Mining of favorable marker alleles for flag leaf inclination in some rice (Oryza sativa L.) accessions by association mapping

Zhang, Dong; Li, Dalu; Hu, Xiaoxiao; Liang, Lijun; Wu, Guocan; Zeng, Siyuan; Liu, Erbao; Wu, Yue; Wang, Hui; Bhanbhro, Lal Bux; Dang, Xiaojing; Hong, Delin

doi:10.1007/s10681-018-2183-6

Cited by 9 publications

(6 citation statements)

References 49 publications

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“…The allele frequency distribution in TRJ was different from that in other subgroups, and the dominant allele GG was the one that controls the large FLA. We speculated that the reason may be due to tropical japonica growth in low-latitude high-altitude mountains in the field, and the light intensity is weaker than that in the plain. The small FLA of temperate japonica rice is beneficial for obtaining high grain yield in pure-line cultivars (Yang et al, 1984 ) but is adverse for hybrid seed production due to the requirement of removing the flag leaf of male-sterile plants to receive pollen from the male parent (Dong Z. Y. et al, 2018 ). Therefore, it is necessary to increase the FLA to facilitate pollination in the F 1 hybrid seed production.…”

Section: Discussionmentioning

confidence: 99%

“…To date, 63 quantitative trait loci (QTLs) for FLA have been identified based on linkage analysis, including 9, 7, 6, 4, 4, 5, 4, 7, 6, 0, 8, and 3 on chromosomes 1–12, respectively ( Supplementary Table 1 ) (Li et al, 1999 ; Yan et al, 1999 ; Dong et al, 2003 ; Kobayashi et al, 2003 ; Luo et al, 2008 ; Zhang et al, 2008 , 2013 ; Cai, 2009 ; Hu et al, 2012 ; Wang et al, 2012 ; Bian et al, 2014 ; Zou et al, 2014 ; Zhu et al, 2016 ; Ham et al, 2019 ). In addition, 100 QTLs for FLA have been detected based on association analysis (Huang et al, 2010 ; Chen et al, 2012 ; Lu et al, 2015 ; Dong H. J. et al, 2018 ; Dong Z. Y. et al, 2018 ). Among these QTLs, only one QTL qFla-8-2 has been fine-mapped and predicted the candidate genes (Zhu et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice (Oryza sativa L.)

Jiang

Zhang

et al. 2022

Front. Plant Sci.

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Flag leaf angle (FLA) is an important outcrossing trait affecting the hybrid seed production in rice (Oryza sativa L.). Natural variation of FLA has been reported in rice, but the molecular basis for this variation is largely unknown. In this study, we investigated the phenotypic values of FLA in 353 rice natural accessions in six environments, which indicated that there was abundant phenotypic variation. We performed a genome-wide association study on FLA using 1.3 million single nucleotide polymorphisms (SNPs). A total of six quantitative trait loci (QTLs) were identified significantly associated with FLA, of which five were located in previously reported QTLs/genes and one was novel. We identified two causal gene loci for FLA, namely, OsFLA6 and OsFLA2; OsFLA6 was co-localized with the gene OsLIC. In addition, the accessions with large and small FLA values have corresponding high and low OsFLA6 expressions. OsFLA2TT allele could increase significantly the seed setting percentage in hybrid F1 seed production by field experiment. We also confirmed that the allele OsFLA2TT increased the FLA compared with that of the isogenic line carrying allele OsFLA2CC by transgenic complementation experiment. The allele frequencies of OsFLA6GGand OsFLA2TT decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement of FLA of parents of hybrid rice.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice (Oryza sativa L.)

Jiang

Zhang

et al. 2022

Front. Plant Sci.

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“…The angle between the foliar normal and the zenith direction, known as the leaf inclination angle, is one of the main canopy structure parameters affecting light interception and photosynthetic efficiency [2]. Many studies have found that the plant leaf inclination angle is mainly regulated by hormones such as BRs [3,4], auxin [5][6][7] and gibberellins (GAs) [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

BcBZR1 Regulates Leaf Inclination Angle in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis Makino)

Lin,

Li,

et al. 2024

Horticulturae

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Brassinosteroids (BRs) play critical roles in plant growth by promoting cell elongation and division, leading to increased leaf inclination angles. BRASSINAZOLE RESISTANT 1 (BZR1) and BRI1-EMS-SUPPRESSOR 1 (BES1) act as transcription factors in the brassinosteroid signaling pathway and are involved in several physiological activities regulated by BRs. In this study, we identified and cloned BcBZR1 from the heitacai non-heading Chinese cabbage (NHCC) cultivar. The sequence analysis showed that the coding sequence length of BcBZR1 is 996 bp, encoding 331 amino acid residues. Subcellular localization assays showed that BcBZR1 is localized in the nucleus and cytoplasm and that BcBZR1 protein is transported to the nucleus after receiving BR signals. Compared with Col-0, the leaf inclination angle was smaller in BcBZR1-OX. The EBR treatment experiment indicated that BRs regulate the differential expression of paclobutrazol resistance1 (PRE1) and ILI1 binding bHLH1 (IBH1) in the adaxial and abaxial cells of the petiole through BZR1, thus regulating the leaf inclination angle. The bimolecular fluorescence complementation (BiFC) assay indicated that BcBZR1 interacts with C-repeat Binding Factor2 (BcCBF2) and CBF3. Taken together, our findings not only validate the function of BcBZR1 in leaf inclination angle distribution in non-heading Chinese cabbage, but also contribute to the mechanism of leaf inclination angle regulation in this species under cold stress.

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“…Six QTLs were identified for heading date and seventeen for low temperature germinability. Dong et al (2018) newly found four loci associated with flag leaf inclination in rice by association mapping. Today, association analysis has become a powerful method of gene digging for complex traits in rice (Zhai et al, 2018;Huang and Han, 2018).…”

Section: Introductionmentioning

confidence: 99%

Association mapping for flag leaf thickness in an indica rice population from South China

Liu¹,

Chen²,

Zhou³

et al. 2019

Afr. J. Agric. Res.

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Flag leaf is the most important source of photosynthate for developing rice grains, and flag leaf thickness is an important morphological trait in rice plant-type breeding programs. In the present study, we carried out association mapping for flag leaf thickness in a local rice population which consisted of 86 cultivars derived from breeding programs and planted in large areas in South China. Phenotyping was conducted in the field using nondestructive leaf thickness measurements. Two hundred and thirtysix SSR markers covering 12 chromosomes were employed to genotype the accessions. The association analysis was carried out using a unified mixed-model approach. The Q+K model was selected for investigating marker-trait associations. A total of eleven marker-trait pairs with significant marker-trait associations were identified which were distributed on eight chromosomes. Four of these loci had already been identified as related to flag leaf thickness in previous studies, while the other seven were novel QTLs. The locus PSM163 had the highest r 2 -marker value of the seven novel loci, explaining 21.54 and 18.49% of the phenotypic variation in 2008 and 2009, respectively. Three of four QTLs, which were detected in a F 2 mapping population in the validation study, could correspond to a significant locus in AM, respectively. The six alleles which had the highest phenotypic values at their respective loci should be considered as favored alleles in breeding programs. Pyramiding the favored alleles for flag leaf thickness identified in the study might be a valuable approach to construct an ideal plant architecture in rice breeding.

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Mining of favorable marker alleles for flag leaf inclination in some rice (Oryza sativa L.) accessions by association mapping

Cited by 9 publications

References 49 publications

An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice (Oryza sativa L.)

An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice (Oryza sativa L.)

BcBZR1 Regulates Leaf Inclination Angle in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis Makino)

Association mapping for flag leaf thickness in an indica rice population from South China

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