Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

Abstract

Background Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109. Results Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7–51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region. Conclusion Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.

QTL Validation and Development of SNP-based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

“…Second is that these QTL might be background speci c which further highlights the importance of this QTL validation exercise. Lastly, in terms of qRCA2.1 and qRCA2.2, the markers targeting them may have not shown effect since these QTL were only shown to be signi cant in IWS conditions (Vinarao et al 2021). Further testing of the designed markers in IWS conditions should be carried out to de nitively check the association of these markers with RCA.…”

“…Of these, six were either released varieties or donors of high importance to the Australian breeding program -IRAT109, Sherpa, Reiziq, Langi, RL11, and Norin PL8. The other 54 genotypes were recombinant inbred lines (RILs) derived from Sherpa/IRAT109 and were previously identi ed to have varying combinations of QTL for RCA (Vinarao et al 2021).…”

“…Three experiments were carried out to evaluate the segregating populations developed above, along with the six varieties/checks following the clear pot method described by Vinarao et al (2021), with some modi cations, at the University of Queensland (UQ) St Lucia (27.4975° S, 153.0137° E) campus. Brie y, single seeds of F 2 s and check genotypes were direct seeded in 4L clear pots (ANOVApot®, 200 mm diameter, 190 mm height, http://www.anovapot.com/php/anovapot.php) lled with pine bark potting media (70% composted pine bark 0-5 mm, 30% coco peat, pH 6.35, EC = 650 ppm, nitrate = 0, ammonia < 6 ppm and phosphorus = 50 ppm) with 3g/L Osmocote Exact 3-4M (19-9-10 + 2MgO + TE, ICL Specialty Fertilizers), 2g/L Osmocote Exact 5-6M (15-9-12 + 2MgO + TE) and 0.82g/L Suscon Maxi Green (Nufarm, Australia).…”

“…IRAT109, an upland tropical japonica (tropjap) genotype, was also utilised to map QTL for RDR in transplanted systems, identifying qRDR-2 as a genomic region located in chromosome 2 (Lou et al 2015). Recently, novel, stable, consistently identi ed across environments and environment-speci c genomic regions conferring narrow RCA were identi ed in AP systems (Vinarao et al 2021). qRCA4 was found to be a major and stable QTL identi ed across all environments tested, and qRCA1.1 was a novel QTL which was also expressed in all environments.…”

QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

“…IRAT109, an upland tropical japonica (tropjap) genotype, was also utilised to map QTL for RDR in transplanted systems, identifying qRDR-2 as a genomic region located in chromosome 2 [ 11 ]. Recently, novel, stable, consistently identified across environments and environment-specific genomic regions conferring narrow RCA were identified in AP systems [ 12 ]. qRCA4 was found to be a major and stable QTL identified across all environments tested, and qRCA1.1 was a novel QTL which was also expressed in all environments.…”