Traits and QTLs for development of dry direct-seeded rainfed rice varieties

Sandhu, Nitika; Torres, Rolando O.; Cruz, Ma Teresa Sta; Maturan, Paul Cornelio; Jain, R. K.; Kumar, Arvind; Henry, Amelia

doi:10.1093/jxb/eru413

Cited by 81 publications

(96 citation statements)

References 63 publications

(69 reference statements)

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“…Although the set of genotypes used in this study was small, we were able to identify genomic regions related to root architectural plasticity traits using a marker class analysis approach, some of which colocate with previously reported QTLs related to phenotypic plasticity in rice. The effectiveness of this approach using just 20 genotypes per population in the field studies is evidenced by the identification of a locus for grain yield at the same locus on chromosome 10 as a QTL for grain yield reported by Sandhu et al (2015) from a population of 300 genotypes. In terms of plasticity, the region on chromosome 1 (loci id1023892 and id1024972) is located near qDTY 1.1 , a major-effect drought-yield QTL that has been observed to confer plastic responses to drought, including increased root growth at depth and regulation of shoot growth (Vikram et al, 2015), as well as a hot spot for root traits including an increased proportion of deep roots by drought in the OryzaSNP panel (Wade et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…This variety was chosen as the recipient parent to investigate the potential for real improvement of one of the best available varieties that can be achieved through the incorporation of root plasticity traits. Of the donor parents, Kali Aus is a medium-duration drought-tolerant aus line from India and drought tolerance donor (Sandhu et al, 2014), and Aus 276 is an earlymaturing drought-tolerant aus pure line from Bangladesh that has been characterized to contribute traits beneficial for direct-seeded conditions (Sandhu et al, 2015). From a set of 294 genotypes from the Kali Aus/2 3 MTU1010 (BC 1 F 4 ; Kali Aus population) and 300 genotypes from the Aus 276/3 3 MTU1010 (BC 2 F 4 ; Aus 276 population) mapping populations grown in the 2012 dry season under reproductive stage stress conditions, the 10 highest and 10 lowest yielding genotypes from each population were selected for the lysimeter, field agronomic, and Rhizoscope studies.…”

Section: Plant Materialsmentioning

confidence: 99%

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Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

et al. 2016

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Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional 3 improved rice populations (Aus 276 3 MTU1010 and Kali Aus 3 MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.

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Section: Discussionmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

et al. 2016

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“…Sandhu et al (2013) reported three QTL for root length in the MASARB25 × Pusa Basmati 1460 and HKR47 × MAS26 mapping populations close to the root QTL identified. Sandhu et al (2013 and2014) and Vikram et al (2012) reported QTL for grain yield close to the QTL identified for grain yield per plant. Other reports are also available for yield QTL on chromosome 8 (Hanamaratti et al 2007;Bernier et al 2008).…”

Section: Discussionmentioning

confidence: 63%

“…Kamoshita et al (2002) also reported three QTL for root thickness at 3.8, 32.8 and 50.7 cM using recombinant inbred lines (RILs) from a lowland indica cross. Sandhu et al (2014) reported a grain yield QTL (at 56.3 cM) in vicinity of root thickness QTL (qRT 8.2 ). Sandhu et al (2013) reported two roots length QTL close to the root thickness QTL identified.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic analysis, correlation studies and linkage mapping of QTL for traits promoting cultivation under dry direct seeded aerobic conditions for the development of water-efficient high yielding rice lines

Kharb

Jain

2016

Cereal Research Communications

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Aerobic adaptation could be an important modification in the traditional rice to cope up with the increasing water scarcity problem. Identification of stable QTL for traits promoting adaptation to aerobic conditions can facilitate the development of water-efficient aerobic rice varieties with better yields. Filial and backcross populations derived from the crosses between high-yielding low-land (HKR47) and aerobic (MAS26) indica rice varieties, were evaluated for various physio-morphological traits including root traits (in case of net house evaluation). Under aerobic field conditions, grain yield per plant showed significant positive correlation with plant height, effective number of tillers/plant and panicle length in all the populations. Grain yield per plant also showed positive correlation with root length in both filial populations and with fresh and dry root weight in F 2 population. Two parental rice varieties displayed polymorphism at 125 of the 803 SSR loci, which were used to map the QTL associated with traits promoting aerobic adaptation. A total of 14 QTL were detected, 10 of them were identified on chromosome 8. Study led to the identification of a number of promising plants with higher grain yield, better root length/biomass under managed aerobic conditions and possessing most of the identified QTL.

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“…These ndings indicate the consistency of the effects of drought grain yield QTLs across diverse germplasm. It is important to take note here that the qDTY 1.1 was reported to have signi cant effect on the grain yield under control non-stress and reproductive stage drought stress in different genetic backgrounds such as Swarna, IR64, MTU1010 under lowland and upland environments (Vikram et al 2011;Sandhu et al 2014;Sandhu et al 2015). The qGY 2-1 and qGY 2-2 reported in the present study were found to be present in the upstream and downstream region of earlier reported qDTY 2.3 , respectively (Sandhu et al 2014;Palanog et al 2014).…”

Section: Mas Optimization Based On Signi Cant Genomic Regions Identi Edmentioning

confidence: 91%

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

Bhandari

Sandhu

Bartholome

et al. 2020

Preprint

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Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

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Traits and QTLs for development of dry direct-seeded rainfed rice varieties

Abstract: Highlight textCharacterization and QTL identification of seedling-stage traits revealed relationships with nutrient uptake and grain yield; these traits may improve the adaptation and productivity of rice under direct-seeded conditions.

Cited by 81 publications

References 63 publications

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

Phenotypic analysis, correlation studies and linkage mapping of QTL for traits promoting cultivation under dry direct seeded aerobic conditions for the development of water-efficient high yielding rice lines

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

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