Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.)

Xie, Yonghong; Yan, Feng; Chen, Qi; Zhao, Feike; Zhou, Shuijuan; Ding, Ying; Song, Xiaoling; Li, Ping; Wang, Baohua

doi:10.1007/s13258-019-00842-6

Cited by 13 publications

(6 citation statements)

References 25 publications

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“…Only a few studies have tried to genetically map salt tolerance in maize (Cui et al ., 2015 ; Luo et al ., 2019b ; Luo et al ., 2019a ; Luo et al ., 2017b ; Sandhu et al ., 2020 ; Xie et al ., 2019 ). The GWAS analysis in this study builds on the results of those studies and allowed us to identify salt tolerance‐related SNP markers throughout the genome.…”

Section: Discussionmentioning

confidence: 99%

“…A genome‐wide association study (GWAS) is a powerful method to study genetic variations associated with complex traits at the genome‐wide level (Huang et al ., 2010 ; Luo et al ., 2019b ; Xie et al ., 2019 ). This method takes into account the historical recombination found in broad panels of diverse germplasm and population‐wide linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs) and QTLs.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method

Luo

Zhang

et al. 2021

Plant Biotechnology Journal

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Salt stress is a major devastating abiotic factor that affects the yield and quality of maize. However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome-wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of >25%. In total, 149 significant SNPs explaining 6.6%-11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co-localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild-type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt-tolerant maize lines.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method

Luo

Zhang

et al. 2021

Plant Biotechnology Journal

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“…Salt stress in per se and its tolerance mechanism in crops at physiological level, cellular level and phenotypical level are more complex ( Farooq et al, 2015 ). In the maize crop, a number of QTLs were reported for rate of seed germination, salt tolerance ranking, shoot fresh and dry weights, shoot K + /Na + ratio, and Na + and K + concentrations in shoots ( Cui et al, 2015 ; Luo et al, 2017 , 2021 ; Zhang et al, 2018 ; Xie et al, 2019 ). However, studies on salt tolerance of maize and reporting of QTLs/genomic regions for salt tolerance are still very limited in field-grown maize crop for a full crop cycle.…”

Section: Introductionmentioning

confidence: 99%

Genomic Regions Associated With Salinity Stress Tolerance in Tropical Maize (Zea Mays L.)

Zaidi

Shahid²,

Seetharam³

et al. 2022

Front. Plant Sci.

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Being a widely cultivated crop globally under diverse climatic conditions and soil types, maize is often exposed to an array of biotic and abiotic stresses. Soil salinity is one of the challenges for maize cultivation in many parts of lowland tropics that significantly affects crop growth and reduces economic yields. Breeding strategies integrated with molecular approach might accelerate the process of identifying and developing salinity-tolerant maize cultivars. In this study, an association mapping panel consisting of 305 diverse maize inbred lines was phenotyped in a managed salinity stress phenotyping facility at International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates (UAE). Wide genotypic variability was observed in the panel under salinity stress for key phenotypic traits viz., grain yield, days to anthesis, anthesis-silking interval, plant height, cob length, cob girth, and kernel number. The panel was genotyped following the genome-based sequencing approach to generate 955,690 SNPs. Total SNPs were filtered to 213,043 at a call rate of 0.85 and minor allele frequency of 0.05 for association analysis. A total of 259 highly significant (P ≤ 1 × 10–5) marker-trait associations (MTAs) were identified for seven phenotypic traits. The phenotypic variance for MTAs ranged between 5.2 and 9%. A total of 64 associations were found in 19 unique putative gene expression regions. Among them, 12 associations were found in gene models with stress-related biological functions.

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“…In the MLM-based methods, population structure is fitted as a fixed effect, while kinship among individuals is incorporated into the variance-covariance structure of individual random effects ( Zhang et al, 2010 ). Since the publication of maize B73 reference genome ( Schnable et al, 2009 ), GWAS has been widely used in maize genetics research, and has played a great role in the analysis of genetic mechanisms such as traditional maize agronomic traits ( Wallace et al, 2016 ; Zhou et al, 2016 ; Li et al, 2017 ; Dai et al, 2018 ; Du et al, 2018 ; Zhou et al, 2018 ; Owens et al, 2019 ), key phenotypes ( Cui et al, 2016 ; Li et al, 2016 ; Liu et al, 2016 ; Zhang et al, 2016a ; Sanchez et al, 2018 ; Guo et al, 2019 ; Mazaheri et al, 2019 ) and stress resistance ( Zhang et al, 2016b ; Shi et al, 2018 ; Cooper et al, 2019 ; Wang et al, 2019 ; Xie et al, 2019 ). However, there are few genetic studies on the phenotype of maize leaf sheath.…”

Section: Introductionmentioning

confidence: 99%

Dissecting the Genetic Structure of Maize Leaf Sheaths at Seedling Stage by Image-Based High-Throughput Phenotypic Acquisition and Characterization

Wang

et al. 2022

Front. Plant Sci.

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The rapid development of high-throughput phenotypic detection techniques makes it possible to obtain a large number of crop phenotypic information quickly, efficiently, and accurately. Among them, image-based phenotypic acquisition method has been widely used in crop phenotypic identification and characteristic research due to its characteristics of automation, non-invasive, non-destructive and high throughput. In this study, we proposed a method to define and analyze the traits related to leaf sheaths including morphology-related, color-related and biomass-related traits at V6 stage. Next, we analyzed the phenotypic variation of leaf sheaths of 418 maize inbred lines based on 87 leaf sheath-related phenotypic traits. In order to further analyze the mechanism of leaf sheath phenotype formation, 25 key traits (2 biomass-related, 19 morphology-related and 4 color-related traits) with heritability greater than 0.3 were analyzed by genome-wide association studies (GWAS). And 1816 candidate genes of 17 whole plant leaf sheath traits and 1,297 candidate genes of 8 sixth leaf sheath traits were obtained, respectively. Among them, 46 genes with clear functional descriptions were annotated by single nucleotide polymorphism (SNPs) that both Top1 and multi-method validated. Functional enrichment analysis results showed that candidate genes of leaf sheath traits were enriched into multiple pathways related to cellular component assembly and organization, cell proliferation and epidermal cell differentiation, and response to hunger, nutrition and extracellular stimulation. The results presented here are helpful to further understand phenotypic traits of maize leaf sheath and provide a reference for revealing the genetic mechanism of maize leaf sheath phenotype formation.

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Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.)

Cited by 13 publications

References 25 publications

Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method

Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method

Genomic Regions Associated With Salinity Stress Tolerance in Tropical Maize (Zea Mays L.)

Dissecting the Genetic Structure of Maize Leaf Sheaths at Seedling Stage by Image-Based High-Throughput Phenotypic Acquisition and Characterization

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