Papers by Abdulqader Jighly
Journal of Experimental Botany
Crop growth models (CGM) can predict the performance of a cultivar in untested environments by sa... more Crop growth models (CGM) can predict the performance of a cultivar in untested environments by sampling genotype-specific parameters (GSPs). As they cannot predict the performance of new cultivars, it has been proposed to integrate CGMs with whole genome prediction (WGP) to combine the benefits of both models. Here, we used a CGM-WGP model to predict the performance of new wheat genotypes that do not have phenotypic records in the reference population. The CGM was designed to predict phenology, nitrogen, and biomass traits. The CGM-WGP simulated more heritable GSPs compared to the CGM and gave smaller errors for the observed phenotypes. The WGP model performed better when predicting yield, grain number and grain protein content, but showed comparable performance to the CGM-WGP for heading and physiological maturity dates. However, the CGM-WGP model was able to predict unobserved traits (for which there were no phenotypic records in the reference population) through the prediction of...
2017 8th International Conference on Information Technology (ICIT)
This research aims at exploring the evolutionary path of selected five grass species to understan... more This research aims at exploring the evolutionary path of selected five grass species to understand how they evolve through time from a computer science perspective, by designing a new algorithm that employs raw data sequences to extract the information necessary for explaining the hypothesis that claims crossing over regions on genomes are responsible of pushing the evolutionary path of plant species. Basic Local Alignment Search Tool (BLAST) and Clustal Omega application were used to perform local alignment and global multiple alignments between species and define the relativity between them in order to approximately determine what species falls in the evolutionary path over time.
Genetics Selection Evolution
Background Meta-analysis describes a category of statistical methods that aim at combining the re... more Background Meta-analysis describes a category of statistical methods that aim at combining the results of multiple studies to increase statistical power by exploiting summary statistics. Different industries that use genomic prediction do not share their raw data due to logistic or privacy restrictions, which can limit the size of their reference populations and creates a need for a practical meta-analysis method. Results We developed a meta-analysis, named MetaGS, that duplicates the results of multi-trait best linear unbiased prediction (mBLUP) analysis without accessing raw data. MetaGS exploits the correlations among different populations to produce more accurate population-specific single nucleotide polymorphism (SNP) effects. The method improves SNP effect estimations for a given population depending on its relations to other populations. MetaGS was tested on milk, fat and protein yield data of Australian Holstein and Jersey cattle and it generated very similar genomic estimat...
Plants
Heat waves are expected to become more frequent and intense, which will impact faba bean cultivat... more Heat waves are expected to become more frequent and intense, which will impact faba bean cultivation globally. Conventional breeding methods are effective but take considerable time to achieve breeding goals, and, therefore, the identification of molecular markers associated with key genes controlling heat tolerance can facilitate and accelerate efficient variety development. We phenotyped 134 accessions in six open field experiments during summer seasons at Terbol, Lebanon, at Hudeiba, Sudan, and at Central Ferry, WA, USA from 2015 to 2018. These accessions were genotyped using genotyping by sequencing (GBS), and 10,794 high quality single nucleotide polymorphisms (SNPs) were discovered. These accessions were clustered in one diverse large group, although several discrete groups may exist surrounding it. Fifteen lines belonging to different botanical groups were identified as tolerant to heat. SNPs associated with heat tolerance using single-trait (ST) and multi-trait (MT) genome-w...
Life, 2022
Triticum aestivum L., also known as common wheat, is affected by many biotic stresses. Root disea... more Triticum aestivum L., also known as common wheat, is affected by many biotic stresses. Root diseases are the most difficult to tackle due to the complexity of phenotypic evaluation and the lack of resistant sources compared to other biotic stress factors. Soil-borne pathogens such as the root-lesion nematodes caused by the Pratylenchus species and crown rot caused by various Fusarium species are major wheat root diseases, causing substantial yield losses globally. A set of 189 advanced spring bread wheat lines obtained from the International Maize and Wheat Improvement Center (CIMMYT) were genotyped with 4056 single nucleotide polymorphisms (SNP) markers and screened for root-lesion nematodes and crown rot resistance. Population structure revealed that the genotypes could be divided into five subpopulations. Genome-Wide Association Studies were carried out for both resistances to Pratylenchus and Fusarium species. Based on our results, 11 different SNPs on chromosomes 1A, 1B, 2A, 3A...
Plants, 2022
The adaptability and stability of 37 faba bean (Vicia faba L.) accessions with different levels o... more The adaptability and stability of 37 faba bean (Vicia faba L.) accessions with different levels of tolerance to metribuzin or imazethapyr was assessed across 12 season–location–herbicide experiments. Significant Genotype x environment (GE) interaction was found for the days to flowering (DFLR), plant height (PLHT) and grain yield (GY). Performance and stability of the accessions regarding PLHT and GY were assessed using four different stability parameters: cultivar superiority, static stability, Wricke’s eco-valence and Finlay and Wilkinson’s regression model. The stability parameters ranked these genotypes differently suggesting that PLHT and GY stability should be assessed not only on a single or a few stability parameters but on a combination of them. GGE biplot analysis indicated that the environments representing metribuzin treatment at Marchouch 2014–2015 and the non-treated treatment at Terbol 2018–2019 are the ideal environments for evaluating faba bean genotypes. GGE biplot...
Scientific Reports, 2022
Weeds represent one of the major constraints for faba bean crop. The identification of molecular ... more Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 an...
Interbull Bulletin, 2019
The accuracy of genomic prediction could be improved by combining datasets across countries, but ... more The accuracy of genomic prediction could be improved by combining datasets across countries, but it is not always possible to combine the individual animal data. This project has tested a meta-analysis, called SNPMace, that mimics the combined analysis but requires only summary statistics, such as estimated SNP effects, from participating countries. The method uses the genetic correlation between a trait measured in different countries to produce country specific estimated SNP effects. We tested this method on data from 6 countries on the protein yield of Brown Swiss cattle and on the milk, fat and protein yields of Australian Holstein and Jersey cattle. In both cases the meta-analysis generated estimated breeding values that had a correlation with those obtained by analyzing the raw data in the range 0.99 to 1. The method is implemented in software called MetaGS which also converts data on a subset of SNPs to a common SNP set for analysis.
PLOS ONE, 2021
Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea... more Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one lo...
Plant, Cell & Environment, 2021
Genotype-by-environment interaction (GEI) is one of the major factors affecting the prediction ac... more Genotype-by-environment interaction (GEI) is one of the major factors affecting the prediction accuracy of genomic selection (GS) models. Standard models have low power to model complex GEI and they fail to predict phenotypes in unobserved environments. Here, we developed a novel prediction model that account for GEI, named 3GS, that combines genotype plus genotype × environment (GGE) analysis with genomic selection. The model calculates the principal components (PCs) of the environmental phenotypes using GGE analysis and predict the performance of these PCs using standard GS models before converting the GEBVs of these PCs (pcGEBVs) back to the original phenotypes. We demonstrated three advantages of the new model. First, 3GS showed significantly higher prediction accuracy primarily for deviated environments that have low to negative correlations to other environments. Second, 3GS can predict new genotypes in unobserved environments with high accuracy. Third, the computational complexity of 3GS increases linearly with increasing the number of environments and the population size, unlike the standard models that exhibit exponential increase, making it hundreds of times faster than the standard models for large datasets. 3GS can improve prediction accuracy with minimal resources in modern breeding programs in which massive populations get multi-environment phenotypes with high-throughput techniques. This article is protected by copyright. All rights reserved.
Scientific Reports, 2020
Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile... more Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QT...
Indexing of DNA sequences is the art of sorting massive genomic data in a user-friendly structure... more Indexing of DNA sequences is the art of sorting massive genomic data in a user-friendly structure to enable rapid accessing and comparing of different patterns in the data. Current genome assemblers use general algorithms for string indexing that do not exploit the special structural arrangement of genomes. Here, I am proposing a new algorithm that indexes only the configuration of microsatellite motifs along reads assuming that the order of microsatellites will be the same in overlapped sequences. The index size is >1000 times smaller than currently used indices and it has higher tolerance to the high error rates produced by third generation sequencing platforms. The results showed that the proposed algorithm can rapidly detect overlaps among considerable proportion of uncorrected long reads (~50% of all simulated base pairs with average read size of 8.16 kb and total error rates of 14.4%) to build large initial contigs. Unassembled reads can be then mapped to these contigs or c...
Frontiers in Ecology and Evolution, 2019
Frontiers in Plant Science, 2019
Breeding schemes that utilize modern breeding methods like genomic selection (GS) and speed breed... more Breeding schemes that utilize modern breeding methods like genomic selection (GS) and speed breeding (SB) have the potential to accelerate genetic gain for different crops. We investigated through stochastic computer simulation the advantages and disadvantages of adopting both GS and SB (SpeedGS) into commercial breeding programs for allogamous crops. In addition, we studied the effect of omitting one or two selection stages from the conventional phenotypic scheme on GS accuracy, genetic gain, and inbreeding. As an example, we simulated GS and SB for five traits (heading date, forage yield, seed yield, persistency, and quality) with different genetic architectures and heritabilities (0.7, 0.3, 0.4, 0.1, and 0.3; respectively) for a tall fescue breeding program. We developed a new method to simulate correlated traits with complex architectures of which effects can be sampled from multiple distributions, e.g. to simulate the presence of both minor and major genes. The phenotypic selection scheme required 11 years, while the proposed SpeedGS schemes required four to nine years per cycle. Generally, SpeedGS schemes resulted in higher genetic gain per year for all traits especially for traits with low heritability such as persistency. Our results showed that running more SB rounds resulted in higher genetic gain per cycle when compared to phenotypic or GS only schemes and this increase was more pronounced per year when cycle time was shortened by omitting cycle stages. While GS accuracy declined with additional SB rounds, the decline was less in round three than in round two, and it stabilized after the fourth SB round. However, more SB rounds resulted in higher inbreeding rate, which could limit long-term genetic gain. The inbreeding rate was reduced by approximately 30% when generating the initial population for each cycle through random crosses instead of generating half-sib families. Our study demonstrated a large potential for additional genetic gain from combining GS and SB. Nevertheless, methods to mitigate inbreeding should be considered for optimal utilization of these highly accelerated breeding programs.
The Plant Journal, 2019
Sequence elimination is one of the main mechanisms that increases the divergence among homoeologo... more 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 natural hexaploid wheat (NHW) genepool that has low genetic diversity. Here, we investigated the deviation 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) got 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 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. SHW derived from Triticum dicoccon or from one of two Aegilops tauschii subpopulations were almost free of RSE while highly admixed parents had higher RSE rate. The rate of RSE in synthetic derivatives was almost double that in primary synthetics. Genome-wide association analysis detected four loci with minor effect on the occurrence of RSE indicating that both parental lines and genetic factors were affecting the occurrence of RSE. Thus, "pre-pre-breeding" strategies should be applied before introducing SHW into pre-breeding programs to ensure genomic stability and avoid undesirable gene loss.
Crop Science, 2019
W heat (Triticum aestivum L.) is one of the most important and widely adapted strategic food crop... more W heat (Triticum aestivum L.) is one of the most important and widely adapted strategic food crop. It provides ?19% of the calories, 55% of carbohydrates, and 21% of protein needs of daily human requirements at the global level (Gupta et al., 1999; Braun et al., 2010). According to FAO (2018), ?749.5 Tg of wheat were produced globally in 2017 on ?220 million ha with a grain yield level of 3.4 t ha −1. In 2050, the world's population is expected to reach 9 billion and the demand for wheat will increase to >900 Tg. Fulfilling this demand will be challenging, especially in developing countries where the effect of climate change is more pronounced through the aggravation of both abiotic and biotic stresses (Dixon et al., 2009; Lobell et al., 2011). High temperature during reproductive stages of wheat causes significant loss in both grain yield and quality in the tropical and subtropical climates
Molecular Ecology Resources, 2018
We have developed the first comprehensive simulator for polyploid genomes (PolySim), and demonstr... more We have developed the first comprehensive simulator for polyploid genomes (PolySim), and demonstrated its value by performing large-scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size, or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating SNPs, minor allele frequency, heterozygosity, R 2 and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. Multivalent formation can homogenise allotetraploid subgenomes, but this homogenisation requires a higher multivalent rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations which, in combination with quantitative genetics tools, can be used to investigate the power of genome-wide association, genomic selection, or breeding program designs in these species.
BMC plant biology, Nov 2, 2017
Barley (Hordeum vulgare L.) is a major cereal crop, which is cultivated under variable environmen... more Barley (Hordeum vulgare L.) is a major cereal crop, which is cultivated under variable environmental conditions and abiotic stresses in marginal areas around the globe. In this study, we evaluated 150 Jordanian landraces obtained from ICARDA Gene Bank and four local checks for yield and yield components related-traits in two locations across Jordan for three growing seasons under rainfed conditions. The study aims to identify superior Jordanian barley genotypes under dry conditions, to understand the genotype × environment (G × E) interactions, to analyze stability parameters and to identify markers associated with yield and yield components under rainfed conditions. The barley accessions exhibited significant variation for all traits studied. Three accessions with high yield, cultivar superiority and stability under specific environments were identified with accession G69 is the highest yielding and superior for Madaba and overall environments and G144 is the highest yielding at Ra...
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Papers by Abdulqader Jighly