Genome-Wide Association Studies (GWAS) for Abiotic Stress Tolerance in Plants

Challa, Surekha; Neelapu, Nageswara Rao Reddy

doi:10.1016/b978-0-12-813066-7.00009-7

Cited by 41 publications

(30 citation statements)

References 39 publications

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“…Previous studies suggested that vast genetic diversity still exists in the germplasms of various crops 12– 14 . GWAS emerged as a powerful tool to identify the genetic basis behind complex phenotypic traits 15, 16 , and it provides high mapping resolution compared with conventional genetic mapping 17, 18 . So far this approach has been applied to major food crops, including wheat 7, 19, 20 , rice 21 , maize 22 , sorghum 23 and Brassica napus L. 24 , to identify the natural variation associated with heat stress and to understand this genetic basis.…”

Section: Mining Of Stress Linked Genesmentioning

confidence: 99%

Functional genomic approaches to improve crop plant heat stress tolerance

et al. 2019

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Heat stress as a yield limiting issue has become a major threat for food security as global warming progresses. Being sessile, plants cannot avoid heat stress. They respond to heat stress by activating complex molecular networks, such as signal transduction, metabolite production and expressions of heat stress-associated genes. Some plants have developed an intricate signalling network to respond and adapt it. Heat stress tolerance is a polygenic trait, which is regulated by various genes, transcriptional factors, proteins and hormones. Therefore, to improve heat stress tolerance, a sound knowledge of various mechanisms involved in the response to heat stress is required. The classical breeding methods employed to enhance heat stress tolerance has had limited success. In this era of genomics, next generation sequencing techniques, availability of genome sequences and advanced biotechnological tools open several windows of opportunities to improve heat stress tolerance in crop plants. This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering novel genes related to heat stress, and their functional validation using both reverse and forward genetic approaches. This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.

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Section: Mining Of Stress Linked Genesmentioning

confidence: 99%

Functional genomic approaches to improve crop plant heat stress tolerance

et al. 2019

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“…A Genome wide association study (GWAS) is a molecular tool used to identify speci c genomic regions or loci governing simple to complex traits. GWAS can be used to determine if a genomic variant is associated with a trait of interest using either germplasm, segregation population, or a collection of diverse genotypes [9,10]. Various candidate genes or quantitative trait loci responsible for traits of interest have been identi ed using GWAS technology in different crops.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

Binagwa

Traore

Egnin

et al. 2020

Preprint

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Background Genome-wide association studies (GWAS) was utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed. Results Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 206 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosome 4 and 10 were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the chromosome 4 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions. Conclusion Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.

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“…A Genome wide association study (GWAS) is a molecular tool used to identify speci c genomic regions or loci governing simple to complex traits. GWAS can be used to determine if a genomic variant is associated with a trait of interest using either germplasm, segregation population, or a collection of diverse genotypes [19,20]. Various candidate genes or quantitative trait loci responsible for traits of interest have been identi ed using GWAS technology in different crops.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

Binagwa

Traore

Egnin

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Genome-wide association studies (GWAS) was utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed. Results: Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for the identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 206 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosomes 4 and 10 (Pv04 and Pv10) were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the chromosome 4 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on Pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on Pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions.Conclusion: Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.

show abstract

Genome-Wide Association Studies (GWAS) for Abiotic Stress Tolerance in Plants

Cited by 41 publications

References 39 publications

Functional genomic approaches to improve crop plant heat stress tolerance

Functional genomic approaches to improve crop plant heat stress tolerance

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

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