Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population

Shen, Yusen; Xiang, Yu‐Tao; Xu, Ensheng; Ge, Xianhong; Li, Zaiyun

doi:10.3389/fpls.2018.00390

Cited by 58 publications

(43 citation statements)

References 60 publications

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“…Meanwhile, the expression of BnGATA2.5 was down-regulated under ABA inducement, drought and cold treatments, indicating its strong response to abiotic stresses ( Figure 7, Table S8). Recently, the association between BnGATA2.5 expression and plant height, branch initiation height and owering time in B. napus was proved (Shen et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Zhu

Guo

Chen

et al. 2020

Preprint

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Background: GATA transcription factors are involved in plant developmental processes, which also respond to environmental stresses through binding DNA regulatory regions to regulate the downstream genes. However, little information of GATA genes is available in Brassica napus, one of important oil crops. The release of B. napus genome sequences provides a good opportunity to perform a genome-wide characterization of GATA family genes in the rapeseed genome. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus. They were classified into four subfamilies on the basis of phylogenetic analysis and the domain structures. The sequences of BnGATAs were obvious divergence among four subfamilies based on their GATA domains, structures and motif compositions. Gene duplication and the synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into the evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distribution analysis suggests functional disparity of GATA family genes in different genotypes of a core collection germplasm.Conclusion: This study examined genomic structures, evolution features, expression patterns and SNP distribution of 96 BnGATAs. The results enriched our knowledge of the GATA genes in rapeseed.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Zhu

Guo

Chen

et al. 2020

Preprint

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“…QTL mapping analysis was performed on three characteristics of wheat flag leaf length, flag leaf width and plant height traits, and six additive QTLs were detected and distributed on chromosome 6 of wheat. QTL analysis of appearance quality traits, such as rice grain length and chalkiness, in two different ecological environments was reported based on this software, and the QTL results showed that 16 appearance-quality QTLs were located in two environments, distributed on chromosomes 1, 2, 3, 5, 9, and 10, and the LOD value was between 2.50-10.98 with a contribution rate of 7.64%-19.89% [18]. Using this method, a high-density genetic map constructed by resequencing parents and simplified genome sequencing of rice RIL populations and QTL mapping of heading stage under two environments, a total of 4 QTLs affecting heading date were located on chromosomes 3, 6, and 8 [19].…”

Section: Discussionmentioning

confidence: 99%

Mapping of QTLs Detected in a Broccoli Double Diploid Population for Plant Height and Leaf Characteristics

Huang¹,

Sun²,

Liu³

et al. 2020

Preprint

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Background The planting density of broccoli can directly affect the yield and overall health of plants. So there is necessary to reveal the regulatory genes of planting density in broccoli by QTL mapping. In this study, the important planting density-dependent factors of broccoli, plant height (PH), maximum outer petiole length (PL) and leaf width (LW), were investigated during 2017 and 2018. The mapping of QTLs for PH, PL and LW were performed, and the interaction between QTLs and the environment was also analyzed by a DH population constructed with 176 genotypes derived from F1 obtained by crossing the broccoli inbred lines 86101 (P1) and 90196 (P2).Results A linkage group including a total of 438 SSR markers were constructed covering a length of 1168.26 cM using QTL IciMapping 4.0 software. Finally, there were mainly four QTLs (phc1, phc2, phc4-1, phc4-2), one QTL (plc6), and two QTLs (lwc1, lwc3) corresponding for PH, PL and LW recurred during the two years. In three environments, inclusive composite interval mapping (ICIM) analysis showed that there was a major QTL for PH at 7.20 cM on chromosome 1 between molecular markers 8C024 and sf4482 with a high explanatory contribution rate of 20.05%. The QTL at the 11.10 cM position of chromosome 6 was located for the PL with a high explanatory contribution rate of 20.02% between the molecular markers sc2170 and sf43960. The QTL at the 147.00 cM position of chromosome 3 was located on LW with a high explanatory contribution rate of 19.97% between molecular markers of Sc52751 and RA2-E12.Conclusions According to the QTL results of planting density in broccoli by a DH population, the possible positions of candidate genes were screened to provide a basis for further locating and cloning genes for plant height, maximum outer petiole and leaf width.

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“…In B. napus, hundreds of QTLs associated with PH have been identified and located on all 19 chromosomes [23][24][25][26][27][28][29][30][31]. Several QTLs on the A3, A6, A9, C5 and C7 chromosomes have been fine-mapped or cloned [21,[32][33][34][35][36].…”

Section: Bnadwfc9 Is a New Locus Associated With Plant Height In B mentioning

confidence: 99%

“…Brassica napus is a tetraploid species, which originated from a hybridization between B. rapa (AA, 2n = 20) and B. oleracea (CC, 2n = 18) around 7500 years ago [22]. In B. napus, many studies have focused on quantitative trait loci (QTLs) detection using linkage mapping or genomewide association studies (GWASs), and hundreds of QTLs have been identified across all 19 chromosomes [23][24][25][26][27][28][29][30][31]. However, most QTLs explain a small percentage of the total phenotypic variance (PV) [23][24][25][26][27][28][29][30][31].…”

mentioning

confidence: 99%

Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L.

Wang

Zheng

Liu

et al. 2020

Biotechnol Biofuels

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Background: Brassica napus provides approximately 13-16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood. Results: A dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F 2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus 'Darmor-bzh' genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in "Darmor-bzh", "Ningyou 7" and "Zhongshuang 11" reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormonerelated signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf. C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D. Conclusions: The combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.

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Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population

Cited by 58 publications

References 60 publications

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Mapping of QTLs Detected in a Broccoli Double Diploid Population for Plant Height and Leaf Characteristics

Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L.

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