Chao, Y.-T. | bioRxiv Science

bioRxiv2022

Phosphate transporter PHT1;1 as a key determinant of phosphorus acquisition in Arabidopsis natural accessions

To understand the genetic basis in governing phosphorus (P) acquisition, we performed genome-wide association studies (GWAS) on a diversity panel of Arabidopsis thaliana by two primary determinants of P acquisition, phosphate (Pi)-uptake activity and PHOSPHATE TRANSPORTER 1 (PHT1) protein abundance. Association mapping revealed a shared significant peak on chromosome 5 (Chr5) where the PHT1;1/2/3 genes reside, suggesting a strong correlation between the regulation of Pi-uptake activity and PHT1 protein abundance. Genes encoding transcription factors, kinases, and a metalloprotease associated with both traits were also identified. Conditional GWAS followed by statistical analysis of genotype-dependent expression of PHT1;1 and transcription activity assays revealed an epistatic interaction between PHT1;1 and MYB DOMAIN PROTEIN 52 (MYB52) on Chr1. Analyses of F1 hybrids generated by crossing two subgroups of natural accessions carrying specific SNPs associated with PHT1;1 and MYB52 further revealed the strong effects of potential variants on PHT1;1 expression and Pi uptake activity. Notably, the soil P contents in A. thaliana habitats were found to coincide with PHT1;1 haplotype, underscoring how fine-tuning of the activity of P acquisition by natural variants allows plants to adapt to their environments. This study sheds light on the complex regulation of P acquisition and offers a framework to systematically assess the effectiveness of GWAS approaches in the study of quantitative traits. One sentence summaryStepwise GWAS analyses reveal insights into the genetic basis in regulating phosphorus acquisition and associations between the phosphate transporter PHT1;1 haplotype and Arabidopsis habitats.

plant biology↗

bioRxiv2021

Comparative genomics of three Colletotrichum scovillei strains and genetic analysis revealed genes involved in fungal growth and virulence on chili pepper

Colletotrichum scovillei is a virulent pathogen and the dominant species causing anthracnose of chili pepper in many Asian countries. Three strains of this pathogen, Coll-524, Coll-153 and Coll-365, show varied virulence on chili pepper fruit. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, in this study, comparative genomic analysis and gene transformation to verify gene function were applied. The genomes of the three strains were sequenced and Coll-524 had 1.3% and 1.5% more genes than Coll-153 and Coll-365, respectively. Compared to Coll-524 and Coll-153, Coll-365 had numerous gene losses including 33 effector genes that are distributed in different scaffolds and a cluster of 14 genes in a 34-kb genomic fragment. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. Gene 15019 encoding a protein related to phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of 15019 with one transcription factor gene 15022 and one C6 zinc finger domain-containing protein gene 15029 was found to enhance the pathogenicity of Coll-365. Introduction of gene 15215, which encodes a LysM domain-containing protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the higher virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365. Author SummaryColletotrichum scovillei is a highly virulent and dominant pathogen causing anthracnose of chili that leads to significant economic loss in chili production in many Asia countries. In this study we focus on finding the gene differences of three C. scovillei strains with different pathogenicity in chili pepper infection and verifying the function of some genes in the lowest virulence strain. We sequenced them and did gene annotation and genome comparison. We setup a simple mathematical method to identify gene variations between strong and weak virulence strains. Our results show that the lowest virulence strain has less pathogenicity-related genes. We also found that the absence of 14 genes in a compact genomic fragment was part of the reason of growth and virulence defect of the lowest virulence strain. We identified four genes that play roles on fungal growth and/or virulence on chili pepper. We also found a group of effector genes that specifically appear in species collected form infected chili in C. acutatum species complex. Our research provides detailed information for why the three strains have different virulence on chili pepper.

genomics↗