Publications by authors named "Francis Ogbonnaya"

23 Publications

  • Page 1 of 1

Multi-dimensional evaluation of response to salt stress in wheat.

PLoS One 2019 30;14(9):e0222659. Epub 2019 Sep 30.

INRES Plant Breeding, Rheinische Friedrich-Wilhelms-University, Bonn, Germany.

Soil salinity is a major threat to crop production worldwide. The global climate change is further accelerating the process of soil salinization, particularly in dry areas of the world. Increasing genetic variability of currently used wheat varieties by introgression of exotic alleles/genes from related progenitors' species in breeding programs is an efficient approach to overcome limitations due to the absence of valuable genetic diversity in elite cultivars. Synthetic hexaploid wheat (SHW) is widely regarded as donor of favourable exotic alleles to improve tolerance against biotic and abiotic stresses such as salinity stress. In this study, synthetic backcross lines (SBLs) winter wheat population "Z86", derived from crosses involving synthetic hexaploid wheat Syn86L with German elite winter wheat cultivar Zentos, was evaluated for salinity tolerance at different developmental stages under controlled and field conditions in three growing seasons. High genetic variability was detected across the SBLs and their parents at various growth stages under controlled as well as under salt stress field trials. Greater performance of Zentos over Syn86L was detected at germination stage across all salt treatments and with respect to shoot dry weight (SDW) and root dry weight (RDW) at seedling stage. Whereas for the root length (RL) and the shoot length (SL) Syn86L surpassed the elite cultivar and most of the progenies. Our experiments revealed for almost all traits that some genotypes among the SBLs showed higher performance than their parents. Furthermore, positive transgressive segregations were detected among the SBLs for germination at high salinity levels, as well as for RDW and SDW at seedling stage. Therefore, the studied Z86 population is a suitable population for assessment of salinity stress on morphological and physiological traits at different plant growth stages. The identified SBLs provide a valuable source for genetic gain through recombination of superior alleles that can be directly applied in breeding programs for efficiently breeding cultivars with improved salinity tolerance and desired agronomic traits.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222659PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768486PMC
March 2020

Population-dependent reproducible deviation from natural bread wheat genome in synthetic hexaploid wheat.

Plant J 2019 11 3;100(4):801-812. Epub 2019 Sep 3.

Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia.

Sequence elimination is one of the main mechanisms that increases the divergence among homoeologous chromosomes after allopolyploidization to enhance the stability of recently established lineages, but it can cause a loss of some economically important genes. Synthetic hexaploid wheat (SHW) is an important source of genetic variation to the natural hexaploid wheat (NHW) genepool that has low genetic diversity. Here, we investigated the change between SHW and NHW genomes by utilizing a large germplasm set of primary synthetics and synthetic derivatives. Reproducible segment elimination (RSE) was declared if a large chromosomal chunk (>5 cM) produced no aligned reads in more than five SHWs. RSE in five genomic regions was the major source of variation between SHW and NHW. One RSE eliminated almost the complete short arm of chromosome 1B, which contains major genes for flour quality, disease resistance and different enzymes. The occurrence of RSE was highly dependent on the choice of diploid and tetraploid parental lines, their ancestral subpopulation and admixture, e.g. SHWs derived from Triticum dicoccon or from one of two Aegilops tauschii subpopulations were almost free of RSE, while highly admixed parents had higher RSE rates. The rate of RSE in synthetic derivatives was almost double that in primary synthetics. Genome-wide association analysis detected four loci with minor effects on the occurrence of RSE, indicating that both parental lines and genetic factors were affecting the occurrence of RSE. Therefore, pre-pre-breeding strategies should be applied before introducing SHW into pre-breeding programs to ensure genomic stability and avoid undesirable gene loss.
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http://dx.doi.org/10.1111/tpj.14480DOI Listing
November 2019

Genome-Wide Analyses Reveal Footprints of Divergent Selection and Drought Adaptive Traits in Synthetic-Derived Wheats.

G3 (Bethesda) 2019 06 5;9(6):1957-1973. Epub 2019 Jun 5.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS) and

Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (-test, Tajima's D, nucleotide diversity (π), , and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 'selective sweeps', out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as (1D) for earliness (Eps), (3D), (6D) and (7D) for grain size, weight and morphology, (5D) influencing drought tolerance, and (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.
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http://dx.doi.org/10.1534/g3.119.400010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553533PMC
June 2019

Unravelling the Complex Genetics of Karnal Bunt () Resistance in Common Wheat () by Genetic Linkage and Genome-Wide Association Analyses.

G3 (Bethesda) 2019 05 7;9(5):1437-1447. Epub 2019 May 7.

Grains Research and Development Corporation, P.O. Box 5367, Kingston, ACT 2604, Australia.

Karnal bunt caused by Mitra [syn. (Mitra) Mundkur] is a significant biosecurity concern for wheat-exporting countries that are free of the disease. It is a seed-, soil-and air-borne disease with no effective chemical control measures. The current study used data from multi-year field experiments of two bi-parental populations and a genome-wide association (GWA) mapping panel to unravel the genetic basis for resistance in common wheat. Broad-sense heritability for Karnal bunt resistance in the populations varied from 0.52 in the WH542×HD29 population, to 0.61 in the WH542×W485 cross and 0.71 in a GWAS panel. Quantitative trait locus (QTL) analysis with seven years of phenotypic data identified a major locus on chromosome 3B (R = 27.8%) and a minor locus on chromosome 1A (R = 12.2%), in the WH542×HD29 population, with both parents contributing the high-value alleles. A major locus (R = 27.8%) and seven minor loci (R = 4.4-15.8%) were detected in the WH542×W485 population. GWA mapping validated QTL regions in the bi-parent populations, but also identified novel loci not previously associated with Karnal bunt resistance. Meta-QTL analysis aligned the results from this study with those reported in wheat over the last two decades. Two major clusters were detected, the first on chromosome 4B, which clustered with , , , and the second on chromosome 3B, which clustered with , and The results provide definitive chromosomal assignments for QTL/genes controlling Karnal bunt resistance in common wheat, and will be useful in pre-emptive breeding against the pathogen in wheat-producing areas that are free of the disease.
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http://dx.doi.org/10.1534/g3.119.400103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505162PMC
May 2019

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat.

Theor Appl Genet 2019 Feb 3;132(2):323-346. Epub 2018 Nov 3.

INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany.

Key Message: SNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties. The dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R = 0.12-63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na and K ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R ≥ 14.7%) and 68.45 cM (R ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na-uptake, shoot K/Na ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na-uptake, shoot Na/K ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.
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http://dx.doi.org/10.1007/s00122-018-3220-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349800PMC
February 2019

Identification of Novel Quantitative Trait Loci Linked to Crown Rot Resistance in Spring Wheat.

Int J Mol Sci 2018 Sep 8;19(9). Epub 2018 Sep 8.

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Ankara 06511, Turkey.

Crown rot (CR), caused by various species, is a major disease in many cereal-growing regions worldwide. is one of the most important species, which can cause significant yield losses in wheat. A set of 126 advanced International Maize and Wheat Improvement Center (CIMMYT) spring bread wheat lines were phenotyped against CR for field crown, greenhouse crown and stem, and growth room crown resistance scores. Of these, 107 lines were genotyped using Diversity Array Technology (DArT) markers to identify quantitative trait loci linked to CR resistance by genome-wide association study. Results of the population structure analysis grouped the accessions into three sub-groups. Genome wide linkage disequilibrium was large and declined on average within 20 cM (centi-Morgan) in the panel. General linear model (GLM), mixed linear model (MLM), and naïve models were tested for each CR score and the best model was selected based on quarantine-quarantine plots. Three marker-trait associations (MTAs) were identified linked to CR resistance; two of these on chromosome 3B were associated with field crown scores, each explaining 11.4% of the phenotypic variation and the third MTA on chromosome 2D was associated with greenhouse stem score and explained 11.6% of the phenotypic variation. Together, these newly identified loci provide opportunity for wheat breeders to exploit in enhancing CR resistance via marker-assisted selection or deployment in genomic selection in wheat breeding programs.
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http://dx.doi.org/10.3390/ijms19092666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165080PMC
September 2018

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat.

Front Genet 2018 6;9:27. Epub 2018 Feb 6.

Grains Research and Development Corporation, Kingston, ACT, Australia.

Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents ( 2n = 4x = 28, AABB subgenomes) with the progenitor species (syn ; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding.
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http://dx.doi.org/10.3389/fgene.2018.00027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807918PMC
February 2018

The goat grass genome's role in wheat improvement.

Nat Plants 2018 02;4(2):56-58

Institute of Crop Science, CAAS, Beijing, China.

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http://dx.doi.org/10.1038/s41477-018-0105-1DOI Listing
February 2018

Wheat genetic resources in the post-genomics era: promise and challenges.

Ann Bot 2018 03;121(4):603-616

Resource Seeds International, Mexico.

Background: Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges.

Perspectives And Conclusion: Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes.
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http://dx.doi.org/10.1093/aob/mcx148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852999PMC
March 2018

Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments.

Theor Appl Genet 2017 Sep 2;130(9):1819-1835. Epub 2017 Jun 2.

Department of Crop Science, University of Nigeria, Nsukka, Nigeria.

Key Message: We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat. We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2-3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4-5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1-2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance.
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http://dx.doi.org/10.1007/s00122-017-2927-zDOI Listing
September 2017

Association analysis of resistance to cereal cyst nematodes () and root lesion nematodes ( and ) in CIMMYT advanced spring wheat lines for semi-arid conditions.

Breed Sci 2016 Dec 25;66(5):692-702. Epub 2016 Oct 25.

Grains Research & Development Corporation (GRDC) , 4/4 National Circuit Barton 2600 ACT , Australia.

To identify loci linked to nematode resistance genes, a total of 126 of CIMMYT advanced spring wheat lines adapted to semi-arid conditions were screened for resistance to , , and , of which 107 lines were genotyped with 1,310 DArT. Association of DArT markers with nematode response was analyzed using the general linear model. Results showed that 11 markers were associated with resistance to (pathotype Ha21), 25 markers with resistance to , and 9 significant markers were identified to be linked with resistance to . In this work we confirmed that chromosome 4A (~90-105 cM) can be a source of resistance to as has been recently reported. Other significant markers were also identified on chromosomal regions where no resistant genes have been reported for both nematodes species. These novel QTL were mapped to chromosomes 5A, 6A, and 7A for ; on chromosomes 1A, 1B, 3A, 3B, 6B, 7AS, and 7D for ; and on chromosomes 1D, 2A, and 5B for and represent potentially new loci linked to resistance that may be useful for selecting parents and deploying resistance into elite germplasm adapted to regions where nematodes are causing problem.
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http://dx.doi.org/10.1270/jsbbs.15158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282747PMC
December 2016

Allelic variations and differential expressions detected at quantitative trait loci for salt stress tolerance in wheat.

Plant Cell Environ 2018 05 7;41(5):919-935. Epub 2017 Mar 7.

INRES Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, D-53115 Bonn, Germany.

The increasing salinization of agricultural lands is a threat to global wheat production. Understanding of the mechanistic basis of salt tolerance (ST) is essential for developing breeding and selection strategies that would allow for increased wheat production under saline conditions to meet the increasing global demand. We used a set that consists of 150 internationally derived winter and facultative wheat cultivars genotyped with a 90K SNP chip and phenotyped for ST across three growth stages and for ionic (leaf K and Na  contents) traits to dissect the genetic architecture regulating ST in wheat. Genome-wide association mapping revealed 187 Single Nucleotide Polymorphism (SNPs) (R  = 3.00-30.67%), representing 37 quantitative trait loci (QTL), significantly associated with the ST traits. Of these, four QTL on 1BS, 2AL, 2BS and 3AL were associated with ST across the three growth stages and with the ionic traits. Novel QTL were also detected on 1BS and 1DL. Candidate genes linked to these polymorphisms were uncovered, and expression analyses were performed and validated on them under saline and non-saline conditions using transcriptomics and qRT-PCR data. Expressed sequence comparisons in contrasting ST wheat genotypes identified several non-synonymous/missense mutation sites that are contributory to the ST trait variations, indicating the biological relevance of these polymorphisms that can be exploited in breeding for ST in wheat.
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http://dx.doi.org/10.1111/pce.12898DOI Listing
May 2018

Global agricultural intensification during climate change: a role for genomics.

Plant Biotechnol J 2016 Apr 11;14(4):1095-8. Epub 2015 Sep 11.

National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Japan.

Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049667PMC
http://dx.doi.org/10.1111/pbi.12467DOI Listing
April 2016

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.

Front Plant Sci 2015 11;6:563. Epub 2015 Aug 11.

Grains Research and Development Corporation Kingston, ACT, Australia.

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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http://dx.doi.org/10.3389/fpls.2015.00563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531421PMC
August 2015

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.).

Plant Biotechnol J 2016 Jan 10;14(1):177-85. Epub 2015 Apr 10.

National Institute of Agricultural Botany, Cambridge, UK.

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5' end of the gene.
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http://dx.doi.org/10.1111/pbi.12371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973813PMC
January 2016

Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm.

Theor Appl Genet 2015 Jul 8;128(7):1277-95. Epub 2015 Apr 8.

International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria.

Key Message: Identified DArT and SNP markers including a first reported QTL on 3AS, validated large effect APR on 3BS. The different genes can be used to incorporate stripe resistance in cultivated varieties. Stripe rust [yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst)] is a serious disease in wheat (Triticum aestivum). This study employed genome-wide association mapping (GWAM) to identify markers linked to stripe rust resistance genes using Diversity Arrays Technology (DArT(®)) and single-nucleotide polymorphism (SNP) Infinium 9K assays in 200 ICARDA wheat genotypes, phenotyped for seedling and adult plant resistance in two sites over two growing seasons in Syria. Only 25.8 % of the genotypes showed resistance at seedling stage while about 33 and 44 % showed moderate resistance and resistance response, respectively. Mixed-linear model adjusted for false discovery rate at p < 0.05 identified 12 DArT and 29 SNP markers on chromosome arms 3AS, 3AL, 1AL, 2AL, 2BS, 2BL, 3BS, 3BL, 5BL, 6AL, and 7DS significantly linked to Pst resistance genes. Of these, the locus on 3AS has not been previously reported to confer resistance to stripe rust in wheat. The QTL on 3AS, 3AL, 1AL, 2AL, and 2BS were effective at seedling and adult plant growth stages while those on 3BS, 3BL, 5BL, 6AL and 7DS were effective at adult plant stage. The 3BS QTL was validated in Cham-6 × Cham-8 recombinant inbred line population; composite interval analysis identified a stripe resistance QTL flanked by the DArT marker, wPt-798970, contributed by Cham-6 parent which accounted for 31.2 % of the phenotypic variation. The DArT marker "wPt-798970" lies 1.6 cM away from the 3BS QTL detected within GWAM. Epistatic interactions were also investigated; only the QTL on 1AL, 3AS and 6AL exhibited interactions with other loci. These results suggest that GWAM can be an effective approach for identifying and improving resistance to stripe rust in wheat.
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http://dx.doi.org/10.1007/s00122-015-2504-2DOI Listing
July 2015

Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat.

PLoS One 2014 25;9(8):e105593. Epub 2014 Aug 25.

International Centre for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria; Research Program, Grains Research and Development Corporation, Barton, Australian Capital Territory, Canberra, Australia.

Use of genetic diversity from related wild and domesticated species has made a significant contribution to improving wheat productivity. Synthetic hexaploid wheats (SHWs) exhibit natural genetic variation for resistance and/or tolerance to biotic and abiotic stresses. Stripe rust caused by (Puccinia striiformis f. sp. tritici; Pst), is an important disease of wheat worldwide. To characterise loci conferring resistance to stripe rust in SHWs, we conducted a genome-wide association study (GWAS) with a panel of 181 SHWs using the wheat 9 K SNP iSelect array. The SHWs were evaluated for their response to the prevailing races of Pst at the seedling and adult plant stages, the latter in replicated field trials at two sites in Ethiopia in 2011. About 28% of the SHWs exhibited immunity at the seedling stage while 56% and 83% were resistant to Pst at the adult plant stage at Meraro and Arsi Robe, respectively. A total of 27 SNPs in nine genomic regions (1 BS, 2 AS, 2 BL, 3 BL, 3 DL, 5A, 5 BL, 6DS and 7A) were linked with resistance to Pst at the seedling stage, while 38 SNPs on 18 genomic regions were associated with resistance at the adult plant stage. Six genomic regions were commonly detected at both locations using a mixed linear model corrected for population structure, kinship relatedness and adjusted for false discovery rate (FDR). The loci on chromosome regions 1 AS, 3 DL, 6 DS and 7 AL appeared to be novel QTL; our results confirm that resynthesized wheat involving its progenitor species is a rich source of new stripe (yellow) rust resistance that may be useful in choosing SHWs and incorporating diverse yellow rust (YR) resistance loci into locally adapted wheat cultivars.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105593PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143293PMC
November 2015

Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis.

BMC Plant Biol 2014 May 9;14:128. Epub 2014 May 9.

Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China.

Background: Grain size and shape greatly influence grain weight which ultimately enhances grain yield in wheat. Digital imaging (DI) based phenomic characterization can capture the three dimensional variation in grain size and shape than has hitherto been possible. In this study, we report the results from using digital imaging of grain size and shape to understand the relationship among different components of this trait, their contribution to enhance grain weight, and to identify genomic regions (QTLs) controlling grain morphology using genome wide association mapping with high density diversity array technology (DArT) and allele-specific markers.

Results: Significant positive correlations were observed between grain weight and grain size measurements such as grain length (r = 0.43), width, thickness (r = 0.64) and factor from density (FFD) (r = 0.69). A total of 231 synthetic hexaploid wheats (SHWs) were grouped into five different sub-clusters by Bayesian structure analysis using unlinked DArT markers. Linkage disequilibrium (LD) decay was observed among DArT loci > 10 cM distance and approximately 28% marker pairs were in significant LD. In total, 197 loci over 60 chromosomal regions and 79 loci over 31 chromosomal regions were associated with grain morphology by genome wide analysis using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. They were mainly distributed on homoeologous group 2, 3, 6 and 7 chromosomes. Twenty eight marker-trait associations (MTAs) on the D genome chromosomes 2D, 3D and 6D may carry novel alleles with potential to enhance grain weight due to the use of untapped wild accessions of Aegilops tauschii. Statistical simulations showed that favorable alleles for thousand kernel weight (TKW), grain length, width and thickness have additive genetic effects. Allelic variations for known genes controlling grain size and weight, viz. TaCwi-2A, TaSus-2B, TaCKX6-3D and TaGw2-6A, were also associated with TKW, grain width and thickness. In silico functional analysis predicted a range of biological functions for 32 DArT loci and receptor like kinase, known to affect plant development, appeared to be common protein family encoded by several loci responsible for grain size and shape.

Conclusion: Conclusively, we demonstrated the application and integration of multiple approaches including high throughput phenotyping using DI, genome wide association studies (GWAS) and in silico functional analysis of candidate loci to analyze target traits, and identify candidate genomic regions underlying these traits. These approaches provided great opportunity to understand the breeding value of SHWs for improving grain weight and enhanced our deep understanding on molecular genetics of grain weight in wheat.
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http://dx.doi.org/10.1186/1471-2229-14-128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057600PMC
May 2014

QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions.

Theor Appl Genet 2013 Apr 27;126(4):971-84. Epub 2012 Dec 27.

CIMMYT Int. Apdo., Postal 6-641, DF Mexico 06600, Mexico.

Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post-anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection.
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http://dx.doi.org/10.1007/s00122-012-2030-4DOI Listing
April 2013

Optimization of sequence alignment for simple sequence repeat regions.

BMC Res Notes 2011 Jul 20;4:239. Epub 2011 Jul 20.

International Center for Agricultural Research in the Dry Areas (ICARDA), P,O, Box 5466, Aleppo, Syria.

Background: Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships.

Findings: To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm.

Conclusions: The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.
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http://dx.doi.org/10.1186/1756-0500-4-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160389PMC
July 2011

Characterization of quantitative trait loci controlling genetic variation for preharvest sprouting in synthetic backcross-derived wheat lines.

Genetics 2008 Mar 3;178(3):1725-36. Epub 2008 Feb 3.

Department of Primary Industries, Primary Industries Research Victoria, Horsham, Victoria 3401, Australia.

Aegilops tauschii, the wild relative of wheat, has stronger seed dormancy, a major component of preharvest sprouting resistance (PHSR), than bread wheat. A diploid Ae. tauschii accession (AUS18836) and a tetraploid (Triticum turgidum L. ssp. durum var. Altar84) wheat were used to construct a synthetic wheat (Syn37). The genetic architecture of PHS was investigated in 271 BC(1)F(7) synthetic backcross lines (SBLs) derived from Syn37/2*Janz (resistant/susceptible). The SBLs were evaluated in three environments over 2 years and PHS was assessed by way of three measures: the germination index (GI), which measures grain dormancy, the whole spike assay (SI), which takes into account all spike morphology, and counted visually sprouted seeds out of 200 (VI). Grain color was measured using both Chroma Meter- and NaOH-based approaches. QTL for PHSR and grain color were mapped and their additive and epistatic effects as well as their interactions with environment were estimated by a mixed linear-model approach. Single-locus analysis following composite interval mapping revealed four QTL for GI, two QTL for SI, and four QTL for VI on chromosomes 3DL and 4AL. The locus QPhs.dpiv-3D.1 on chromosome 3DL was tightly linked to the red grain color (RGC) at a distance of 5 cM. The other locus on chromosome 3D, "QPhs.dpiv-3D.2" was independent of RGC locus. Two-locus analysis detected nine QTL with main effects and 18 additive x additive interactions for GI, SI, and VI. Two of the nine main effects QTL and two epistatic QTL showed significant interactions with environments. Both additive and epistatic effects contributed to phenotypic variance in PHSR and the identified markers are potential candidates for marker-assisted selection of favorable alleles at multiple loci. SBLs derived from Ae. tauschii proved to be a promising tool to dissect, introgress, and pyramid different PHSR genes into adapted wheat genetic backgrounds. The enhanced expression of PHS resistance in SBLs enabled us to develop white PHS-resistant wheat germplasm from the red-grained Ae. tauschii accession.
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http://dx.doi.org/10.1534/genetics.107.084939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278070PMC
March 2008

Haplotype diversity of preharvest sprouting QTLs in wheat.

Genome 2007 Feb;50(2):107-18

Department of Primary Industries, Primary Industries Research Victoria, Private Bag 260, Horsham Victoria 3401, Australia.

Preharvest sprouting (PHS) is one of the most important factors affecting wheat production worldwide in environments characterized by rainfall and high humidity at harvest. In such environments, the incorporation of seed dormancy of a limited duration is required to minimize losses associated with PHS. A global collection of 28 PHS-resistant and -susceptible wheat germplasm was characterized with microsatellite markers flanking the genomic regions associated with PHS-resistance quantitative trait loci (QTLs), particularly on chromosomes 3D and 4A. The genetic diversity analysis revealed 380 alleles at 54 microsatellite loci, with an average of 7.0 alleles per locus, among the 28 wheat genotypes. Gower's genetic similarity values among all possible pairs of genotypes varied from 0.44 to 0.97, indicating that there is considerable diversity in the PHS germplasm evaluated. Cluster and principal coordinates analysis of genetic similarity estimates differentiated the genotypes into groups, according to their source of PHS resistance. Three major SSR haplotypes were observed on chromosome 4AL, designated RL4137-type allele, Aus1408-type allele, and synthetic-hexaploid-type allele. The RL4137-type allele was prevalent in Canadian cultivars, mostly in cluster 6, followed by the Aus1408-type and its derivatives in clusters 4 and 5. The Syn36 and Syn37 alleles on chromosome 4AL were rare. On chromosome 3DL, the SSRs haplotypes derived from Syn36 and Syn37 were also rare, and proved unique to the Aegilops tauschii - derived synthetic hexaploids. They are therefore likely carrying resistance genes different from those previously reported. Based on genetic relationships, PHS resistance might be improved by selecting parental genotypes from different clusters.
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http://dx.doi.org/10.1139/g06-142DOI Listing
February 2007

The cre1 and cre3 nematode resistance genes are located at homeologous loci in the wheat genome.

Mol Plant Microbe Interact 2003 Dec;16(12):1129-34

CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.

Differential responses in host-nematode pathotype interactions occur in wheat lines carrying different cereal cyst nematode resistance (Cre) genes. Cre1, located on chromosome 2B, confers resistance to most European nematodes and the sole Australian pathotype, while Cre3, present on chromosome 2D, is highly resistant to the Australian pathotype and susceptible to a number of European pathotypes. Genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) proteins that cosegregate with the Cre3 locus cross hybridize to homologues whose restriction fragment length polymorphism (RFLP) patterns distinguish near-isogenic Cre1 nematode-resistant wheat lines. Genetic mapping showed that the NBS-LRR gene members that distinguished the Cre1 near-isogenic lines were located on chromosome 2BL at a locus, designated Xcsl107, that cosegregates with the Cre1 locus. A haplotype of NBS-LRR genes from the Xcsl107 locus provides a diagnostic marker for the presence of Cre1 nematode resistance in a wide collection of wheat lines and segregating families. Genetic analysis of NBS-LRR haplotypes that cosegregate with Cre1 and Cre3 resistance, together with flanking cDNA markers and other markers from homoeologous group 2 chromosomes, revealed a conserved gene order that suggests Cre1 and Cre3 are homeoloci.
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http://dx.doi.org/10.1094/MPMI.2003.16.12.1129DOI Listing
December 2003