Developing green super rice varieties with high nutrient use efficiency by phenotypic selection under varied nutrient conditions

Jewel, Zilhas Ahmed; Ali, Jauhar; Pang, Yongzhen; Mahender, Anumalla; Acero, Bart; Hernandez, Jose E.; Xu, Jianlong; Li, Zhikang

doi:10.1016/j.cj.2019.01.002

Cited by 28 publications

(24 citation statements)

References 24 publications

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“…A population of 230 BC 1 F 6 backcross recombinant inbred lines (BRILs) derived from a cross between indica line WTR1 and japonica cultivar Hao-an-nong was produced using single seed descent at the International Rice Research Institute (IRRI), Los Baños, Philippines. For detailed information regarding the population development, see (Jewel et al 2019). As tolerance and accumulation was a non-target trait that was not considered during the development of the BRILs population which was used in this study.…”

Section: Methodsmentioning

confidence: 99%

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Murugaiyan

Ali

Mahender

et al. 2019

Rice

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Background Arsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice ( Oryza sativa L . ) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 ( indica) and Hao-an-nong (japonica ) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As. Results Arsenic toxicity leads to significantly negative plant responses, including reduced biomass, stunted plant growth, reduced leaf chlorophyll content, and increased shoot As concentration ranging from 9 to 20 mg kg − 1 . Marker-trait association was determined for seven As-related traits using 704 single nucleotide polymorphism (SNP) markers generated from a 6 K SNP-array. One QTL was mapped on chromosome 1 for relative chlorophyll content, two QTLs for As content in roots were mapped on chromosome 8, and six QTLs for As content in shoots were mapped on chromosomes 2, 5, 6, and 9. Using the whole-genome sequence of the parents, we narrowed down the number of candidate genes associated with the QTL intervals based on the existence of a non-synonymous mutation in genes between the parental lines. Also, by using publicly available gene expression profiles for As stress, we further narrowed down the number of candidate genes in the QTL intervals by comparing the expression profiles of genes under As stress and control conditions. Twenty-five genes showing transcription regulation were considered as candidate gene nominees for As toxicity-related traits. Conclusions Our study provides insight into the genetic basis of As tolerance and uptake in the early seedling stage of rice. Comparing our findings with the previously reported QTLs for As toxicity stress in rice, we identified some novel and co-localized QTLs associated with As stress. Also, the mapped QTLs harbor gene models of known function associated with stress responses, metal homeostasis, and transporter activity in rice. Overall, our findings will assist breeders with initial marker information to develop suitable varieties for As-contaminated ecosystems. Electronic supplementary material The online version of this article (10.1186/s12284-019-0321-y) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Murugaiyan

Ali

Mahender

et al. 2019

Rice

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“…The experiment was conducted at the International Rice Research Institute (IRRI), Los Baños, Philippines (14°1 1 N, 121°15 E) during 2015 using an early backcross mapping population of 230 BC 1 F 7 lines developed by single backcross with recipient parent WTR-1 and HNG as the pollen (donor) parent. The population was developed by using single seed descent method at IRRI, and further detailed information of this breeding scheme and population development were explained in Jewel et al (2019) and Murugaiyan et al (2019). Both parents showed 100% germination rate under control conditions (27°C and 19°C day/night temperature), whereas, at LT (14°C/12°C), the former showed a low germination rate and the latter a high germination rate.…”

Section: Plant Materialsmentioning

confidence: 99%

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

et al. 2020

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An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BC I F 7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were

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“…In the improvement of the tolerance of rice cultivars of single biotic and abiotic stresses, tremendous progress has been achieved [ 8 , 17 , 18 , 19 , 20 , 21 ]. However, these tolerant varieties have not been able to succeed to attain higher grain yields under both the irrigated and rainfed ecosystems.…”

Section: Introductionmentioning

confidence: 99%

Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (Oryza sativa L.)

Jewel

Ali

Mahender

et al. 2019

IJMS

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The development of rice cultivars with nutrient use efficiency (NuUE) is highly crucial for sustaining global rice production in Asia and Africa. However, this requires a better understanding of the genetics of NuUE-related traits and their relationship to grain yield. In this study, simultaneous efforts were made to develop nutrient use efficient rice cultivars and to map quantitative trait loci (QTLs) governing NuUE-related traits in rice. A total of 230 BC1F5 introgression lines (ILs) were developed from a single early backcross population involving Weed Tolerant Rice 1, as the recipient parent, and Hao-an-nong, as the donor parent. The ILs were cultivated in field conditions with a different combination of fertilizer schedule under six nutrient conditions: minus nitrogen (–N), minus phosphorus (–P), (–NP), minus nitrogen phosphorus and potassium (–NPK), 75% of recommended nitrogen (75N), and NPK. Analysis of variance revealed that significant differences (p < 0.01) were noted among ILs and treatments for all traits. A high-density linkage map was constructed by using 704 high-quality single nucleotide polymorphism (SNP) markers. A total of 49 main-effect QTLs were identified on all chromosomes, except on chromosome 7, 11 and 12, which are showing 20.25% to 34.68% of phenotypic variation. With further analysis of these QTLs, we refined them to four top hotspot QTLs (QTL harbor-I to IV) located on chromosomes 3, 5, 9, and 11. However, we identified four novel putative QTLs for agronomic efficiency (AE) and 22 QTLs for partial factor productivity (PFP) under –P and 75N conditions. These interval regions of QTLs, several transporters and genes are located that were involved in nutrient uptake from soil to plant organs and tolerance to biotic and abiotic stresses. Further, the validation of these potential QTLs, genes may provide remarkable value for marker-aided selection and pyramiding of multiple QTLs, which would provide supporting evidence for the enhancement of grain yield and cloning of NuUE tolerance-responsive genes in rice.

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Developing green super rice varieties with high nutrient use efficiency by phenotypic selection under varied nutrient conditions

Cited by 28 publications

References 24 publications

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (Oryza sativa L.)

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