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

Abstract

Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome‐wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome‐wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP‐glucose‐1‐phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor‐like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.

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

“…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.…”

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

“…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).…”

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

“…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 ).…”