Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

Guo, Qi; Meng, Shu; Zhang, Xianggui; Xu, Zhenzhen; Guo, Wangzhen; Shen, Xinlian

doi:10.1186/s12864-020-07321-3

Cited by 36 publications

(22 citation statements)

References 55 publications

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“…Salt tolerance is a complex quantitative trait, which is controlled by multiple genes and involves a variety of physiological and biochemical metabolic pathways in cotton [ 6 ]. Quantitative trait locus (QTL) mapping of salt-related traits has become an effective approach.…”

Section: Introductionmentioning

confidence: 99%

“…Many QTLs were mapped on A05, A08, A09, A11, D01, D08, D09, D10 and D12 for salt tolerance in tetraploid cotton. Xu et al (2021) found a locus on chromosome A13 and D08 associated with relative plant height (RPH), and loci on A07 for relative shoot fresh matter weight (RSFW); A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments and the increase in GH_A13G0171-silenced plants’ salt tolerance under salt stress indicated its negative function in regulating the salt stress response [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Zheng

Zhang

Gong

et al. 2021

Plants

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Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline–alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Zheng

Zhang

Gong

et al. 2021

Plants

View full text Add to dashboard Cite

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“…Growth parameters, such as SRW, SDW, RFW, and RDW, have been used to determine salt stress responses and tolerance in various species, such as cotton [31], maize [32,33], tomato [34], wheat [35], eggplant [36], and rice [9]. RWC and CMS have also been used to assess salt tolerance.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations

Kojonna

Suttiyut

Khunpolwattana

et al. 2022

IJMS

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Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice.

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“…GWAS was conducted to identify a study’s salt tolerance-related QTLs/genes in cotton cultivars. They performed a GBS of 217 cotton cultivars and identified 12 candidate salt-tolerant genes that can be used in the breeding program for cotton improvement [ 28 ].…”

Section: Advancements In Molecular Breeding Techniquesmentioning

confidence: 99%

Integrating speed breeding with artificial intelligence for developing climate-smart crops

Krishna

2022

Mol Biol Rep

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Introduction In climate change, breeding crop plants with improved productivity, sustainability, and adaptability has become a daunting challenge to ensure global food security for the ever-growing global population. Correspondingly, climate-smart crops are also the need to regulate biomass production, which is imperative for the maintenance of ecosystem services worldwide. Since conventional breeding technologies for crop improvement are limited, time-consuming, and involve laborious selection processes to foster new and improved crop varieties. An urgent need is to accelerate the plant breeding cycle using artificial intelligence (AI) to depict plant responses to environmental perturbations in real-time. Materials and methods The review is a collection of authorized information from various sources such as journals, books, book chapters, technical bulletins, conference papers, and verified online contents. Conclusions Speed breeding has emerged as an essential strategy for accelerating the breeding cycles of crop plants by growing them under artificial light and temperature conditions. Furthermore, speed breeding can also integrate marker-assisted selection and cutting-edged gene-editing tools for early selection and manipulation of essential crops with superior agronomic traits. Scientists have recently applied next-generation AI to delve deeper into the complex biological and molecular mechanisms that govern plant functions under environmental cues. In addition, AIs can integrate, assimilate, and analyze complex OMICS data sets, an essential prerequisite for successful speed breeding protocol implementation to breed crop plants with superior yield and adaptability.

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Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

Cited by 36 publications

References 55 publications

Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations

Integrating speed breeding with artificial intelligence for developing climate-smart crops

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