Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw

Panahabadi, Rahele; Ahmadikhah, Asadollah; McKee, Lauren S.; Ingvarsson, Pär K.; Farrokhi, Naser

doi:10.1002/tpg2.20174

Cited by 8 publications

(4 citation statements)

References 115 publications

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“…The studied plant panel consisted of 197 rice accessions collected from 70 countries (Supplemental Table S1). The grains from these accessions were previously analyzed in another GWAS project to understand the genetic control of starch and (1,3;1,4)‐β‐glucan content in grain (Panahabadi et al., 2021) and cellulose, lignin, and fermentable sugars in rice straw (Panahabadi et al., 2022). Our new analyses present major monosaccharides composition (including arabinose, xylose, mannose, galactose, fucose, and rhamnose) in whole grain of the same accessions.…”

Section: Resultsmentioning

confidence: 99%

Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study

2023

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The simplest form of carbohydrates are monosaccharides which are the building blocks for the synthesis of polymers or complex carbohydrates. Monosaccharide contents of 197 rice accessions were quantified by HPAEC‐PAD in rice (Oryza sativa L.) whole grain (RWG). A genome‐wide association study (GWAS) was carried out using 33,812 single nucleotide polymorphisms (SNPs) to identify corresponding genomic regions influencing neutral monosaccharides contents. In total, 49 GWAS signals contained in 17 genomic regions (quantitative trait loci [QTLs]) on seven chromosomes of rice were determined to be associated with monosaccharides contents of whole grain. The QTLs were found for fucose (1), mannose (1), xylose (2), arabinose (2), galactose (4), and rhamnose (7) contents, all of which are novel. Based on co‐location of annotated rice genes in the vicinity of GWAS signals, the constituents of the whole grain were associated with the following candidate genes: arabinose content with α‐N‐arabinofuranosidase, pectinesterase inhibitor, and glucosamine‐fructose‐6‐phosphate aminotransferase 1; xylose content with ZOS1‐10 (a C2H2 zinc finger transcription factor [TF]); mannose content with aldose 1‐epimerase‐like protein and a MYB family TF; galactose content with a GT8 family member (galacturonosyltransferase‐like 3), a GRAS family TF, and a GH16 family member (xyloglucan endotransglucosylase/hydrolase xyloglucan 23); fucose content with gibberellin 20 oxidase and a lysine‐rich arabinogalactan protein 19, and finally rhamnose content with myo‐inositol‐1‐phosphate synthase, UDP‐arabinopyranose mutase, and COBRA‐like protein precursor. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in the biosynthesis, regulation, and turnover of monosaccharides in RWG, aiming to enhance the nutritional value of rice grain and impact the related industries.

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Section: Resultsmentioning

confidence: 99%

Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study

2023

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“…PtrLAC12 is a kind of laccase from poplar; it is well known that laccase can participate in the synthesis and degradation of lignin in the xylem, and it is also directly related to the formation and modification of the cell wall (W. Bao et al., 1993; LaFayette et al., 1999; Y. Liu et al., 2020; Sharma et al., 2020). AtVLN2 belongs to the Villin family, members of this family are associated with SCW formation and thickening (Panahabadi et al., 2022). In studies of Arabidopsis , it was found that there was a significant reduction in the cell numbers in the cortex, inter‐fascicular fibers, xylem, and pith in vln2 vln3 double mutants, it means that AtVLN2 may involve in secondary xylem development (C. Bao et al., 2012).…”

Section: Discussionmentioning

confidence: 99%

Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar

Wang,

Wu,

Zhang

et al. 2024

The Plant Genome

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MicroRNAs (miRNAs) and DNA methylation are both vital regulators of gene expression. DNA methylation can affect the transcription of miRNAs, just like coding genes, through methylating the CpG islands in the gene regions of miRNAs. Although previous studies have shown that DNA methylation and miRNAs can each be involved in the process of wood formation, the relationship between the two has been relatively little studied in plant wood formation. Studies have shown that the second internode (IN2) (from top to bottom) of 3‐month‐old poplar trees can represent the primary stage of poplar stem development and IN8 can represent the secondary stage. There were also significant differences in DNA methylation patterns and miRNA expression patterns obtained from PS and SS. In this study, we first interactively analyzed methylation and miRNA sequencing data to identify 43 differentially expressed miRNAs regulated by differential methylation from the primary stage and secondary stage, which were found to be involved in multiple biological processes related to wood formation by enrichment analysis. In addition, six miRNA/target gene modules were finally identified as potentially involved in secondary xylem development of poplar stems through degradome sequencing and functional analysis. In conclusion, this study provides important reference information on the mechanism of interaction between different regulatory pathways of wood formation.

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“…Micro‐checker software was used to check scoring errors, stutter, or null alleles (Van Oosterhout et al, 2004 ). Gametic disequilibrium between all pairs of microsatellite loci was tested using POPGENE (Version: 1.32; Panahabadi et al, 2021 , 2022 ; Yeh 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 ).…”

Section: Methodsmentioning

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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Genome‐wide association study for lignocellulosic compounds and fermentable sugar in rice straw

Cited by 8 publications

References 115 publications

Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study

Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study

Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar

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

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