Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems

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Abstract

In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.

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Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.

Weiya Xue, Yongzhong Xing, Xiaoyu Weng … (2008)

Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.

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Improving photosynthetic efficiency for greater yield.

Xin-Guang Zhu, Stephen P Long, Donald Ort (2010)

Increasing the yield potential of the major food grain crops has contributed very significantly to a rising food supply over the past 50 years, which has until recently more than kept pace with rising global demand. Whereas improved photosynthetic efficiency has played only a minor role in the remarkable increases in productivity achieved in the last half century, further increases in yield potential will rely in large part on improved photosynthesis. Here we examine inefficiencies in photosynthetic energy transduction in crops from light interception to carbohydrate synthesis, and how classical breeding, systems biology, and synthetic biology are providing new opportunities to develop more productive germplasm. Near-term opportunities include improving the display of leaves in crop canopies to avoid light saturation of individual leaves and further investigation of a photorespiratory bypass that has already improved the productivity of model species. Longer-term opportunities include engineering into plants carboxylases that are better adapted to current and forthcoming CO(2) concentrations, and the use of modeling to guide molecular optimization of resource investment among the components of the photosynthetic apparatus, to maximize carbon gain without increasing crop inputs. Collectively, these changes have the potential to more than double the yield potential of our major crops.

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Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene.

Wolfgang Spielmeyer, Marc H. Ellis, Peter Chandler (2002)

The introduction of semidwarf rice (Oryza sativa L.) led to record yield increases throughout Asia in the 1960s. The major semidwarfing allele, sd-1, is still extensively used in modern rice cultivars. The phenotype of sd-1 is consistent with dwarfism that results from a deficiency in gibberellin (GA) plant growth hormones. We propose that the semidwarf (sd-1) phenotype is the result of a deficiency of active GAs in the elongating stem arising from a defective 20-oxidase GA biosynthetic enzyme. Sequence data from the rice genome was combined with previous mapping studies to locate a putative GA 20-oxidase gene (Os20ox2) at the predicted map location of sd-1 on chromosome 1. Two independent sd-1 alleles contained alterations within Os20ox2: a deletion of 280 bp within the coding region of Os20ox2 was predicted to encode a nonfunctional protein in an indica type semidwarf (Doongara), whereas a substitution in an amino acid residue (Leu-266) that is highly conserved among dioxygenases could explain loss of function of Os20ox2 in a japonica semidwarf (Calrose76). The quantification of GAs in elongating stems by GC-MS showed that the initial substrate of GA 20-oxidase activity (GA53) accumulated, whereas the content of the major product (GA20) and of bioactive GA1 was lower in semidwarf compared with tall lines. We propose that the Os20ox2 gene corresponds to the sd-1 locus.

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Author and article information

Contributors

Arvind Kumar: a.kumar@irri.org

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 27 June 2019

Publication date PMC-release: 27 June 2019

Publication date Collection: 2019

Volume: 9

Electronic Location Identifier: 9334

Affiliations

[1 ]ISNI 0000 0001 0729 330X, GRID grid.419387.0, Rice Breeding Platform, , International Rice Research Institute, ; Metro Manila, Philippines

[2 ]ISNI 0000 0000 9323 1772, GRID grid.419337.b, International Rice Research Institute, , South Asia Hub, ICRISAT, ; Patancheru, Hyderabad India

[3 ]ISNI 0000 0000 9323 1772, GRID grid.419337.b, Center of Excellence in Genomics and System Biology, , International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ; Patancheru Hyderabad, India

[4 ]ICAR Research Complex for Eastern Region, Patna, Bihar India

[5 ]ISNI 0000 0004 1787 6463, GRID grid.418317.8, Bihar Agricultural University, ; Sabour, Bhagalpur, Bihar India

[6 ]GRID grid.460993.1, Agriculture and Forestry University, ; Rampur, Chitwan Nepal

[7 ]National Rice Research Program, Hardinath, Nepal

[8 ]ISNI 0000 0001 2176 2352, GRID grid.412577.2, Punjab Agricultural University, ; Ludhiana, India

Author information

Rajeev K. Varshney http://orcid.org/0000-0002-4562-9131

Article

Publisher ID: 45770

DOI: 10.1038/s41598-019-45770-3

PMC ID: 6597570

PubMed ID: 31249338

SO-VID: 8c7ba828-926d-4f2c-80fd-07f053db0703

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 1 October 2018

Date accepted : 13 June 2019

Funding

Funded by: FundRef https://doi.org/10.13039/100004425, Asian Development Bank (ADB);

Award ID: TA8441

Award Recipient : Nitika Sandhu Sushil Raj Subedi Vikas Kumar Singh Pallavi Sinha Santosh Kumar Surya Kant Ghimire Madhav Pandey Ram Baran Yadaw Rajeev K. Varshney

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ScienceOpen disciplines: Uncategorized

Keywords: genomics,genome-wide association studies

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ScienceOpen disciplines: Uncategorized

Keywords: genomics, genome-wide association studies

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Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems

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Most cited references 62

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.

Improving photosynthetic efficiency for greater yield.

Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene.

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