Genome-Wide Association Study of Early Vigour-Related Traits for a Rice (Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions.

Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.

Low canopy temperature and high stomatal conductance contribute to high grain yield of contrasting japonica rice under aerobic conditions.

Water limitation is a major concern in rice production. It has been suggested that with adapted genotypes, aerobic rice production offers the maintenance of grain yield while saving water. However, there has been limited exploration of japonica germplasm adapted for high-yield aerobic environments. Therefore, three aerobic field experiments with different levels of relatively high-water availability were conducted across two seasons to explore genetic variation in grain yield and physiological traits that contributed to high yield. In the first season, a japonica rice diversity set was explored under well-watered (WW20) conditions. While in the second season, a well-watered (WW21) experiment and an intermittent water deficit (IWD21) experiment were conducted to examine the performance of a subset of 38 genotypes selected for low (mean of -6.01°C) and high (mean of -8.22°C) canopy temperature depression (CTD). In WW20, CTD explained 19% of the variation in grain yield which was similar to the variation explained by plant height, lodging, and leaf death response to heat. In WW21, a relatively high average grain yield (9.09 t ha-1) was achieved, while a 31% reduction was achieved in IWD21. Compared with the low CTD group, the high CTD group had 21% and 28% higher stomatal conductance, 32% and 66% higher photosynthetic rate, and 17% and 29% higher grain yield in the WW21 and IWD21, respectively. This work demonstrated the advantage of higher stomatal conductance and cooler canopy temperature which resulted in higher photosynthetic rate and higher grain yield. Two promising genotypes with high grain yield, cooler canopy temperature, and high stomatal conductance were identified as donor genotypes for use by the rice breeding program when aerobic rice production is a target. Field screening for cooler canopies within a breeding program with high-throughput phenotyping tools would be of value for genotype selection for aerobic adaption.

Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice (Oryza sativa L.) in Australian breeding material.

Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109.

Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.

Effects of variety, early harvest, and germination on pasting properties and cooked grain texture of brown rice.

Brown rice is superior to white rice in nutritional value and in the prevention of chronic diseases. However, it is not the preference of consumers and the relative consumption of brown rice is limited due to a number of factors including chewiness and perceived hard texture after cooking. While both early harvested brown rice and germinated brown rice have been shown to contain superior nutritional components, there is limited knowledge on textural properties of these types of brown rice relative to standard brown rice, and how varieties may affect such properties. Thus, the present study examined the effect of variety, early harvest, and germination on those properties of eight rice varieties with contrasting amylose content and known texture in terms of milled rice. Early harvest and germination decreased pasting viscosities and cooked grain hardness. However, their effect on the characteristics of flour and whole grains differed, in which germination had a greater effect on pasting properties, while early harvest on the texture of cooked grains. The softer texture of brown rice, about 32% lower, could be achieved by germination and 46% by harvesting early. There was a good relationship between pasting characteristics, particularly setback and hardness among different varieties in brown rice, germinated brown rice, and also in early harvest brown rice. This is the first time the comparison of texture between the three brown rice types has been reported. The results also provide new options for the selection of desired characteristics for food processing and brown rice consumption.

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.

Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4's effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.

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

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.