Relationships Among Arsenic-Related Traits, Including Rice Grain Arsenic Concentration and Straighthead Resistance, as Revealed by Genome-Wide Association

Abstract

There is global concern that rice grains and foods can contain harmful amounts of arsenic (As), motivating breeders to produce cultivars that restrict As accumulation in grains to protect human health. Arsenic is also toxic to plants, with straighthead disorder (StHD), causing panicle sterility, being observed in rice. The genetic variation in StHD resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, or detoxification/sequestration. Because these mechanisms could also underlie the wide (3- to 100-fold) differences in grain As concentration (grain-As) observed among diverse rice genotypes, it was hypothesized that some genes reduce both grain-As content and StHD susceptibility and may be detectable as co-located StDH and As quantitative trait loci (QTL). We used a machine-learning Bayesian network approach plus high-resolution genome-wide association study (GWAS) to identify QTL for grain-As and StHD resistance within the USDA Rice Minicore Collection (RMC). Arsenic enters roots through phosphorus (P) and silica (Si) transporters, As detoxification involves sulfur (S), and cell signaling to activate stress tolerance mechanisms is impacted by Si, calcium (Ca), and copper (Cu). Therefore, concentrations of Si, P, S, Ca, and Cu were included in this study to elucidate physiological mechanisms underlying grain-As and StHD QTL. Multiple QTL (from 9 to 33) were identified for each of the investigated As-associated traits. Although the QTL for StHD, Si, and grain-As did not overlap as heavily as our hypothesis predicted (4/33 StHD and 4/15 As QTL co-located), they do provide useful guidance to future research. Furthermore, these are the first StHD and Si QTL to be identified using high-density mapping, resulting in their being mapped to shorter, more precise genomic regions than previously reported QTL. The candidate genes identified provide guidance for future research, such as gene editing or mutation studies to further investigate the role of antioxidants and ROS scavenging to StHD resistance, as indicated by candidate genes around the commonly reported qStHD8-2 QTL. Other genes indicated for future study for improving grain-As and StHD include several multidrug and toxic compound extrusion (MATE) genes, F-box genes, and NIPs not documented to date to transport As.

Genome wide association studies and candidate gene mining for understanding genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

“…A total of 4 out of the 14 MTAs, on chromosomes 3, 4 and 5, namely qSSi3.2, qSSi4.2, qSSi5.1, qSSi5.2, respectively, were simultaneously found to be signi cant in 5 out of the 6 ML-GWAS models. Six MTAs identi ed in our study have been found to be co-localized with QTLs from other mapping studies for silica content(Dai et al 2005;Wu et al 2006;Pinson et al 2022), thus providing analytical corroboration to our current study (Table2). Trait Associations (MTAs)/Single Nucleotide Polymorphisms (SNPs) associated with straw silica content in O. nivara accessions, along with previously reported QTLs for Silica, Arsenic (As) and Germanium (Ge)…”

“…Further, our study found three QTLs to be co-localizing with previously reported QTLs for As content. qSSi4.2 was found to be co-localized with qAs4, while qSSi11.1 and qSSi11.2 co-localized with qAs11-2 identi ed by Pinson et al (2022). In addition, qSSi11.1 was found to be co-localized with qGAs18 and qGAs22 identi ed by Liu et al…”

“…The spatial and temporal nuances and synchronies in the expression of these genes is responsible for uptake and accumulation of silicon from the soil. A few QTL mapping studies have also been conducted (Dai et al 2005;Wu et al 2006;Bryant et al 2011;Pinson et al 2022) to identify genomic regions associated with silica content in rice. All these studies have not encompassed the validated transporter genes Lsi1, Lsi2 and Lsi6, except Pinson et al (2022) who have reported association of Lsi1, 2 MB away from the peak SNP in one of the QTLs.…”

“…A few QTL mapping studies have also been conducted (Dai et al 2005;Wu et al 2006;Bryant et al 2011;Pinson et al 2022) to identify genomic regions associated with silica content in rice. All these studies have not encompassed the validated transporter genes Lsi1, Lsi2 and Lsi6, except Pinson et al (2022) who have reported association of Lsi1, 2 MB away from the peak SNP in one of the QTLs. This also indicates the presence of a wide natural variation for the genes involved in silicon transport and regulation present in rice germplasm.…”

“…Also, qSSi3.2 bears another interesting gene which encodes a BTB-domain containing gene, Os03g0686050. OsTAZ24 gene, which encodes a BTB-domain protein was found to be responsible for promoting plant resistance against various heavy metals (Shalmani et al 2021;Pinson et al 2022). Hence, it has been considered as a candidate gene in relation to response to As or Si.…”