Genome-wide association study (GWAS) of seed germination-related traits in rice and identification of candidate genes

Panhabadi, Rahele; Ahmadikhah, Asadollah; Farokhi, Naser; Bagheri, Nadali

doi:10.21203/rs.3.rs-312154/v1

Cited by 2 publications

(2 citation statements)

References 128 publications

(146 reference statements)

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“…Gametic disequilibrium between all pairs of microsatellite loci was tested using POPGENE (Version: 1.32; Panahabadi et al, 2021Panahabadi et al, , 2022Yeh Francis et al, 1999). Null alleles and deviations from Hardy-Weinberg equilibrium for each locus were estimated using Genepop (Version 4.2.1; Panhabadi et al, 2022;Rousset, 2008). Unbiased gene diversity per locus and inbreeding coefficient (F IS ) were estimated using FSTAT (Version 1.2; Goudet, 1995;v.4.2), with the Bonferroni correction provided by FSTAT to infer significant values.…”

Section: Population Genetic Analysismentioning

confidence: 99%

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

Asadi Aghbolaghi,

Keyghobadi,

Azarakhsh

et al. 2023

Ecology and Evolution

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For the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.

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Section: Population Genetic Analysismentioning

confidence: 99%

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

Asadi Aghbolaghi,

Keyghobadi,

Azarakhsh

et al. 2023

Ecology and Evolution

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“…There are no reports of GWAS on GABA content in rice; however, GWAS has been used to identify genetic variants associated with numerous phenotypes, including those occurring during germination and seedling growth. Panhabadi et al (2022) reported that the results of GWAS identified several plausible candidate genes for features related to germination and seedling development, which will significantly advance our understanding of the genetic complexity underlying the relevant phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Gamma-aminobutyric acid contents and glutamate decarboxylase activity in local Thai rice and transgenic rice overexpressing oscam1-1 gene

Kanchitanurak

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In rice grain, many considerable nutrients are shown to have potential functional food benefits. GABA is a metabolic�product that is primarily produced by the decarboxylation of L-glutamic acid (L-Glu), catalyzed by glutamate decarboxylase (GAD), which is a cytosolic enzyme regulated by Ca2+-calmodulin (CaM) complex. The accumulation of GABA is related to the activity of GAD and substrate concentration of L-Glu. In this study, analysis of GABA contents in local Thai rice (Oryza sativa L.) during 0-72 h of germination revealed that GABA concentrations rapidly increased and the pattern of increment varied among different rice varieties. Genome-wide association mapping using 2,009,083 SNPs from a population of 100 varieties based on the GABA concentrations 48 hours after germination was carried out. As a result, 23 SNPs associated to five genes were identified. LOC Os02g40320, LOC Os02g40330, and LOC Os11g35580 were three genes having significant SNPs in their coding regions. The additional genes with upstream significant SNPs were LOC_Os01g18390�and LOC_Os04g13480. The protein encoded by LOC_Os02g40320 was related to numerous other proteins by STRING analysis, including nitrate reductase 1 (NIA1) and sucrose synthase 6. (SUS6). The response regulator receiver domain protein, which is encoded by LOC_Os4g13480 and functions in the His-to-Asp phosphorelay signal transduction pathway, was discovered to interact with a number of proteins in the two-component system responding to cytokinin, which has previously been shown to have a functional relationship with GABA. To investigate the role of calmodulin in GABA accumulation, GABA contents in the three transgenic Khoa Dawk Mali 105' (KDML105) rice overexpressing OsCaM1-1 gene (L1, L2, and L7) were examined compared with the wild-type KDML105' (WT), which are differing in salt tolerance. Under normal condition, GABA contents in the transgenic rice overexpressing OsCam1-1 calmodulin gene increased in the first 24 hr of germination while that of WT did not. Under salt stress (100 mM NaCl), their levels slightly increased and were not different among the rice lines. After 4 days with visible sprouting under both normal and salt stress conditions, GABA contents in all rice lines rapidly increased. GABA contents under salt stress condition continued to increase and reached higher levels at day 6 and 8 in all transgenic overexpressing lines when compared with that of WT. After 10 and 12 days, GABA levels under normal condition then rapidly increased whereas those under salt stress when the seedlings were severely affected significantly decreased. In addition, GAD activity in all transgenic rice lines and WT appeared to increase in the first week of germination and those of the transgenic rice were higher than WT at day 12 after germination. Together these results indicated that higher GABA content in the transgenic rice overexpressing OsCam1-1 gene may result from the induced GAD activity, which in turn confers the salt tolerance ability to the transgenic rice.

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Genome-wide association study (GWAS) of seed germination-related traits in rice and identification of candidate genes

Cited by 2 publications

References 128 publications

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

Gamma-aminobutyric acid contents and glutamate decarboxylase activity in local Thai rice and transgenic rice overexpressing oscam1-1 gene

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