Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition

Subedi, Sudeep; Sandhu, Nitika; Singh, Vikas K.; Sinha, Pallavi; Kumar, Santosh; Singh, Suresh Prasad; Ghimire, Surya Kant; Pandey, Madhav Prasad; Yadaw, Ram Baran; Varshney, Rajeev K.; Kumar, Arvind

doi:10.1186/s12864-019-5840-9

Cited by 31 publications

(43 citation statements)

References 72 publications

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“…Different significant MTAs in the two subpanels of the study, indica and japonica were detected using mixed model approach with structure control and kinship among the studied landraces. GWAS performed by Subedi et al ( 2019 ) reported 37 highly significant MTAs for 20 traits including plant and root morphological traits, nutrient uptake, yield and its components in MAGIC population of 5 diverse parents for increased adaptability in dry direct seeded rice (DDSR) system.…”

Section: Discussionmentioning

confidence: 99%

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

Rice

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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 200 kb 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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Section: Discussionmentioning

confidence: 99%

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

Rice

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“…The locus on chromosome 6 encodes the Heading Date ( Hd1 ) locus that was also previously associated with plant height in vegetative rice plants (Zhang et al, 2012; Yang et al, 2014). Subedi et al (2019) performed a GWAS on plant height at plant maturity and found peaks on chromosome 1 and 11, which could indicate that at different developmental stages plant height is determined by different genomic regions. However, Subedi et al (2019) used a specifically constructed genetic population stemming from six parents and this could explain why very different loci were identified.…”

Section: Discussionmentioning

confidence: 99%

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Huber

Julkowska

et al. 2021

Preprint

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Rice feeds more than half of the world's human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant's ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.

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“…Similarly, in other study conducted for same traits on MAGIC population, Subedi et al . (2019) identified a total of 37 MTAs for 20 traits and 9 putative QTLs related to different DDSR traits, among which 15 MTAs were located in the proximity of earlier identified candidate gene. Further, they identified seven promising progenies with better root morphology, nutrient‐uptake and higher grain yield to be deployed in developing DDSR varieties through genomic breeding.…”

Section: Transcending From Qtls/genes To Superior Haplotypes For Devementioning

confidence: 98%

More and more of less and less: Is genomics‐based breeding of dry direct‐seeded rice (DDSR) varieties the need of hour?

Sagare¹,

Abbai

Jain³

et al. 2020

Plant Biotechnology Journal

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Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotypebased breeding.

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Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition

Cited by 31 publications

References 72 publications

Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

More and more of less and less: Is genomics‐based breeding of dry direct‐seeded rice (DDSR) varieties the need of hour?

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