Genetic analysis of germinating ability under alkaline and neutral salt stress by a high-density bin genetic map in rice

Luo, Xin; Deng, Haodong; Wang, Peng; Zhang, Xiangyu; Li, Caijing; Li, Cuijuan; Tan, Jingai; Wu, Guangliang; Wang, Yanning; Cheng, Qiqun; He, Haohua; Bian, Jianmin

doi:10.1007/s10681-020-02623-9

Cited by 13 publications

(11 citation statements)

References 24 publications

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“…The genetic basis of these traits is complex and controlled by multiple genes (Xia et al 2018;Shi et al, Shi et al 2018;Ruan et al 2020). With the rapid development of next-generation sequencing technology, through whole-genome resequencing, a bin-marker mapping based on chromosome fragments covering the genome has been perfomed and precise QTL positioning has been applied in many species (Liu et al 2015a;Jiang et al 2017;Luo et al 2020). A large number of SNPs and InDel markers were detected by resequencing with the advantages of high genome coverage and high density, which can improve the The phylogenetic tree was constructed by MEGA 6.0 using the neighbor-joining method with 1000 replications accuracy of QTL mapping, and obtain relatively small chromosome reference intervals.…”

Section: Discussionmentioning

confidence: 99%

qTGW12a, a naturally varying QTL, regulates grain weight in rice

Zhou

et al. 2021

Theor Appl Genet

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Key message A stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation. Abstract Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality. Therefore, the discovery and identification of rice grain size genes can provide pathways for the cultivation of high-yielding varieties. In the present work, 45,607 SNP markers were used to construct a high-density genetic map of rice recombinant inbred lines, and hence a total of 14 quantitative trait loci (QTLs) were detected based on the phenotypic data of grain weight, grain length and grain width under four different environments. qTGW12a and qGL12 are newly detected QTLs related to grain weight, and are located between 22.43 Mb and 22.45 Mb on chromosome 12. Gene annotation shows that the QTL region contains the LOC_Os12g36660 annotated gene, which encodes the multidrug and toxic compound extrusion (MATE) transporter. Mutations in exons and the splice site were responsible for the changes in grain type and weight. Gene knockout experiments were used to verify these results. Hence, these results provide a basis for the cloning of qTGW12a. This discovery provides new insights for studying the genetic mechanism of rice grain morphology, and reveals a promising gene to ultimately increase rice yield.

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Section: Discussionmentioning

confidence: 99%

qTGW12a, a naturally varying QTL, regulates grain weight in rice

Zhou

et al. 2021

Theor Appl Genet

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“…To better understand the genetic mechanism of salt tolerance in rice at the germination stage, many QTLs have been identified by using traditional QTL mapping methods in biparental populations. A total of 16 QTLs were detected during the germination stage under 100 mM NaCl conditions from a RILs that were derived from a cross between Jiucaiqing (salt-tolerant) and IR26 (salt-susceptible; Wang et al, 2011); a total of 11 QTLs were identified for their salt tolerance (1.5% NaCl) at the germination stage by using linkage mapping from a BC 2 F 2 : 3 population including 190 accessions that were derived from Dongnong 425 and Changbai 10 (Zheng et al, 2014); 17 QTLs that were related to germination traits under salt stress (80 mM NaCl) in an F2:4 population were detected, which were derived from a cross between the salt-tolerant variety "Gharib" and salt-sensitive variety "Sepidroud" (Mardani et al, 2014); 10 QTLs for five salt stress (0.01 mol L −1 )-related traits were detected a population of backcross inbred lines, which was derived from a cross between Changhui 891 and 02428 with 3,057 bin markers (Luo et al, 2020); 13 QTLs were identified under H 2 O conditions and salt conditions (300 mM NaCl) by using a BC1F2 population that derived from a WJZ/Nip cross (Zeng et al, 2021); 23 QTLs for germination parameters were detected under 18 dS m −1 NaCl solution conditions by using a BIL population that was derived from a backcross of an African rice, ACC9, as the donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent (Nakhla et al, 2021). Biparental populations, although, have played an important role in the past to provide a resource for researchers to work with; construction of populations entails major investments in time, which has therefore limited the number of genes identified to date (Bian et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Zou

et al. 2022

Front. Plant Sci.

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Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

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“…Genes encoding Na + transport proteins are involved in regulating Na + transport under alkaline salt stress [21]. A quantitative trait locus (QTL) detected from NaCl and NaHCO 3treated rice suggested that the genes controlling the transport of Na + , in the form of NaCl and NaHCO 3 , may be different or induced in an uncoordinated manner by salt stress [22]. The vacuolar proton pump ATPase (V-H + -ATPase) is a multisubunit membrane protein complex that plays a major role in the activation of ion and nutrient transport.…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

Zhang

Duo

Wang

et al. 2021

Preprint

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Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

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Genetic analysis of germinating ability under alkaline and neutral salt stress by a high-density bin genetic map in rice

Cited by 13 publications

References 24 publications

qTGW12a, a naturally varying QTL, regulates grain weight in rice

qTGW12a, a naturally varying QTL, regulates grain weight in rice

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

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