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

Abstract Background Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. Results A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL, other than NIS1, were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. Conclusions Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.

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Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽

10.3390/genes12121897 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1897

Author(s):

Endale G. Tafesse ◽

Krishna K. Gali ◽

V. B. Reddy Lachagari ◽

Rosalind Bueckert ◽

Thomas D. Warkentin

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Adaptive Traits ◽

Flowering Duration ◽

Genome Wide ◽

A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

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Dissection of coleoptile elongation in japonica rice under submergence through integrated genome‐wide association mapping and transcriptional analyses

Plant Cell & Environment ◽

10.1111/pce.13540 ◽

2019 ◽

Vol 42 (6) ◽

pp. 1832-1846 ◽

Cited By ~ 11

Author(s):

Khac Nhu Nghi ◽

Alessandro Tondelli ◽

Giampiero Valè ◽

Andrea Tagliani ◽

Caterina Marè ◽

...

Keyword(s):

Association Mapping ◽

Genome Wide Association ◽

Japonica Rice ◽

Genome Wide ◽

Coleoptile Elongation

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

Genes ◽

10.3390/genes10100829 ◽

2019 ◽

Vol 10 (10) ◽

pp. 829 ◽

Cited By ~ 1

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.

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Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping

Phytopathology ◽

10.1094/phyto-10-19-0372-r ◽

2020 ◽

Vol 110 (4) ◽

pp. 881-891 ◽

Cited By ~ 5

Author(s):

Anke Martin ◽

Paula Moolhuijzen ◽

Yongfu Tao ◽

Judy McIlroy ◽

Simon R. Ellwood ◽

...

Keyword(s):

Association Mapping ◽

Population Level ◽

Genome Wide Association ◽

Pyrenophora Teres ◽

Barley Cultivars ◽

Genome Wide ◽

A Genome ◽

Sexual Recombination ◽

Parastagonospora Nodorum ◽

Genomic Regions

Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.

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Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v2 ◽

2019 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Sclerotinia Sclerotiorum ◽

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

The Impact

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

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Eagle for better genome-wide association mapping

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab204 ◽

2021 ◽

Author(s):

Andrew W George ◽

Arunas Verbyla ◽

Joshua Bowden

Keyword(s):

Association Mapping ◽

Genome Wide Association Study ◽

R Package ◽

Study Data ◽

Single Locus ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Trait Associations

Abstract Eagle is an R package for multi-locus association mapping on a genome-wide scale. It is unlike other multi-locus packages in that it is easy-to-use for R users and non-users alike. It has two modes of use, command line and GUI. Eagle is fully documented and has its own supporting website, http://eagle.r-forge.r-project.org/index.html. Eagle is a significant improvement over the method-of-choice, single-locus association mapping. It has greater power to detect SNP-trait associations. It is based on model selection, linear mixed models, and a clever idea on how random effects can be used to identify SNP-trait associations. Through an example with real mouse data, we demonstrate Eagle’s ability to bring clarity and increased insight to single-locus findings. Initially, we see Eagle complementing single-locus analyses. However, over time, we hope the community will make, increasingly, multi-locus association mapping their method-of-choice for the analysis of genome-wide association study data.

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Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen.

10.21203/rs.3.rs-35252/v2 ◽

2020 ◽

Author(s):

Mathias Frontini ◽

Arnaud Boisnard ◽

Julien Frouin ◽

Malika Ouikene ◽

Jean-Benoit Morel ◽

...

Keyword(s):

Nitrogen Fertilization ◽

Rice Blast ◽

Genome Wide Association ◽

Japonica Rice ◽

High Nitrogen ◽

Initial Finding ◽

Blast Fungus ◽

Genome Wide ◽

A Genome ◽

Low Nitrogen

Abstract Background: Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. Results: A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. Conclusions: Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.

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Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v4 ◽

2020 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Sclerotinia Sclerotiorum ◽

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

The Impact

Abstract Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. Conclusion: These results suggest that the new region on chromosome 1 harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

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Genome-wide association mapping for wheat blast resistance in CIMMYT’s international screening nurseries evaluated in Bolivia and Bangladesh

Scientific Reports ◽

10.1038/s41598-020-72735-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Philomin Juliana ◽

Xinyao He ◽

Muhammad R. Kabir ◽

Krishna K. Roy ◽

Md. Babul Anwar ◽

...

Keyword(s):

Association Mapping ◽

Blast Resistance ◽

Genome Wide Association ◽

Aegilops Ventricosa ◽

Wheat Blast ◽

Genome Wide ◽

Large Panel ◽

The Mean ◽

Association Mapping Study ◽

Genomic Regions

Abstract Wheat blast caused by the fungus Magnaporthe oryzae pathotype Triticum (MoT) is an emerging threat to wheat production. To identify genomic regions associated with blast resistance against MoT isolates in Bolivia and Bangladesh, we performed a large genome-wide association mapping study using 8607 observations on 1106 lines from the International Maize and Wheat Improvement Centre’s International Bread Wheat Screening Nurseries (IBWSNs) and Semi-Arid Wheat Screening Nurseries (SAWSNs). We identified 36 significant markers on chromosomes 2AS, 3BL, 4AL and 7BL with consistent effects across panels or site-years, including 20 markers that were significant in all the 49 datasets and tagged the 2NS translocation from Aegilops ventricosa. The mean blast index of lines with and without the 2NS translocation was 2.7 ± 4.5 and 53.3 ± 15.9, respectively, that substantiates its strong effect on blast resistance. Furthermore, we fingerprinted a large panel of 4143 lines for the 2NS translocation that provided excellent insights into its frequency over years and indicated its presence in 94.1 and 93.7% of lines in the 2019 IBWSN and SAWSN, respectively. Overall, this study reinforces the effectiveness of the 2NS translocation for blast resistance and emphasizes the urgent need to identify novel non-2NS sources of blast resistance.

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