studied traits indicated that these traits could be used for selection for high yielding and drought tolerance. The four drought tolerant genotypes can be used for a further breeding program to improve drought tolerance in barley.
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104
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Genome-Wide Genetic Diversity and Population Structure of Tunisian Durum Wheat Landraces Based on DArTseq Technology. Int J Mol Sci 2019; 20:ijms20061352. [PMID: 30889809 PMCID: PMC6471223 DOI: 10.3390/ijms20061352] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 12/26/2022] Open
Abstract
Tunisia, being part of the secondary center of diversity for durum wheat, has rich unexploited landraces that are being continuously lost and replaced by high yielding modern cultivars. This study aimed to investigate the genetic diversity and population structure of 196 durum wheat lines issued from landraces collected from Tunisia using Diversity Array Technology sequencing (DArTseq) and to understand possible ways of introduction in comparing them to landraces from surrounding countries. A total of 16,148 polymorphic DArTseq markers covering equally the A and B genomes were effective to assess the genetic diversity and to classify the accessions. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish five distinct groups that matched well with the farmer's variety nomenclature. Interestingly, Mahmoudi and Biskri landraces constitute the same gene pool while Jenah Zarzoura constitutes a completely different group. Analysis of molecular variance (AMOVA) showed that the genetic variation was among rather than within the landraces. DAPC analysis of the Tunisian, Mediterranean and West Asian landraces confirmed our previous population structure and showed a genetic similarity between the Tunisian and the North African landraces with the exception of Jenah Zarzoura being the most distant. The genomic characterization of the Tunisian collection will enhance their conservation and sustainable use.
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Luo Z, Brock J, Dyer JM, Kutchan T, Schachtman D, Augustin M, Ge Y, Fahlgren N, Abdel-Haleem H. Genetic Diversity and Population Structure of a Camelina sativa Spring Panel. FRONTIERS IN PLANT SCIENCE 2019; 10:184. [PMID: 30842785 PMCID: PMC6391347 DOI: 10.3389/fpls.2019.00184] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/05/2019] [Indexed: 05/20/2023]
Abstract
There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36-47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa's agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs.
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Affiliation(s)
- Zinan Luo
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
- *Correspondence: Zinan Luo, Hussein Abdel-Haleem,
| | - Jordan Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - John M. Dyer
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
| | - Toni Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Daniel Schachtman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Megan Augustin
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Yufeng Ge
- Department of Biological and Agricultural Engineering, University of Nebraska, Lincoln, NE, United States
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hussein Abdel-Haleem
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
- *Correspondence: Zinan Luo, Hussein Abdel-Haleem,
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106
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Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:164-181. [PMID: 30466152 DOI: 10.1111/tpj.14170] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe-related traits were developed in the relatively simple context of binary host-microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome-wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant-microbe interactions will influence the choice of traits to be mapped.
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Affiliation(s)
- Kathleen Beilsmith
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Manus P M Thoen
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Benjamin Brachi
- BIOGECO, INRA, University of Bordeaux, 33610, Cestas, France
| | - Andrew D Gloss
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Mohammad H Khan
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
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107
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Yang Q, Yang Z, Tang H, Yu Y, Chen Z, Wei S, Sun Q, Peng Z. High-density genetic map construction and mapping of the homologous transformation sterility gene (hts) in wheat using GBS markers. BMC PLANT BIOLOGY 2018; 18:301. [PMID: 30477426 PMCID: PMC6258151 DOI: 10.1186/s12870-018-1532-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/16/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Homologous transformation sterility-1 (HTS-1) is a novel wheat mutant that exhibits pistillody, the transformation of stamens into pistils or pistil-like structures. More extreme phenotypes of this mutation can have six pistils or pistil-like structures without any stamens in a floret. Thus, HTS-1 is highly valuable for studies of wheat hybrid breeding and flower development. Previous studies have shown that two major genes (Pis1 and hts) control pistillody in HTS-1. The Pis1 gene controls the three-pistil trait in the three-pistil wheat mutant and has been mapped on chromosome 2D, but the hts gene has not been mapped or identified. To do so, we crossed HTS-1 with CM28TP (three-pistil mutant) and constructed a high-density linkage map with the F2 population (200 individuals). RESULTS The map covered 2779.96 cM, and the genetic distance per chromosome ranged from 37.59 cM to 318.95 cM. The average distance between markers was 1.04 cM. We then mapped hts between GBS-SNP markers 4A_109 and 4A_119, separated by 2.0 cM and 5.2 Mb. To find the candidate genes, the hts region was enlarged to 7.2 Mb, encompassing 752 protein-coding genes. We identified TaWin1 as a possible candidate gene after comparing the 752 genes with 206 common differentially expressed genes between pistillody stamens (PS) versus normal stamens (S) and pistils (P) versus S. Real-time PCR indicated that TaWin1 was highly expressed in HTS-1 during the pistil-and-stamen-differentiating stage, at levels approximately 120 times greater than those in CM28TP. Further analysis indicated that TaWin1 was mainly expressed in HTS-1 PS, supporting its status as a candidate gene of hts. Thus, TaWin1 overexpression probably leads to the transformation of stamens into pistils in wheat. CONCLUSIONS The results of this study provide a foundation for further research on stamen and pistil development, with implications for wheat-hybrid breeding programs.
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Affiliation(s)
- Qian Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Haifeng Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Yan Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zhenyong Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Shuhong Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Qinxu Sun
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, 615000 Sichuan China
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108
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Sallam A, Amro A, El-Akhdar A, Dawood MFA, Kumamaru T, Stephen Baenziger P. Genetic diversity and genetic variation in morpho-physiological traits to improve heat tolerance in Spring barley. Mol Biol Rep 2018; 45:2441-2453. [PMID: 30411192 DOI: 10.1007/s11033-018-4410-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/26/2018] [Indexed: 02/04/2023]
Abstract
Heat stress is one of the abiotic stresses that limit the production and productivity of barley. Understanding the genetic variation, changes in physiological processes and level of genetic diversity existing among genotypes are needed to produce new cultivars not only having a high tolerance to heat stress, but also displaying high yield. To address this challenge, a set of 60 highly homozygous, diverse barley genotypes were evaluated under normal and heat stress conditions in two seasons of 2014/2015 and 2015/2016. Seedling vigor (SV) as a morphological trait was visually scored under normal conditions. Plant height (Ph), days to flowering (DOF), 1000-kernel weight (TKW), grain yield per spike (GYPS), yield per plot (YPP) and biological yield (BY) were measured. Moreover, proline content (ProC), soluble carbohydrate content (SCC), starch content, soluble protein (SP), and amino acid (AA) content as physiological parameters were analyzed from the grains. High genetic variation was observed among genotypes for all traits scored in this study. All traits had high broad-sense heritability estimates ranging from 0.59 (SV) to 0.97 (TKW) for yield traits. Seedling vigor was significantly correlated with all yield traits under both conditions. Among all physiological traits, the increase in ProC and reduction in starch content due to heat stress had significant correlations with the reduction due to heat stress in YPP, GYPS, TKW, and BY. Furthermore, the genetic diversity based on genetic distance (GD) among genotypes was investigated using 206 highly polymorphic SSR marker alleles. The GD ranged from 0.70 to 0.98 indicating that these genotypes are highly and genetically dissimilar. The combination of analyses using molecular markers, genetic variation in yield traits, and changes in physiological traits provided useful information in identifying the tolerant genotypes which can be used to improve heat tolerance in barley through breeding.
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Affiliation(s)
- Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt. .,Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
| | - Ahmed Amro
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| | - Ammar El-Akhdar
- Field Crop Research Institute, Agricultural Research Center, 9 Gama St., Giza, Egypt.,Institute of Genetic Resources, Kyushu University, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan
| | - Mona F A Dawood
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Kyushu University, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan
| | - P Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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