Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Yuan, Jing; Wang, Xueqiang; Zhao, Yan; Khan, Najeeb Ullah; Zhao, Zhiqiang; Zhang, Yanhong; Wen, Xiaorong; Tang, Fusen; Wang, Fengbin; Li, Zichao

doi:10.1038/s41598-020-66604-7

Cited by 82 publications

(60 citation statements)

References 39 publications

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“…Also, the LD block could show the LD level between each SNP, as well the multiple SNPs make a haplotype block by strong LD level, which is contributed to identified novel haplotype and functional genes. In Yuan's study, they identified multiple strong LD regions in candidate regions using the diverse model and diverse subspecies [66]. Two candidate genes, OsSTL1 and OsSTL2, were identified from strong LD regions in GWAS results.…”

Section: Ld Haplotype and Functional Snp Analysismentioning

confidence: 99%

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Zhang

San

Jang

et al. 2020

Genes

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Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement.

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Section: Ld Haplotype and Functional Snp Analysismentioning

confidence: 99%

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Zhang

San

Jang

et al. 2020

Genes

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“…Lekklar et al conducted a GWAS for salt tolerance during rice reproduction, and more than 73% of the identified loci overlapped with the previously reported salt QTLs [92]. Yuan et al performed a GWAS using 664 cultivated rice accessions from the 3000 Rice genomes, and twenty-one salt-tolerant QTLs and two candidate genes were identified [93]. These studies indicate that GWAS is a powerful strategy for mapping QTLs of salt tolerance in rice.…”

Section: Biotechnology Promises To Accelerate Breeding Of Salt-toleramentioning

confidence: 95%

Advances and Challenges in the Breeding of Salt-Tolerant Rice

Qin

Huang

2020

IJMS

127

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Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

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“…In contrast, salt tolerance in varieties like IR29, Fatmawati, Pokkali, Cheriviroppu, FL478, IR651, CSR27, FL30, Fontan, SR86, IR9884-54-3 results from ion exclusion, osmotic and tissue tolerance with multiple genes involved in the process, which confers agronomic stability of this trait (Qin et al, 2020;Reddy et al, 2017;Takagi et al, 2015;. The orchestrated stress system can be targeted for achieving salt tolerance by mutating genes encoding key transcription factors, specifically OsRR22 (Os06g0183100), STL1 (Os04g0110600), and the zinc finger transcription factor encoded by DST (Os03g0786400) (Cui et al, 2015;Santosh Kumar et al, 2020;Yuan et al, 2020;. Other transcription factors are critical in stress adaptation, which results in stress sensitivity when inactivated.…”

Section: Stress Tolerancementioning

confidence: 99%

Rice breeding in the new era: comparison of useful agronomic traits

Hernández-Soto

Echeverría-Beirute

Abdelnour-Esquivel

et al. 2021

Preprint

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Understanding agronomic traits at a genetic level enables the leveraging of this knowledge to produce crops that are more productive and resilient, have better quality and are adjusted for consumer preferences. In the last decade, rice has become a model to validate the function of specific genes, resulting in valuable but scattered information. Here, we aimed to identify particular genes in rice related to traits that can be targeted by different mutation techniques in the breeding of crops. We selected gain of function, misfunction, and specific mutations associated with phenotypes of agronomic interest. The review includes specific trait-related genes involved in domestication, stress, herbicide tolerance, pathogen resistance, grain number/quality/weight, plant structure, nitrogen use, and others. The information presented can be used for rice, other cereals, and orphan crops to achieve a superior and sustainable production in challenging farming conditions.

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Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Cited by 82 publications

References 39 publications

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Advances and Challenges in the Breeding of Salt-Tolerant Rice

Rice breeding in the new era: comparison of useful agronomic traits

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