Population structure, marker-trait association and identification of candidate genes for terminal heat stress relevant traits in bread wheat (Triticum aestivum L. em Thell)

2020 ◽  
Vol 18 (3) ◽  
pp. 168-178
Author(s):  
Devender Sharma ◽  
Jai Prakash Jaiswal ◽  
Navin Chander Gahtyari ◽  
Anjana Chauhan ◽  
Rashmi Chhabra ◽  
...  
Keyword(s):  
Population Structure ◽  
Heat Stress ◽  
Candidate Genes ◽  
Bread Wheat ◽  
Ssr Markers ◽  
Stress Responses ◽  
Vegetation Index ◽  
Association Studies ◽  
Trait Association

AbstractGenetic improvement along with widened crop base necessitates for the detailed understanding of the genetic diversity and population structure in wheat. The present investigation reports the discovery of a total of 182 alleles by assaying 52 simple sequence repeats (SSRs) on 40 genotypes of bread wheat. Unweighted neighbour-joining method grouped these genotypes into two main clusters. Highly heat tolerant and intermediate tolerant cultivars were grouped in the same cluster, whereas remaining genotypes, particularly sensitive ones, were assigned different cluster. Similarly, the entire population was structured into two sub-populations (K = 2), closely corresponding with the other distance-based clustering patterns. The marker-trait association was discovered for four important physiological parameters, viz. canopy temperature depression, membrane thermostability index (MSI), normalized difference vegetation index and heat susceptibility index, indicating for heat stress (HS) tolerance in wheat. Both general and mixed linear models of association studies during 2017 and 2018, revealed the association of SSR markers, wmc222 (17.60%, PV) and gwm34 (20.70%, PV) with the mean phenotypic value of MSI. Likewise, SSR markers barc183, gwm75, gwm11 and cfd7 revealed a unique relationship with four selected physiological traits. Candidate genes discovered using in silico tools had nine SSR markers within the genic regions reported to play a role in heat and drought stress responses in plants. The information generated about these genic regions may be explored further in expression studies in-vivo to impart HS tolerance in bread wheat.

Genetic diversity and population structure using linked SSR markers for heat stress tolerance in rice

2017 ◽  
Vol 54 (2) ◽  
pp. 158
Author(s):  
Sudipti Mohapatra ◽  
E Pandit ◽  
SR Barik ◽  
BC Patra ◽  
J Meher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Heat Stress Tolerance

scholarly journals Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

2021 ◽  
Vol 12 ◽  
Author(s):  
Pooja Sihag ◽  
Vijeta Sagwal ◽  
Anuj Kumar ◽  
Priyanka Balyan ◽  
Reyazul Rouf Mir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Wheat Varieties ◽  
Wheat Genotypes ◽  
Wheat Germplasm ◽  
Heat Tolerant

A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR markers (miRNA-SSRs) in wheat, which were found as key players in various abiotic stresses. In the present study, we identified 104 heat-stress-responsive miRNAs reported in various crops. Out of these, 70 miRNA-SSR markers have been validated on a set of 20 terminal heat-tolerant and heat-susceptible wheat genotypes. Among these, only 19 miRNA-SSR markers were found to be polymorphic, which were further used to study the genetic diversity and population structure. The polymorphic miRNA-SSRs amplified 61 SSR loci with an average of 2.9 alleles per locus. The polymorphic information content (PIC) value of polymorphic miRNA-SSRs ranged from 0.10 to 0.87 with a mean value of 0.48. The dendrogram constructed using unweighted neighbor-joining method and population structure analysis clustered these 20 wheat genotypes into 3 clusters. The target genes of these miRNAs are involved either directly or indirectly in providing tolerance to heat stress. Furthermore, two polymorphic markers miR159c and miR165b were declared as very promising diagnostic markers, since these markers showed specific alleles and discriminated terminal heat-tolerant genotypes from the susceptible genotypes. Thus, these identified miRNA-SSR markers will prove useful in the characterization of wheat germplasm through the study of genetic diversity and population structural analysis and in wheat molecular breeding programs aimed at terminal heat tolerance of wheat varieties.

scholarly journals Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0231063
Author(s):  
Sandhya Tyagi ◽  
Anuj Kumar ◽  
Tinku Gautam ◽  
Renu Pandey ◽  
Sachin Rustgi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Allelic Diversity ◽  
Abiotic Factor ◽  
Wheat Genotypes ◽  
Mirna Genes ◽  
Heat Tolerant

Heat stress is an important abiotic factor that limits wheat production globally, including south-east Asia. The importance of micro (mi) RNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, specifically simple sequence repeats (SSRs), play an important role in the wheat improvement breeding programs. Given the role of miRNAs in heat stress-induced transcriptional regulation and acclimatization, the development of miRNA-derived SSRs would prove useful in studying the allelic diversity at the heat-responsive miRNA-genes in wheat. In the present study, efforts have been made to identify SSRs from 96 wheat heat-responsive miRNA-genes and their characterization using a panel of wheat genotypes with contrasting reactions (tolerance/susceptible) to heat stress. A set of 13 miRNA-derived SSR markers were successfully developed as an outcome. These miRNA-SSRs are located on 11 different common wheat chromosomes (2A, 3A, 3B, 3D, 4D, 5A, 5B, 5D, 6A, 6D, and 7A). Among 13 miRNA-SSRs, seven were polymorphic on a set of 37 selected wheat genotypes. Within these polymorphic SSRs, three makers, namely HT-169j, HT-160a, and HT-160b, were found promising as they could discriminate heat-tolerant and heat-susceptible genotypes. This is the first report of miRNA-SSR development in wheat and their deployment in genetic diversity and population structure studies and characterization of trait-specific germplasm. The study suggests that this new class of molecular makers has great potential in the marker-assisted breeding (MAB) programs targeted at improving heat tolerance and other adaptability or developmental traits in wheat and other crops.

scholarly journals Identification of QTLs affecting post-anthesis heat stress responses in European bread wheat

2022 ◽  
Author(s):  
Gaëtan Touzy ◽  
Stéphane Lafarge ◽  
Elise Redondo ◽  
Vincent Lievin ◽  
Xavier Decoopman ◽  
...  
Keyword(s):  
Heat Stress ◽  
Bread Wheat ◽  
Heat Tolerance ◽  
Stress Responses ◽  
Grain Weight ◽  
High Yield ◽  
Wheat Varieties ◽  
Stay Green ◽  
A Genome ◽  
Main Effect

Abstract Key message The response of a large panel of European elite wheat varieties to post-anthesis heat stress is influenced by 17 QTL linked to grain weight or the stay-green phenotype. Abstract Heat stress is a critical abiotic stress for winter bread wheat (Triticum aestivum L.) especially at the flowering and grain filling stages, limiting its growth and productivity in Europe and elsewhere. The breeding of new high-yield and stress-tolerant wheat varieties requires improved understanding of the physiological and genetic bases of heat tolerance. To identify genomic areas associated with plant and grain characteristics under heat stress, a panel of elite European wheat varieties (N = 199) was evaluated under controlled conditions in 2016 and 2017. A split-plot design was used to test the effects of high temperature for ten days after flowering. Flowering time, leaf chlorophyll content, the number of productive spikes, grain number, grain weight and grain size were measured, and the senescence process was modeled. Using genotyping data from a 280 K SNP chip, a genome-wide association study was carried out to test the main effect of each SNP and the effect of SNP × treatment interaction. Genotype × treatment interactions were mainly observed for grain traits measured on the main shoots and tillers. We identified 10 QTLs associated with the main effect of at least one trait and seven QTLs associated with the response to post-anthesis heat stress. Of these, two main QTLs associated with the heat tolerance of thousand-kernel weight were identified on chromosomes 4B and 6B. These QTLs will be useful for breeders to improve grain yield in environments where terminal heat stress is likely to occur.

scholarly journals Genomic analysis for heat and combined heat–drought resilience in bread wheat under field conditions

2021 ◽  
Author(s):  
Michael O. Itam ◽  
Ryosuke Mega ◽  
Yasir S. A. Gorafi ◽  
Yuji Yamasaki ◽  
Izzat S. A. Tahir ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Vegetation Index ◽  
Isotope Composition ◽  
Association Studies ◽  
Canopy Temperature ◽  
Kernel Weight ◽  
Field Conditions ◽  
Genome Wide Association Studies ◽  
D Genome ◽  
Genome Wide

Abstract Key message GWAS on a bread wheat panel with high D genome diversity identified novel alleles and QTLs associated with resilience to combined heat and drought stress under natural field conditions. Abstract As heat (H) and drought stresses occur concurrently under field conditions, studying them separately offers limited opportunities for wheat improvement. Here, a wheat diversity panel containing Aegilops tauschii introgressions was evaluated under H and combined heat–drought (HD) stresses to identify quantitative trait loci (QTLs) associated with resilience to the stresses, and to assess the practicability of harnessing Ae. tauschii diversity for breeding for combined stress resilience. Using genome-wide analysis, we identified alleles and QTLs on chromosomes 3D, 5D, and 7A controlling grain yield (GY), kernel number per spike, and thousand-kernel weight, and on 3D (521–549 Mbp) controlling GY alone. A strong marker–trait association (MTA) for GY stability on chromosome 3D (508.3 Mbp) explained 20.3% of the variation. Leaf traits—canopy temperature, vegetation index, and carbon isotope composition—were controlled by five QTLs on 2D (23–96, 511–554, and 606–614 Mbp), 3D (155–171 Mbp), and 5D (407–413 Mbp); some of them were pleiotropic for GY and yield-related traits. Further analysis revealed candidate genes, including GA20ox, regulating GY stability, and CaaX prenyl protease 2, regulating canopy temperature at the flowering stage, under H and HD stresses. As genome-wide association studies under HD in field conditions are scarce, our results provide genomic landmarks for wheat breeding to improve adaptation to H and HD conditions under climate change.

scholarly journals Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 494
Author(s):  
Christina Schumacher ◽  
Christoph Tim Krannich ◽  
Lisa Maletzki ◽  
Karin Köhl ◽  
Joachim Kopka ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Association Studies ◽  
Solanum Tuberosum L ◽  
Potato Cultivars ◽  
Candidate Gene Approach ◽  
Improved Performance ◽  
High Yields

Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields under limited water supplies. A candidate gene approach was used to develop functional simple sequence repeat (SSR) markers for association studies in potato with the aim to enhance breeding for drought tolerance. SSR primer combinations, mostly surrounding interrupted complex and compound repeats, were derived from 103 candidate genes for drought tolerance. Validation of the SSRs was performed in an association panel representing 34 mainly starch potato cultivars. Seventy-five out of 154 SSR primer combinations (49%) resulted in polymorphic, highly reproducible banding patterns with polymorphic information content (PIC) values between 0.11 and 0.90. Five SSR markers identified allelic differences between the potato cultivars that showed significant associations with drought sensitivity. In all cases, the group of drought-sensitive cultivars showed predominantly an additional allele, indicating that selection against these alleles by marker-assisted breeding might confer drought tolerance. Further studies of these differences in the candidate genes will elucidate their role for an improved performance of potatoes under water-limited conditions.

Synonymous mutation of miR396a target sites in Growth Regulating Factor 15 (GRF15) enhances photosynthetic efficiency and heat tolerance in poplar

2021 ◽  
Author(s):  
Yiyang Zhao ◽  
Jianbo Xie ◽  
Sha Wang ◽  
Weijie Xu ◽  
Sisi Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Stress Responses ◽  
Photosynthetic Efficiency ◽  
Time Course ◽  
Growth Traits ◽  
Association Studies ◽  
Rna Seq ◽  
Gene Association ◽  
Target Sites

Abstract Heat stress damages plant tissues and induces multiple adaptive responses. Complex and spatiotemporally specific interactions among transcription factors (TFs), microRNAs (miRNAs), and their target genes play crucial roles in regulating stress responses. To explore these interactions and identify the regulatory networks in perennial woody plants, we integrated time-course RNA-seq, small RNA-seq, degradome sequencing, weighted gene correlation network analysis, and multi-gene association approaches in poplar. The results allowed for constructing a three-layer, highly interwoven regulatory network involving 15 TFs, 45 miRNAs, and 77 photosynthetic genes. Candidate gene association studies in the population of Populus tomentosa identified 114 significant associations and 696 epistatic SNP–SNP pairs which were linked to 29 photosynthetic and growth traits (P < 0.0001, q < 0.05). Finally, we identified miR396a and its target, Growth-Regulating Factor 15 (GRF15) as an important regulatory module in the heat stress response. Transgenic oxPagGRF15 plants expressing a GRF15 mRNA that lacks miR396a target sites exhibited enhanced heat tolerance and photosynthetic efficiency compared to wild-type plants. Together, these observations demonstrate that GRF15 plays a crucial role in responding to heat stress and validate the power of this new, multifaceted approach for identifying regulatory nodes in plants.

scholarly journals Shared genetic architecture underlying root metaxylem phenotypes under drought stress in cereals

2020 ◽  
Author(s):  
Stephanie P. Klein ◽  
Jenna E. Reeger ◽  
Shawn M. Kaeppler ◽  
Kathleen M. Brown ◽  
Jonathan P. Lynch
Keyword(s):  
Water Stress ◽  
Drought Stress ◽  
Candidate Genes ◽  
Stress Responses ◽  
Genetic Architecture ◽  
Association Studies ◽  
Multiple Root ◽  
Stress Conditions ◽  
Genome Wide Association Studies ◽  
New Strategy

AbstractRoot metaxylem are phenotypically diverse structures whose function is related to their anatomy, particularly under drought stress. Much research has dissected the genetic machinery underlying metaxylem phenotypes in dicots, but monocots are relatively unexplored. In maize (Zea mays), a robust pipeline integrated a GWAS of root metaxylem phenes under well-watered and water stress conditions with a gene co-expression network to identify candidate genes most likely to impact metaxylem phenotypes. We identified several promising candidate genes in 14 gene co-expression modules inferred to be functionally relevant to xylem development. We also identified five gene candidates that co-localized in multiple root metaxylem phenes in both well-watered and water stress conditions. Using a rice GWAS conducted in parallel, we detected overlapping genetic architecture influencing root metaxylem phenotypes by identifying eight pairs of syntenic candidate genes significantly associated with metaxylem phenes. There is evidence that the genes of these syntenic pairs may be involved in biosynthetic processes related to the cell wall, hormone signaling, oxidative stress responses, and drought responses. Our study demonstrates a powerful new strategy for identifying promising gene candidates and suggests several gene candidates that may enhance our understanding of vascular development and responses to drought in cereals.One sentence summaryCross-species genome-wide association studies and a gene coexpression network identified genes associated with root metaxylem phenotypes in maize under water stress and non-stress and rice.

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