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

Genome-wide association studies unveils the genetic basis of cell wall composition and saccharification of cassava pulp

Cassava (Manihot esculenta Crantz) is a key crop for starch and biofuels production. This study focuses on the polysaccharide composition and saccharification efficiency in cassava pulp through genome-wide association studies (GWAS), targeting the improvement of root characteristics for industrial use. We analyzed 135 partially inbred lines population, performing monosaccharide composition and saccharification analyses to reveal substantial variability in storage root biomass. Among 33 traits examined, 128 significant SNPs were associated with 23 biomass traits, highlighting a complex genetic architecture. Saccharification potential varied from 39 to 95 nmol Glu mg-1 h-1, with high broad-sense heritability for saccharification and several monosaccharide traits, indicating a strong genetic control. Our findings revealed that cassava pulp comprises similar proportions of pectin, hemicellulose, and cellulose in all genotypes. Correlation analysis showed significant associations between cellulose content and saccharification, suggesting that enhancing these traits can improve bioconversion efficiency. Negative correlations with glucose and glucuronic acid in hemicellulose and pectin fractions imply these components may inhibit saccharification. We identified 118 candidate genes associated with 21 traits, with many involved in stress responses affecting cell wall composition. This study verified 12 key candidate genes through sequence and expression analysis, including MANES_07G081200, a YTH domain-containing protein associated with saccharification. Several stress-response genes, such as MANES_04G118600 and MANES_09G174600, were linked to monosaccharide traits, suggesting that adaptive stress pathways influence biomass characteristics. This study provides insights into the genetic determinants of cassava pulp's saccharification and polysaccharide composition, aiding breeding efforts to develop cassava varieties optimized for industrial applications.

Genome-wide association study identifies the genetic basis of key agronomic traits in 207 sugar beet accessions

Sugar beet (Beta vulgaris) has emerged as one of the two primary crops, alongside sugarcane, for global sugar production. Comprehensively understanding sucrose synthesis, transport, and accumulation in sugar beet holds great significance for enhancing sugar production. In this study, we collected a diverse set of 269 sugar beet accessions worldwide and measured 12 phenotypes, comprising biomass, soluble sugar content, and 10 taproot-related traits. We re-sequenced 207 accessions to explore genetic diversity and population structure. Then we employed a genome-wide association study (GWAS) and RNA-seq to identify single-nucleotide polymorphisms and genes associated with natural phenotypic variations. Our findings revealed a panel of genes potentially regulating biomass and sugar accumulation, notably the dual-role gene UDP-glucose 4-epimerase, which genetically balances sugar accumulation and cell wall synthesis. In summary, this study provides a foundation for molecular breeding in sugar beet.

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

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.

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

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.

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

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.