scholarly journals Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1088
Author(s):  
Thao Duc Le ◽  
Floran Gathignol ◽  
Huong Thi Vu ◽  
Khanh Le Nguyen ◽  
Linh Hien Tran ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Transport Systems ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Salinity Stress Tolerance

Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.

scholarly journals A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 829 ◽  
Author(s):  
Muhammad Yasir ◽  
Shoupu He ◽  
Gaofei Sun ◽  
Xiaoli Geng ◽  
Zhaoe Pan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Stress Tolerance ◽  
Salinity Stress ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Salinity Stress Tolerance

Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.

scholarly journals Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rami AlTameemi ◽  
Harsimardeep S. Gill ◽  
Shaukat Ali ◽  
Girma Ayana ◽  
Jyotirmoy Halder ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Stagonospora Nodorum ◽  
Complex Nature ◽  
Breeding Programs ◽  
Stagonospora Nodorum Blotch ◽  
Genome Wide ◽  
A Genome

AbstractStagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single‐nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions (‘Pioneer-2180’ and ‘Shocker’) with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 759 ◽  
Author(s):  
Caleb Manamik Breria ◽  
Ching-Hsiang Hsieh ◽  
Tsair-Bor Yen ◽  
Jo-Yi Yen ◽  
Thomas J. Noble ◽  
...  
Keyword(s):  
Salt Stress ◽  
Association Study ◽  
Stress Tolerance ◽  
Vigna Radiata ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Salt Stress Tolerance ◽  
Genome Wide ◽  
A Genome

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

scholarly journals Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190964 ◽  
Author(s):  
Julien Frouin ◽  
Antoine Languillaume ◽  
Justine Mas ◽  
Delphine Mieulet ◽  
Arnaud Boisnard ◽  
...  
Keyword(s):  
Association Mapping ◽  
Calcium Signaling ◽  
Salinity Stress ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Mapping Study ◽  
Genome Wide ◽  
A Genome ◽  
Association Mapping Study

Linking osmotic adjustment and stomatal characteristics with salinity stress tolerance in contrasting barley accessions

2015 ◽  
Vol 42 (3) ◽  
pp. 252 ◽  
Author(s):  
Min Zhu ◽  
Meixue Zhou ◽  
Lana Shabala ◽  
Sergey Shabala
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Osmotic Adjustment ◽  
Inorganic Ions ◽  
Plant Performance ◽  
Hordeum Vulgare L ◽  
Stomatal Characteristics ◽  
Stomata Density ◽  
Salinity Stress Tolerance

Salinity tolerance is a complex trait – both physiologically and genetically – and the issue of which mechanism or trait has bigger contribution towards the overall plant performance is still hotly discussed in the literature. In this work, a broad range of barley (Hordeum vulgare L. and Hordeum spontaneum L.) genotypes contrasting in salinity stress tolerance were used to investigate the causal link between plant stomatal characteristics, tissue ion relations, and salinity tolerance. In total, 46 genotypes (including two wild barleys) were grown under glasshouse conditions and exposed to moderate salinity stress (200mM NaCl) for 5 weeks. The overall salinity tolerance correlated positively with stomata density, leaf K+ concentration and the relative contribution of inorganic ions towards osmotic adjustment in the shoot. At the same time, no correlation between salinity tolerance and stomatal conductance or leaf Na+ content in the shoot was found. Taken together, these results indicate the importance of increasing stomata density as an adaptive tool to optimise efficiency of CO2 assimilation under moderate saline conditions, as well as benefits of the predominant use of inorganic osmolytes for osmotic adjustment in barley. Another finding of note was that wild barleys showed rather different strategies dealing with salinity, as compared with cultivated varieties.

scholarly journals Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 559
Author(s):  
Ashutosh Kumar Yadav ◽  
Aruna Kumar ◽  
Nitasha Grover ◽  
Ranjith Kumar Ellur ◽  
Haritha Bollinedi ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide ◽  
Trait Associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

scholarly journals Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

BMC Genetics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Dariga Batayeva ◽  
Benedick Labaco ◽  
Changrong Ye ◽  
Xiaolin Li ◽  
Bakdaulet Usenbekov ◽  
...  
Keyword(s):  
Association Study ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Temperate Japonica ◽  
Rice Germplasm ◽  
Genome Wide

Genetics and molecular mapping for salinity stress tolerance at seedling stage in lentil ( Lens culinaris Medik)

Crop Science ◽  
2020 ◽  
Vol 60 (3) ◽  
pp. 1254-1266
Author(s):  
Dharmendra Singh ◽  
Chandan Kumar Singh ◽  
Ram Sewak Singh Tomar ◽  
Shristi Sharma ◽  
Sourabh Karwa ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Lens Culinaris ◽  
Molecular Mapping ◽  
Seedling Stage ◽  
Salinity Stress Tolerance

scholarly journals GABA operates upstream of H+-ATPase and improves salinity tolerance in Arabidopsis by enabling cytosolic K+ retention and Na+ exclusion

2019 ◽  
Vol 70 (21) ◽  
pp. 6349-6361 ◽  
Author(s):  
Nana Su ◽  
Qi Wu ◽  
Jiahui Chen ◽  
Lana Shabala ◽  
Axel Mithöfer ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Plant Roots ◽  
Transcript Levels ◽  
Root Epidermis ◽  
Beneficial Effects ◽  
Salinity Stress Tolerance ◽  
Increased Activity

GABA has beneficial effects on salinity stress tolerance in Arabidopsis linked to increased activity of H+-ATPase, reduced ROS-induced K+ efflux from root epidermis, and increased SOS1 and NHX1 transcript levels in plant roots.

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