Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

Abstract

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers

“…The samples used in their study were obtained from 14 provinces across China, demonstrating a broad geographical distribution. Diverse environmental conditions and ecological system characteristics exist in different geographical regions, leading to genetic variations in species as they adapt to varying environmental conditions and respond to different selection pressures [ 81 , 82 ]. Adaptive differences may lead to different genetic variation within different geographic regions, thereby increasing overall genetic diversity.…”

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron

“…The paired-end sequencing with a read length of 150 base pairs was conducted according to the manufacturer's guidelines for whole genome sequencing, utilizing the Illumina HiSeq 2500 sequencer on the Illumina HiSeq 2500 platform (San Diego, CA, United States), achieving a 100-fold sequencing depth. After the completion of Illumina sequencing, the raw data undergo a series of data analysis operations, including quality control, statistical analysis, genome assessment, and de novo assembly (Akbar et al, 2021;Dang et al, 2022).…”

Analysis of genetic relationship and inbreeding coefficient of Hetian Qing donkey based on simplified genome sequencing

“…Genetic diversity analysis includes effective population content (Ne), which refers to the ideal population content with the same gene frequency variance or inbreeding coefficient increment (heterozygosity decay rate) as the actual population [13]. It is usually estimated based on the linkage disequilibrium (LD) of the population [14].…”