Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping

Wang, Xiaoliang; Li, Jinquan; Sun, Jiwei; Gu, Shuang; Wang, Jingbo; Su, Chang; Li, Yueting; Ma, Dianrong; Zhao, Ming‐Hui; Chen, Wenfu

doi:10.3389/fpls.2022.847863

Cited by 4 publications

(3 citation statements)

References 74 publications

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“…Many genes that affect agronomic traits have been discovered in rice core collections [226][227][228][229]; these include Rc, waxy, and GS3 genes, which were found to be associated with grain color, amylose content, and grain length, respectively [230]. In addition, 65 QTLs and four candidate genes (LOC_Os06g47720, LOC_Os06g47820, LOC_Os06g47850, LOC_Os06g47970) were identified for salt tolerance [212]. Soybean core collections have also been genotyped using SNP markers to study linkage disequilibrium and associations with agronomic, yield and yield components; 12 genes, 19 SNPs, and five haplotypes were identified and linked to these traits [216,217].…”

Section: Gene Discovery and Allele Miningmentioning

confidence: 99%

Developments on Core Collections of Plant Genetic Resources: Do We Know Enough?

Fan

Wei

et al. 2023

Forests

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The core collection is a small subset that minimizes genetic redundancy while preserving the maximum genetic diversity of the entire population. Research on the core collection is crucial for the efficient management and utilization of germplasm resources. In this paper, the concept of the core collection and the research progress of its construction have briefly been summarized. Subsequently, some perspectives have been proposed in this research field for the near future. Four novel opinions have been presented, (1) the effective integration of multiple data types and accurate phenotyping methods need to be focused on; (2) the sampling strategy and bioinformatics software should be given attention; (3) the core collection of afforestation tree and bamboo species, with a wide natural distribution range and a large planting area, need to be carried out as soon as possible; (4) we should place a high priority on the study of genes discoveries and utilize these with a rapid, precise and high-throughput pattern based on re-sequencing technology. This paper provides a theoretical and technological reference for further study and the application of the plant core collection.

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Section: Gene Discovery and Allele Miningmentioning

confidence: 99%

Developments on Core Collections of Plant Genetic Resources: Do We Know Enough?

Fan

Wei

et al. 2023

Forests

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“…This core set can provide a starting point for enhancing genetic gains and employing phenomic and genomic tools in less time ( Tripathi et al., 2022 ). An economical, time-effective, and labor-saving approach for studying physiological or molecular response mechanisms using phenotypic traits of the core collection or trait-marker associations has been widely used ( Guo et al., 2022 ; Wang et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Salt tolerance evaluation and mini-core collection development in Miscanthus sacchariflorus and M. lutarioriparius

Tang,

Li,

Zerpa-Catanho

et al. 2024

Front. Plant Sci.

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Marginal lands, such as those with saline soils, have potential as alternative resources for cultivating dedicated biomass crops used in the production of renewable energy and chemicals. Optimum utilization of marginal lands can not only alleviate the competition for arable land use with primary food crops, but also contribute to bioenergy products and soil improvement. Miscanthus sacchariflorus and M. lutarioriparius are prominent perennial plants suitable for sustainable bioenergy production in saline soils. However, their responses to salt stress remain largely unexplored. In this study, we utilized 318 genotypes of M. sacchariflorus and M. lutarioriparius to assess their salt tolerance levels under 150 mM NaCl using 14 traits, and subsequently established a mini-core elite collection for salt tolerance. Our results revealed substantial variation in salt tolerance among the evaluated genotypes. Salt-tolerant genotypes exhibited significantly lower Na+ content, and K+ content was positively correlated with Na+ content. Interestingly, a few genotypes with higher Na+ levels in shoots showed improved shoot growth characteristics. This observation suggests that M. sacchariflorus and M. lutarioriparius adapt to salt stress by regulating ion homeostasis, primarily through enhanced K+ uptake, shoot Na+ exclusion, and Na+ sequestration in shoot vacuoles. To evaluate salt tolerance comprehensively, we developed an assessment value (D value) based on the membership function values of the 14 traits. We identified three highly salt-tolerant, 50 salt-tolerant, 127 moderately salt-tolerant, 117 salt-sensitive, and 21 highly salt-sensitive genotypes at the seedling stage by employing the D value. A mathematical evaluation model for salt tolerance was established for M. sacchariflorus and M. lutarioriparius at the seedling stage. Notably, the mini-core collection containing 64 genotypes developed using the Core Hunter algorithm effectively represented the overall variability of the entire collection. This mini-core collection serves as a valuable gene pool for future in-depth investigations of salt tolerance mechanisms in Miscanthus.

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“…However, the resolution of these studies is low, time-consuming and costly due to the need to create large-scale segregation populations and high-density genetic maps. With the development of next-generation sequencing (NGS) technology, the genome-wide association study (GWAS) has become an effective approach to map QTLs related to complex traits of crops and has been applied in various crops, such as rice, soybean, and B. napus [14][15][16]. Some QTLs and candidate genes associated with salt-tolerance-related traits at the germination and seedling stages [17][18][19][20][21][22][23] and yield-related traits [24][25][26] have gradually been identified through GWAS in B. napus.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L.

Zhang

et al. 2022

IJMS

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Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.

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Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping

Cited by 4 publications

References 74 publications

Developments on Core Collections of Plant Genetic Resources: Do We Know Enough?

Developments on Core Collections of Plant Genetic Resources: Do We Know Enough?

Salt tolerance evaluation and mini-core collection development in Miscanthus sacchariflorus and M. lutarioriparius

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L.

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