Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles

Zhang, Guangchen; Liu, Youhong; Gui, Rui; Wang, Ziming; Li, Zhuan; Han, Yang; Guo, Xiaohong; Sun, Jian

doi:10.1016/j.ygeno.2021.07.021

Cited by 13 publications

(10 citation statements)

References 52 publications

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“…Based on the genotypic data of 210 polymorphic markers, the overall introgression (heterozygosity) in the initially selected 126 BC 2 F 4 plants was 0.108 (0.013), 0.137 (0.069), and 0.122 (0.027) in populations CY1/Bg90-2, CY1/X21, and CY1/X22, respectively, largely fitting the Mendelian expectations ( Table S4 ), but was 0.216 (0.086) in population CY1/Q5, significantly higher than the Mendelian expectations. To understand the genetic basis of ST in the selected ILs, we adopted the strategy of selective introgression (Zhang et al, 2021 [ 22 ]) to detect the donor genomic segments that were strongly associated with the significantly improved ST in the 78 ST ILs from the four inter-subspecific populations. Because only two lines from cross CY1/SN265 were confirmed to have significantly improved ST, this population was not used for genetic mapping because of the low power in QTL detection.…”

Section: Resultsmentioning

confidence: 99%

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Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

Tian

Zhang

et al. 2023

CIMB

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Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC2F4 populations from inter-subspecific crosses between an elite Geng (japonica) recipient and four Xian (indica) donors at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. Genome-wide characterization of donor introgression identified 35 ST QTLs, 25 of which harbor 38 cloned ST genes as the most likely QTL candidates. Thirty-four are Xian-Geng differentiated ones with the donor (Xian) alleles associated with ST, suggesting differentiated responses to salt stress were one of the major phenotypic differences between the two subspecies. At least eight ST QTLs and many others affecting yield traits were identified under salt/non-stress conditions. Our results indicated that the Xian gene pool contains rich ‘hidden’ genetic variation for developing superior Geng varieties with improved ST and YP, which could be efficiently exploited by selective introgression. The developed ST ILs and their genetic information on the donor alleles for ST and yield traits would provide a useful platform for developing superior ST and high-yield Geng varieties through breeding by design in the future.

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Section: Resultsmentioning

confidence: 99%

“…Researchers identified several QTLs on rice chromosomes 1, 7, 8 and 12 for ST at the reproductive stage using a recombinant inbred population. Furthermore, (Takehisa et al, 2004) reported 17 ST QTLs identified in BC 1 F 9 to BC 1 F 12 populations of Nipponbare/Kasalath [ 22 ]. Two of these QTLs showed strong epistatic effects.…”

Section: Introductionmentioning

confidence: 99%

Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

Tian

Zhang

et al. 2023

CIMB

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“…The fact that many of the analyzed genes resulted to be co-responsive under the different conditions implies that the signaling pathways are closely interconnected with each other, and most probably involve ABA [ 120 ]. Similar considerations were drawn from another study where transcriptomics of weedy and cultivated rice grown under hypoxia were compared [ 119 ]. Additionally, in this case, oxidative phosphorylation was enhanced in weedy rice compared to that in cultivated rice, indicative of more effective energy metabolism during hypoxia.…”

Section: Transcriptomics Scenario In Relation To Rice Germinationmentioning

confidence: 90%

“…This is possible because seedlings prioritize the elongation of coleoptile over the development of roots, allowing the coleoptile to reach the aerated water surface and then promote oxygenation of developmental tissues [ 114 , 115 ]. Several recent studies have looked into the transcriptomics overview of rice germination under hypoxia, anoxia, and reoxygenation [ 116 , 117 , 118 , 119 , 120 ]. For instance, a microarray transcriptomics profile was carried out in rice (cv.…”

Section: Transcriptomics Scenario In Relation To Rice Germinationmentioning

confidence: 99%

Transcriptomics View over the Germination Landscape in Biofortified Rice

Dueñas

Slamet‐Loedin

Macovei

2021

Genes

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Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.

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“…The anaerobic germination tolerance of rice was presented at elongation ability of coleoptiles under flooded water. This ability of rice cultivars is regulated by both division and elongation capacity of cells, with the latter being the major in rice as well as other monocot (Zhang et al 2021). Cell division plays an important role at the first phase of anaerobic germination, then cell elongation occurs and goes on until the tip of the coleoptile reaches the surface of flooded water.…”

Section: Introductionmentioning

confidence: 99%

Effects of flooding conditions and phytohormones on coleoptile elongation in Indica rice varieties

Nghi,

Trinh

2024

J Plant Biotechnol

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The unpredictable scenarios of current climate change pose great challenges for global food security. Climate change triggers submergence, a natural disaster that affects cereal production in the Mekong Delta of Vietnam. Among cereals, rice is a unique species in its ability to germinate and develop a long coleoptile under water. Several previous studies indicated that the capacity of japonica rice is better than indica rice cultivars. Herein, we assessed the ability of coleoptile elongation and the role of exogenous auxin (IAA) in promoting rice coleoptile length under dark, flooded conditions using 20 indica rice varieties collected from the Mekong Delta. We germinated 20 rice seeds per variety under water (with and without adding auxin at different concentrations) for several days and measured the coleoptile length at two different timepoints of submergence. We found that the ability to develop a long coleoptile under water was not related to the rice subspecies. The average coleoptile length at day 8 and the growth curve from the beginning to day 8 of the submergence experiment of our rice cultivars were the same. We also found that 10 µM of IAA concentration expressed a significant effect on the capacity of coleoptile elongation in both long and short coleoptile-harboring indica rice subspecies. Our results suggested that OM108, OM5451, and ĐT8 are promising rice cultivars for rice production in the Mekong Delta of Vietnam.

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Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles

Cited by 13 publications

References 52 publications

Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

Transcriptomics View over the Germination Landscape in Biofortified Rice

Effects of flooding conditions and phytohormones on coleoptile elongation in Indica rice varieties

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