Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

Candidate Genes and Favorable Haplotypes Associated with Iron Toxicity Tolerance in Rice

Iron (Fe) toxicity is a major issue adversely affecting rice production worldwide. Unfortunately, the physiological and genetic mechanisms underlying Fe toxicity tolerance in rice remain relatively unknown. In this study, we conducted a genome-wide association study using a diverse panel consisting of 551 rice accessions to identify genetic mechanisms and candidate genes associated with Fe toxicity tolerance. Of the 29 quantitative trait loci (QTL) for Fe toxicity tolerance detected on chromosomes 1, 2, 5, and 12, five (qSH_Fe5, qSFW_Fe2.3, qRRL5.1, qRSFW1.1, and qRSFW12) were selected to identify candidate genes according to haplotype and bioinformatics analyses. The following five genes were revealed as promising candidates: LOC_Os05g40160, LOC_Os05g40180, LOC_Os12g36890, LOC_Os12g36900, and LOC_Os12g36940. The physiological characteristics of rice accessions with contrasting Fe toxicity tolerance reflected the importance of reactive oxygen species-scavenging antioxidant enzymes and Fe homeostasis for mitigating the negative effects of Fe toxicity on rice. Our findings have clarified the genetic and physiological mechanisms underlying Fe toxicity tolerance in rice. Furthermore, we identified valuable genetic resources for future functional analyses and the development of Fe toxicity-tolerant rice varieties via marker-assisted selection.

Field Evaluation of Rice Lines Derived from Suakoko 8 X Bao Thai for Iron Tolerance in the South Saharan African Farming System

Rice is a major grain crop in numerous countries. In lowland areas, high iron levels in the soil severely hinder its cultivation. The current study explored high-yielding and Fe-toxicity-tolerant irrigated lowland rice (340 lines) among a population derived from a cross between Suakoko 8 and Bao Thai in Edozighi and Ibadan, Nigeria. In contrast to Ibadan, the soils in Edozighi contain a significant amount of iron. For the stated purpose, we carried out a two-year experiment using an alpha lattice design. The data showed significant differences between genotypes for the days to heading, plant height, number of tillers per plant, number of panicles per plant, panicle length, and grain yield. The results revealed that multiple characteristics had both direct and indirect effects on cultivated rice yields. There was a direct and positive influence on the number of days in the 50% heading period (0.31), a direct and negative effect on plant height (-0.94), a direct and positive effect on tiller and panicle numbers, and a direct but negative effect on panicle length (-0.56). The leaf bronzing score was adversely correlated with yield, panicle length, and plant height, while it was positively correlated with the number of panicles, tillers, and days to heading. The findings showed significant changes in yield and yield characteristics between genotypes. Grain yields ranged from 283 to 11,700 kg/ha in the absence of iron in the soil, contrary to 0 to 8230 kg/ha in soil with iron toxicity, with losses estimated between 6 and 94%, demonstrating the resulting disaster. In contrast to the elite parents and varieties used in this study, the ten top genotypes exhibited smaller losses in yield. The authors strongly recommend using these lines for further studies as donors or releasing them in farmer fields in Africa.

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)

Rice is the staple food for more than half of the world's population. Iron toxicity limits rice production in several regions of the world. Breeding Fe-tolerant rice varieties is an excellent approach to address the problem of Fe toxicity. Rice responds differently to Fe toxicity at different stages. Most QTLs associated with Fe toxicity have been identified at the seedling stage, and there are very few studies on Fe toxicity across different stages. In this study, we investigated agro-morphological and physiological traits in response to Fe toxicity in a rice diversity panel at seedling, vegetative, and reproductive stages and applied GWAS to identify QTLs/genes associated with these traits. Among agro-morphological and physiological parameters, leaf bronzing score (LBS) is a key parameter for determining Fe toxicity response at all stages, and SDW could be a promising parameter at the seedling stage. A total of 29 QTLs were identified on ten chromosomes. Among them, three colocalized QTLs were identified on chromosome 5, 6, and 11. Several QTLs identified in this study overlapped with previously identified QTLs from bi-parental QTL mapping and association mapping. Two genes previously reported to be associated with iron homeostasis were identified, i.e., LOC_Os01g72370 (OsIRO2, OsbHLH056) and LOC_Os04g38570 (OsABCB14). In addition, based on gene-based haplotype analysis, LOC_Os05g16670 was identified as a candidate gene for the colocalized QTL on chromosome 5 and LOC_Os11g18320 was identified as a candidate gene for the colocalized QTL on chromosome 11. The QTLs and candidate genes identified in this study could be useful for rice breeding programs for Fe toxicity tolerance.