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.

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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

10.21203/rs.3.rs-636404/v1 ◽

2021 ◽

Author(s):

Ricky Vinarao ◽

Christopher Proud ◽

Peter Snell ◽

Shu Fukai ◽

Jaquie Mitchell

Keyword(s):

Molecular Markers ◽

Production Systems ◽

Genotypic Variation ◽

Cone Angle ◽

Subsequent Development ◽

Genomic Region ◽

Rice Production ◽

Future Research ◽

Breeding Programs ◽

Qtl Validation

Abstract BackgroundAerobic rice production (AP) is a potential solution to the imminent global water crisis as it consumes less water than traditional permanent water culture. Narrow root cone angle (RCA) and subsequent development of deeper rooting systems are considered AP adaptation traits by enabling water uptake at depth. Quantitative trait loci (QTL), such as qRCA4, contributing to RCA variation in AP systems have been previously identified. However, their usefulness depends on validation in a range of genetic backgrounds, development of associated molecular markers, and identification of possible donors in other subpopulations. Results Using three F2 bi-parental populations derived from IRAT109 crossed with three different genetic backgrounds, and genotypes with known qRCA composition, QTL validation were performed and molecular markers developed. qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation in the populations tested and the introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetive allele specific PCR (KASP) molecular markers have been developed associated with narrow RCA. Core molecular marker quality metrics have shown robustness and breeding program specific utility of up to 83%. qRCA4 was further fine mapped into a 720 kb region. Analysis of candidate genes identified those related with plant response to abiotic stress stimulus together with root development. Available public database search found 178 potential donors representing major rice subpopulations and may be used readily by breeding programs. ConclusionThis study validated qRCA4’s effect in multiple genetic backgrounds further strengthening its value in improvement of rice genotypes for AP adaptation. Furthermore, the development of novel KASP markers has ensured the opportunity for its seamless introgression across pertinent breeding programs. Future research in metabolomic and transcriptomic analysis of QTL positive genotypes should improve the understanding of the physiological mechanisms underpinning narrow RCA and development of deeper rooting. Finally, this work provides the tools and opportunity to accelerate the 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.

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

Rice ◽

10.1186/s12284-021-00471-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ricky Vinarao ◽

Christopher Proud ◽

Xiaolu Zhang ◽

Peter Snell ◽

Shu Fukai ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Oryza Sativa L ◽

Genotypic Variation ◽

Cone Angle ◽

Rice Production ◽

Aerobic Rice ◽

Deep Roots ◽

Stimulus Response ◽

Trait Loci

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.

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

10.21203/rs.3.rs-148668/v1 ◽

2021 ◽

Author(s):

Ricky Vinarao ◽

Christopher Proud ◽

Xiaolu Zhang ◽

Peter Snell ◽

Shu Fukai ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Oryza Sativa L ◽

Genotypic Variation ◽

Cone Angle ◽

Rice Production ◽

Aerobic Rice ◽

Deep Roots ◽

Stimulus Response ◽

Trait Loci

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. ConclusionStable 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.

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Studies on nitrogenase activity of diazotrophic isolates from different rice production systems

Journal of Applied and Natural Science ◽

10.31018/jans.v8i1.787 ◽

2016 ◽

Vol 8 (1) ◽

pp. 284-289

Author(s):

S. Kanimoli ◽

K. Kumar

Keyword(s):

Acetylene Reduction ◽

Tamil Nadu ◽

Production Systems ◽

Nitrogenase Activity ◽

Rice Production ◽

Lowland Rice ◽

Aerobic Rice ◽

Marked Variation ◽

Reduction Assay ◽

First Time

The present study was carried out to evaluate the nitrogen fixing ability of diazotrophs isolated from the rhizosphere soils of rice which were grown in three different rice growing systems. A total of hundred and ten isolates obtained were subjected to Acetylene Reduction Assay (ARA) and ninety eight isolates recorded significant amount of nitrogenase activity in a range of 185.73 to 3794.55 nmoles of ethylene mg of protein-1 h-1. The highest nitrogenase activity was recorded by Derxia (3794.55 nmoles of ethylene mg of protein-1 h-1) isolated from Trichy (lowland). Among the three different rice production systems, isolates obtained from lowland rice (Derxia â€“ 3794.5 nmoles of ethylene mg of protein-1 h-1) recorded higher nitrogenase activity followed by Aerobic (Pseudomonas - 2194.89 nmoles of ethylene mg of protein-1 h-1) and SRI (Azotobacter - 1971.85 nmoles of ethylene mg of protein-1 h-1) rice isolates. The results revealed marked variation in the ARA of the diazotrophic isolates obtained from lowland, SRI and Aerobic rice. The nitrogenase activity of diazotrophs from rice fields have been reported earlier but the nitrogenase activity of diazotrophs from three different rice production systems from various parts of Tamil Nadu is reported for the first time from India.

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Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties

Plants ◽

10.3390/plants9111531 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1531

Author(s):

Kyeong-Seong Cheon ◽

Young-Min Jeong ◽

Hyoja Oh ◽

Jun Oh ◽

Do-Yu Kang ◽

...

Keyword(s):

Agronomic Traits ◽

High Impact ◽

Japonica Rice ◽

Rice Varieties ◽

Breeding Programs ◽

Temperate Japonica ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr ◽

Kasp Markers

Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

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System of Crop Rotation: A Prospective Strategy Alleviating Grain Yield Penalty in Sustainable Aerobic Rice Production

International Journal of Plant Production ◽

10.1007/s42106-021-00163-3 ◽

2021 ◽

Author(s):

A. Ghosh ◽

O. N. Singh ◽

J. Berliner ◽

S. Pokhare

Keyword(s):

Grain Yield ◽

Crop Rotation ◽

Rice Production ◽

Aerobic Rice ◽

Yield Penalty

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Plant breeding in the semiarid region of Brazil: examples of success

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332012000500007 ◽

2012 ◽

Vol 12 (spe) ◽

pp. 57-66 ◽

Cited By ~ 1

Author(s):

Manoel Abílio de Queiroz ◽

Levi de Moura Barros ◽

Luiz Paulo de Carvalho ◽

Jonas de Araújo Candeia ◽

Edinardo Ferraz

Keyword(s):

Cotton Fiber ◽

Production Systems ◽

Rio Grande ◽

Semiarid Region ◽

Breeding Programs ◽

Caatinga Biome ◽

Colored Cotton ◽

Nut Production ◽

Production Area ◽

Naturally Colored Cotton

The Northeastern region of Brazil comprises the Caatinga biome (900,000 km²) part of which is a semiarid region with rainfed and irrigated production systems. Among the successful breeding programs are cashew and cotton. The first led to a substantial increase in nut production in Ceará, Rio Grande do Norte and Piauí and the second bred a naturally colored cotton fiber, now processed in small clothing industries in Paraiba, exporting to 11 countries. In the lower-middle São Francisco valley, the previously grown onion was replaced by improved varieties, on 90% of the production area, and by industrial tomato, introduced by research in 1972, which came to be used on more than 80% of the area at the time. The participation of the private sector and continuity of breeding programs were crucial for the success. More examples of success are expected with the establishment of postgraduate courses in Agricultural Sciences in the Semiarid region.

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