GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley – A review

Alqudah, Ahmad M.; Sallam, Ahmed; Baenziger, P. S.; Börner, Andreas

doi:10.1016/j.jare.2019.10.013

Cited by 290 publications

(244 citation statements)

References 102 publications

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“…GWAS was able to identify three SNPs significant at 5% at the chromosome-wide level and 54 suggestive SNPs associated with the prolificacy trait. The power of GWAS to detect the true association is determined by many factors such as phenotypic variation, the number of individuals, and allele frequency [52]. The indirect associations are the result of disequilibrium between multiple factors affecting a trait, whereas lack of statistical power can produce spurious associations that are only distantly linked to causal polymorphisms [53].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Hernández-Montiel

Martínez-Núñez

Ramón-Ugalde

et al. 2020

Animals

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The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10−3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Hernández-Montiel

Martínez-Núñez

Ramón-Ugalde

et al. 2020

Animals

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“…The threshold p-value (p = .0001) was indicated by dotted red line for each track of low frequency alleles from GWAS analysis is mainly due to lack of resolution to detect association signals for functional alleles present in low frequency (usually they are ignored in analysis). Otherwise, rare alleles could significantly explain genetic variations in phenotypic traits (Alqudah, Sallam, Baenziger, & Börner, 2020). These rare variants that are unique to a specific group of individuals and would only be detected in GWAS if the frequency was greater (Brachi et al, 2011).…”

Section: F I G U R Ementioning

confidence: 99%

Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing

Edae

Rouse

2020

The Plant Genome

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The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the seedling stage with a total of seven isolates including TKKTP, TKTTF, TKTTF, TRTTF, TTRTF, TTKSK, and TTKTT. The lines were genotyped by a GBS platform and 9,042 SNPs were used for identification of chromosome regions associated with resistance against the seven isolates. Strong association signals were detected on chromosomes 6BL (Sr11 gene region) and 4AL, likely Sr7a, for resistance against both TKKTP and TKTTF. Similarly, association signals were also detected on chromosomes 4AL (race TTRTF resistance) and 4BS (race TTKSK and TTKTT resistance). Association analysis based on mean phenotypic differences between closely related isolates identified QTL that were not elucidated by direct association mapping of the responses, individually. Overall, with the exception of race TRTTF, each race shared at least one association signal with another race. However, the number of race-specific association signals are larger than that of association signals common among races suggesting the need for identifying and characterizing QTL/genes for newly emerging stem rust pathogen races. There was also high concordance between PCA-based GWAS association signals and association signals from that of both single and multilocus mixed models.

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“…In crops such as wheat and barley, QTLs related to drought have been identified and introgressed from wild relative species [ 132 ], allowing the inclusion of new favorable alleles in the breeding populations. Another approach to identifying regions that explain the phenotypic variation of traits (e.g., drought tolerance) in plants is the Genome-Wide Association Study (GWAS), where it is possible to associate a specific single-nucleotide polymorphism (SNP)/gene with a phenotypic variation of any trait [ 133 ]. The GWAS combines phenotypic and genomic information to identify statistical associations in order to explain the phenotypic variations of the target trait.…”

Section: Methods and Approaches To Improve Crop Tolerance To Drougmentioning

confidence: 99%

A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency

Rosero

Granda

Berdugo-Cely

et al. 2020

Plants

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Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; in accordance, agricultural systems have to be optimized. Several concepts and strategies should be considered to improve crop yield and quality, particularly in vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two strategies aiming to increase drought stress tolerance: (i) the use of natural genes that have evolved over time and are preserved in crop wild relatives and landraces for drought tolerance breeding using conventional and molecular methods and (ii) exploiting the reservoir of neglected and underutilized species to identify those that are known to be more drought-tolerant than conventional staple crops while possessing other desired agronomic and nutritive characteristics, as well as introducing them into existing cropping systems to make them more resilient to water deficiency conditions. In the past, the existence of drought tolerance genes in crop wild relatives and landraces was either unknown or difficult to exploit using traditional breeding techniques to secure potential long-term solutions. Today, with the advances in genomics and phenomics, there are a number of new tools available that facilitate the discovery of drought resistance genes in crop wild relatives and landraces and their relatively easy transfer into advanced breeding lines, thus accelerating breeding progress and creating resilient varieties that can withstand prolonged drought periods. Among those tools are marker-assisted selection (MAS), genomic selection (GS), and targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration of these two major strategies, the advances in conventional and molecular breeding for the drought tolerance of conventional staple crops, and the introduction of drought-tolerant neglected and underutilized species into existing production systems has the potential to enhance the resilience of agricultural production under conditions of water scarcity.

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GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley – A review

Cited by 290 publications

References 102 publications

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing

A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency

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